Wikiomics:Bioinfo tutorial (exercises)

text only/raw sequence
DNA CGGGAGGCGGCAGCGGCTGCAGCGTTGGTAGCATCAGCATCAGCATCAGCGGCAGCGGCAGCGGCCTCGG GCGGGGCCGGCCGGACGGACAGGCGGACAGAAGGCGCCAGGGGCGCGCGTCCCGCCCGGGCCGGCCATGG AGGGCGCCTCCTTCGGCGCGGGCCGCGCAGGGGCCGCCCTGGACCCCGTGAGCTTTGCGCGGCGGCCCCA GACCCTGCTCCGGGTCGCGTCCTGGGTGTTCTCCATCGCCGTCTTCGGGCCCATCGTCAACGAGGGCTAC GTGAACACCGACAGCGGCCCCGAGCTGCGCTGCGTGTTCAACGGGAACGCGGGCGCCTGCCGCTTCGGCG

Protein MEGASFGAGRAGAALDPVSFARRPQTLLRVASWVFSIAVFGPIV NEGYVNTDSGPELRCVFNGNAGACRFGVALGLGAFLACAAFLLLDVRFQQISSVRDRR RAVLLDLGFSGLWSFLWFVGFCFLTNQWQRTAPGPATTQAGDAARAAIAFSFFSILSW VALTVKALQRFRLGTDMSLFATEQLSTGASQAYPGYPVGSGVEGTETYQSPPFTETLD TSPKGYQVPAY

single FASTA
>gi|22091456|ref|NM_004209.4| Homo sapiens synaptogyrin 3 (SYNGR3), mRNA CGGGAGGCGGCAGCGGCTGCAGCGTTGGTAGCATCAGCATCAGCATCAGCGGCAGCGGCAGCGGCCTCGG GCGGGGCCGGCCGGACGGACAGGCGGACAGAAGGCGCCAGGGGCGCGCGTCCCGCCCGGGCCGGCCATGG AGGGCGCCTCCTTCGGCGCGGGCCGCGCAGGGGCCGCCCTGGACCCCGTGAGCTTTGCGCGGCGGCCCCA GACCCTGCTCCGGGTCGCGTCCTGGGTGTTCTCCATCGCCGTCTTCGGGCCCATCGTCAACGAGGGCTAC GTGAACACCGACAGCGGCCCCGAGCTGCGCTGCGTGTTCAACGGGAACGCGGGCGCCTGCCGCTTCGGCG

multiple FASTA
>homoSYNGR1a_NP_004702.2 MEGGAYGAGKAGGAFDPYTLVRQPHTILRVVSWLFSIVVFGSIVNEGYLNSASEGEEFCIYNRNPNACSY GVAVGVLAFLTCLLYLALDVYFPQISSVKDRKKAVLSDIGVSAFWAFLWFVGFCYLANQWQVSKPKDNPL NEGTDAARAAIAFSFFSIFTWAGQAVLAFQRYQIGADSALFSQDYMDPSQDSSMPYAPYVEPTGPDPAGM GGTYQQPANTFDTEPQGYQSQGY

>X.laev_syngr1_BAB79596.1 MEGGAYGAGKAGGAFDPQTFIRQPHTILRMVSWVFSIVVFGCIINEGYINSSTEEEEHCIFNRNPSACSY GVTVGVLAFLTCLLYLAVDIYFPQISSVKDRKKTVISDIAVSALWAFFWFVGFCFLANQWQVSNPNDNPM NEGADAARAAITFSFFSIFTWAGQAVLAYQQYRLGSDSALFSQDYMDPSQDQGPPYPPYASNEDLDPSAG YQQPPTEAYDAGSHGYQTQDY

>X.trop_syngr1_NP_001016195.1 MEGGAYGAGKAGGAFDPQTFVRQPHTVLRMVSWVFSIVVFGCIINEGYINASTEAEEHCIFNRNSSACAY GVTVGVLAFLTCLLYLAVDVYFPQISSVKDRKKTVISDIAVSGLWAFFWFVGFCFLANQWQVSNPNDNPM NEGADAARAAIAFSFFSIFTWAGQAVLAYQRYRLGSDSALFSQDYMDPSQDQGPPYPPYASNEDLDPSAG YQQPPSDAYDAGSQGYQTQDY

GenBank format
LOCUS      NM_004209               2054 bp    mRNA    linear   PRI 24-SEP-2005 DEFINITION Homo sapiens synaptogyrin 3 (SYNGR3), mRNA. ACCESSION  NM_004209 VERSION    NM_004209.4  GI:22091456 KEYWORDS. SOURCE     Homo sapiens (human) ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo. REFERENCE  1  (bases 1 to 2054) AUTHORS  Kedra,D., Pan,H.Q., Seroussi,E., Fransson,I., Guilbaud,C., Collins,J.E., Dunham,I., Blennow,E., Roe,B.A., Piehl,F. and Dumanski,J.P. TITLE     Characterization of the human synaptogyrin gene family JOURNAL  Hum. Genet. 103 (2), 131-141 (1998)  PUBMED   9760194 COMMENT    REVIEWED REFSEQ: This record has been curated by NCBI staff. The reference sequence was derived from BC014087.2 and BG699055.1. On Aug 2, 2002 this sequence version replaced gi:21361084. Summary: This gene encodes an integral membrane protein. The gene belongs to the synaptogyrin gene family. Like other members of the family the protein contains four transmembrane regions. The exact function of this protein is unclear. COMPLETENESS: complete on the 3' end. FEATURES            Location/Qualifiers source         1..2054 /organism="Homo sapiens" /mol_type="mRNA" /db_xref="taxon:9606" /chromosome="16" /map="16p13" gene           1..2054 /gene="SYNGR3" /note="synonym: MGC:20003" /db_xref="GeneID:9143" /db_xref="HGNC:11501" /db_xref="HPRD:06801" /db_xref="MIM:603927" CDS            137..826 /gene="SYNGR3" /go_component="integral to plasma membrane [pmid 9760194];                    membrane" /codon_start=1 /product="synaptogyrin 3" /protein_id="NP_004200.2" /db_xref="GI:6631112" /db_xref="CCDS:CCDS10456.1" /db_xref="GeneID:9143" /db_xref="HGNC:11501" /db_xref="HPRD:06801" /db_xref="MIM:603927" /translation="MEGASFGAGRAGAALDPVSFARRPQTLLRVASWVFSIAVFGPIV                    NEGYVNTDSGPELRCVFNGNAGACRFGVALGLGAFLACAAFLLLDVRFQQISSVRDRR                     RAVLLDLGFSGLWSFLWFVGFCFLTNQWQRTAPGPATTQAGDAARAAIAFSFFSILSW                     VALTVKALQRFRLGTDMSLFATEQLSTGASQAYPGYPVGSGVEGTETYQSPPFTETLD                     TSPKGYQVPAY" STS            1230..1360 /gene="SYNGR3" /standard_name="D3S3542" /db_xref="UniSTS:4004" STS            1396..2025 /gene="SYNGR3" /standard_name="SYNGR3_8904" /db_xref="UniSTS:467928" STS            1739..1859 /gene="SYNGR3" /standard_name="RH66376" /db_xref="UniSTS:7190" STS            1914..2013 /gene="SYNGR3" /standard_name="SHGC-61093" /db_xref="UniSTS:61380" polyA_signal   2001..2006 /gene="SYNGR3" polyA_site     2029 /gene="SYNGR3" /experiment="experimental evidence, no additional details                    recorded" ORIGIN 1 cgggaggcgg cagcggctgc agcgttggta gcatcagcat cagcatcagc ggcagcggca 61 gcggcctcgg gcggggccgg ccggacggac aggcggacag aaggcgccag gggcgcgcgt 121 cccgcccggg ccggccatgg agggcgcctc cttcggcgcg ggccgcgcag gggccgccct

GCG
from !!NA_SEQUENCE 1.0

H.sapiens fau mRNA

HSFAU Length: 518  Type: N  Check: 2981 ..

1 ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc

51 gccaatatgc agctctttgt ccgcgcccag gagctacaca ccttcgaggt

101 gaccggccag gaaacggtcg cccagatcaa ggctcatgta gcctcactgg

151 agggcattgc cccggaagat caagtcgtgc tcctggcagg cgcgcccctg

201 gaggatgagg ccactctggg ccagtgcggg gtggaggccc tgactaccct

251 ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc

301 gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag

351 aagaagaaga agacaggtcg ggctaagcgg cggatgcagt acaaccggcg

401 ctttgtcaac gttgtgccca cctttggcaa gaagaagggc cccaatgcca

451 actcttaagt cttttgtaat tctggctttc tctaataaaa aagccactta

501 gttcagtcaa aaaaaaaa

XML
here

EXP
ID  xb61c6.s1 EN   xb61c6.s1 LN   xb61c6.s1.ztr LT  ZTR QR  446 AQ  54.180000 SQ GCTTTACTGC CTTAGGGTCG ACTCTAGAGG ATCCCCTAAA TTATTATTTT AAATTGACAT TTTGAAAATT TCCCCCGTAA TTTTATTGCA ATTTTAATTG AAAGTTTATT AATTGTGAAA TGTGCTTTTT AAGATGTTGC AAACACCTAA TTACTATT-T CACTTTTGAG ATATGT-AAT T-CTAAA-AA CTTTT-T--A ATTTCCTAA- --GAATTT-C AAAAG-CAAA A-AACAAACG AATTT-ATAA AAG--AAAAG -GCAAACT-A CCTG-TAACT -ACA-T-CCG G-CCA-T-AT CAAAATTAAT TTTTCCGTTG G-ATTAACTT TTT-G-AT-T TTCCT-GGGG GG-CTTGACT TT-CCGC-AT TGGTTGGTT- GGGTTCGCGG AATTTTTTTA CCAGGGGTTC TTTGGG-GGA G-G-AAG-C- TT-A-AAC-C GGGTT // SF  /home6/jkb/work/course/t/m13mp18.vector CF  /home6/jkb/work/course/t/lorist6.vector TN  xb61c6 PR  1 SC  6249 SP  41 SI  1400..2000 CH  0 QR  159 QL  0 SL  36 SR  446

GFF
from ##sequence-region  ctg123 1 1497228 ctg123. gene           1000  9000. + .  ID=gene00001;Name=EDEN ctg123. TF_binding_site 1000 1012. + .  ID=tfbs00001;Parent=gene00001 ctg123. mRNA           1050  9000. + .  ID=mRNA00001;Parent=gene00001;Name=EDEN.1 ctg123. five_prime_UTR 1050  1200. + .  Parent=mRNA0001 ctg123. CDS            1201  1500. + 0  Parent=mRNA0001 ctg123. CDS            3000  3902. + 0  Parent=mRNA0001 ctg123. CDS            5000  5500. + 0  Parent=mRNA0001 ctg123. CDS            7000  7600. + 0  Parent=mRNA0001 ctg123. three_prime_UTR 7601 9000. + .  Parent=mRNA0001 ctg123. cDNA_match 1050 1500 5.8e-42  +. ID=match0001;Target=cdna0123+12+462 ctg123. cDNA_match 5000 5500 8.1e-43  +. ID=match0001;Target=cdna0123+463+963 ctg123. cDNA_match 7000 9000 1.4e-40  +. ID=match0001;Target=cdna0123+964+2964
 * 1) gff-version  3

MSF
PileUp

MSF:   265   Type: P    Check:   214852   ..

Name: homoSYNGR1a_NP_ Len:  265  Check: 17794  Weight:  1.000 Name: X_laev_syngr1_B Len:  265  Check: 17613  Weight:  1.000 Name: X_trop_syngr1_N Len:  265  Check: 17610  Weight:  1.000 Name: homo_SYNGR3_NP_ Len:  265  Check: 17422  Weight:  1.000 Name: homo_SYNGR2_AAH Len:  265  Check: 17128  Weight:  1.000 Name: D_rerio_XP_6969 Len:  265  Check: 18054  Weight:  1.000 Name: T_nigr_CAF89717 Len:  265  Check: 18574  Weight:  1.000 Name: D_mela_NP_61090 Len:  265  Check: 18339  Weight:  1.000 Name: D_rerio_syngr1_ Len:  265  Check: 16771  Weight:  1.000 Name: E_eleg_NP_50923 Len:  265  Check: 18759  Weight:  1.000 Name: A_gamb_EAA05258 Len:  265  Check: 16202  Weight:  1.000 Name: chick_syngr1_XP Len:  265  Check: 9780  Weight:  1.000 Name: bee_XP_624778_1 Len:  265  Check: 10806  Weight:  1.000

//

homoSYNGR1a_NP_ .........M E.GGAYGAGK AGGAFDPYTL VRQPHTILRV VSWLFSIVVF X_laev_syngr1_B .........M E.GGAYGAGK AGGAFDPQTF IRQPHTILRM VSWVFSIVVF X_trop_syngr1_N .........M E.GGAYGAGK AGGAFDPQTF VRQPHTVLRM VSWVFSIVVF homo_SYNGR3_NP_ .........M E.GASFGAGR AGAALDPVSF ARRPQTLLRV ASWVFSIAVF homo_SYNGR2_AAH .........M E.SGAYGAAK AGGSFDLRRF LTQPQVVARA VCLVFALIVF D_rerio_XP_6969 .......MES R.SVAYGASL AGAGFDLVKF IKQPQTVVRF LSWVFAIVVF T_nigr_CAF89717 .........M DGVGSFGAGR TGSAVDPIAF AKQPQTILRV LSWIFSLVVF D_mela_NP_61090 MDMLNQILSI NNGGAYGGGK AGGAFDPLTF AMKPQVVIRA LCWLFSVVVF D_rerio_syngr1_ MDQ....... ....AYGAGK AGGTFDPITF FQQPQTILRI VSWIFSIVIF E_eleg_NP_50923 .........M ENVRAYGAGL AGANFDKNTF FKKPTVLFRC AALLFGLILW A_gamb_EAA05258 .NEANR.SKM DIGGAYGGGK AGGAFDPIAF VQRPTVILRA VCWLFAIIVF chick_syngr1_XP .......... .......... .......... .......... ...VFSIVVF bee_XP_624778_1 .......... .......... .......... .......... ..........

homoSYNGR1a_NP_ GSIVNEGYLN SASEGEEFCI YNRNPNACSY GVAVGVLAFL TCLLYLALDV X_laev_syngr1_B GCIINEGYIN SSTEEEEHCI FNRNPSACSY GVTVGVLAFL TCLLYLAVDI X_trop_syngr1_N GCIINEGYIN ASTEAEEHCI FNRNSSACAY GVTVGVLAFL TCLLYLAVDV homo_SYNGR3_NP_ GPIVNEGYVN TDSGPELRCV FNGNAGACRF GVALGLGAFL ACAAFLLLDV homo_SYNGR2_AAH SCIYGEGYSN AHESKQMYCV FNRNEDACRY GSAIGVLAFL ASAFFLVVDA D_rerio_XP_6969 SSITAEGYVN STDEAEVRCV FNRNDGACHY GVGIGVIAFL ACVGFLLADA T_nigr_CAF89717 ASIVNEGYVN IGSE.RLYCV FNKNADACNY GVFVGLVGLL ACSFFGLLDY D_mela_NP_61090 GCISSEGWTE K.DG.KEYCL YNGDGMACKY GNMVGVFGFL ASMGFMGGEF D_rerio_syngr1_ GCIANEGYVN RPDEVEEFCI FNRNQNACNY AVGMGALDFL CCAAFLALDI E_eleg_NP_50923 YSVSKGGWHK PSDAIHPVCL YGRSSSTCSF ATAVGFFAVC GAIVLIVLDA A_gamb_EAA05258 GCISSEGWRE EANG.KEYCI INRDGNACNY AVGIGVIAFL AAMGFIAGEY chick_syngr1_XP GSIVNEGYVN RLDESEEHCI FNRNRNACNY GITVGVLAFL SCLLYLALDA bee_XP_624778_1 .......... .......... .......... .......... ..........

homoSYNGR1a_NP_ YFPQISSVKD RKKAVLSDIG VSAFWAFLWF VGFCYLANQ. ..WQVSKPKD X_laev_syngr1_B YFPQISSVKD RKKTVISDIA VSALWAFFWF VGFCFLANQ. ..WQVSNPND X_trop_syngr1_N YFPQISSVKD RKKTVISDIA VSGLWAFFWF VGFCFLANQ. ..WQVSNPND homo_SYNGR3_NP_ RFQQISSVRD RRRAVLLDLG FSGLWSFLWF VGFCFLTNQ. ..WQRTAPGP homo_SYNGR2_AAH YFPQISNATD RKYLVIGDLL FSALWTFLWF VGFCFLTNQ. ..WAVTNPKD D_rerio_XP_6969 ILPLISNAQE RKYIVMADLA FSGCWTFLWF VCFCLTADQ. ..WSKTSDRS T_nigr_CAF89717 KFSSISSIKD RKKAVMLEIG FSGFWTFLYF VSFCFLANQ. ..WSRTTPDE D_mela_NP_61090 LFERMSSVKS RKRYVMADMG FSALWTFMYF VAFLYLWSQ. ..WSSSAPPP D_rerio_syngr1_ YFPQISSVKD RKKAVLADIG VSAFWSFVWF VGFCFLANQ. ..WQVANPED E_eleg_NP_50923 KMDQISSVPT RRRAVLADLV VSAIFTAIFL IGFFTFWSKL SAFEVDEDDE A_gamb_EAA05258 LFEQMSSVKT RKHYVLADLG FSAFWSFLFF IGFCYLTNQ. ..WGKADDPP chick_syngr1_XP YFPQISSVKD RKKAVLSDIG VSAFWAFLWF VGFCFLTNQ. ..WQASKEED bee_XP_624778_1 ....MSSVKT RKHFVLLDLG FSGFWAFLYF VGFCYLTNA. ..WNKSETPK

homoSYNGR1a_NP_ NPLNEGTDAA RAAIAFSFFS IFTWAGQAVL AFQRYQIGAD SAL...FSQD X_laev_syngr1_B NPMNEGADAA RAAITFSFFS IFTWAGQAVL AYQQYRLGSD SAL...FSQD X_trop_syngr1_N NPMNEGADAA RAAIAFSFFS IFTWAGQAVL AYQRYRLGSD SAL...FSQD homo_SYNGR3_NP_ ATTQ.AGDAA RAAIAFSFFS ILSWVALTVK ALQRFRLGTD M.....SLFA homo_SYNGR2_AAH VLV..GADSV RAAITFSFFS IFSWGVLASL AYQRYKAGVD D.....FIQN D_rerio_XP_6969 GI...PTDAV HAVIAFSFFS IASWGALTYF AVVRFRQGVE E.....VTQS T_nigr_CAF89717 VPLDQGADAA RAAIAFSFFS IITWAGLTVR AVQKYLLGTD MSL...FTTE D_mela_NP_61090 LGI..GAGSM KTAIWFCLFS IVSWALCALM AYKRFLIGAG DEF...TSAF D_rerio_syngr1_ NPLKEGADAA RAAITFAFFS IFTWAGQAFF GFQRYKLGSS SSL...FSQD E_eleg_NP_50923 NPI..KTNNA KFGILSALLS FLAWGGAAFF AWRRYEEGNQ ATHEPNYDEH A_gamb_EAA05258 NGE..GVNNV QASIVFSFFS IFTWAGCAYF AFLRFKAGVD PSF...SSTY chick_syngr1_XP NPMNEGGDAA RAAITFSFFS IFTWV..... .......... .......... bee_XP_624778_1 DNY..GVNNV QSAIAFSFFS IFTWAACAWF AFQRFKQGTD AAF...APSY

homoSYNGR1a_NP_ YMDPSQDSSM PYAP..YVEP TGPDPAGMGG TYQQPANTF. DTEP..QGYQ X_laev_syngr1_B YMDPSQDQGP PYPP..YASN EDLDPS...A GYQQPPTEAY DAGS..HGYQ X_trop_syngr1_N YMDPSQDQGP PYPP..YASN EDLDPS...A GYQQPPSDAY DAGS..QGYQ homo_SYNGR3_NP_ TEQLSTGASQ AYPG..YPVG SGVEGT...E TYQSPPFTET LDTSP.KGYQ homo_SYNGR2_AAH YVDPTPDPNT AYAS..YPGA S....V...D NYQQPPFTQN AETT..EGYQ D_rerio_XP_6969 YTDPPPDLSS PYPSTYTPPT YPSFQNTGAD IYQQPPFTPN PDPSGQTSFQ T_nigr_CAF89717 HLDGAAPTQR LPLQLTCRRH RRDHGGLPEP PLHREQRSTH LPGSHLLDQG D_mela_NP_61090 ETDPANV... VHQQAYGYSM DNDNDQYSAS PFGQPQQGGM EQQQSGMEYQ D_rerio_syngr1_ YTDPSQDPAA APSE...... .....GTEYT GYNADMEANY DGS...GGYQ E_eleg_NP_50923 FGQVSTDVQD GYGY...... .GGDSTGIGH VGAPPPQSSY QSGAAPQTMQ A_gamb_EAA05258 ESDPSAAQQY AAYP...... ....ASNEND QFQEAPF... .......... chick_syngr1_XP .......... .......... .......... .......... .......... bee_XP_624778_1 EADPVGGTGY TSYP...... .....DATDT GYQEPPFGQQ QQQQQ.QQQQ

homoSYNGR1a_NP_ .SQGY..... ..... X_laev_syngr1_B .TQDY..... ..... X_trop_syngr1_N .TQDY..... ..... homo_SYNGR3_NP_ .VPAY..... ..... homo_SYNGR2_AAH PPPVY..... ..... D_rerio_XP_6969 .PPVY..... ..... T_nigr_CAF89717 .SPRRARSSA K.... D_mela_NP_61090 .QPTY..... ..... D_rerio_syngr1_ .NQDY..... ..... E_eleg_NP_50923 QPPSNPYTQS EGYGY A_gamb_EAA05258 .......... ..... chick_syngr1_XP .......... ..... bee_XP_624778_1 QQQQQRMPDF RAPAY

ALN
CLUSTAL FORMAT for T-COFFEE Version_3.93, CPU=12.81 sec, SCORE=52, Nseq=13, Len=276

A.gamb_EAA05258.2            -NEANRS-KMDIG-GAYGGGKAGGAFDPIAFVQRPTVILRAVCWLFAIIVFGCISSEGWR bee_XP_624778.1 D.mela_NP_610908.1           MDMLNQILSINNG-GAYGGGKAGGAFDPLTFAMKPQVVIRALCWLFSVVVFGCISSEGWT E.eleg_NP_509239.1           -MENV-RAYGAGLAGANFDKNTFFKKPTVLFRCAALLFGLILWYSVSKGGWH D.rerio_XP_696934.1          MESRS-VAYGASLAGAGFDLVKFIKQPQTVVRFLSWVFAIVVFSSITAEGYV homo_SYNGR2_AAH00407.1       --MES-GAYGAAKAGGSFDLRRFLTQPQVVARAVCLVFALIVFSCIYGEGYS D.rerio_syngr1_AAH83255.1    --M-D-QAYGAGKAGGTFDPITFFQQPQTILRIVSWIFSIVIFGCIANEGYV X.laev_syngr1_BAB79596.1     --MEG-GAYGAGKAGGAFDPQTFIRQPHTILRMVSWVFSIVVFGCIINEGYI X.trop_syngr1_NP_001016195.1 --MEG-GAYGAGKAGGAFDPQTFVRQPHTVLRMVSWVFSIVVFGCIINEGYI chick_syngr1_XP_423200.1     VFSIVVFGSIVNEGYV homoSYNGR1a_NP_004702.2      --MEG-GAYGAGKAGGAFDPYTLVRQPHTILRVVSWLFSIVVFGSIVNEGYL T.nigr_CAF89717.1            --MDGVGSFGAGRTGSAVDPIAFAKQPQTILRVLSWIFSLVVFASIVNEGYV homo_SYNGR3_NP_004200.2      --MEG-ASFGAGRAGAALDPVSFARRPQTLLRVASWVFSIAVFGPIVNEGYV

A.gamb_EAA05258.2            EEANG-KEYCIINRDGNACNYAVGIGVIAFLAAMGFIAGEYLFEQMSSVKTRKHYVLADL bee_XP_624778.1              -MSSVKTRKHFVLLDL D.mela_NP_610908.1           EKD-G-KEYCLYNGDGMACKYGNMVGVFGFLASMGFMGGEFLFERMSSVKSRKRYVMADM E.eleg_NP_509239.1           KPSDAIHPVCLYGRSSSTCSFATAVGFFAVCGAIVLIVLDAKMDQISSVPTRRRAVLADL D.rerio_XP_696934.1          NSTDEAEVRCVFNRNDGACHYGVGIGVIAFLACVGFLLADAILPLISNAQERKYIVMADL homo_SYNGR2_AAH00407.1       NAHESKQMYCVFNRNEDACRYGSAIGVLAFLASAFFLVVDAYFPQISNATDRKYLVIGDL D.rerio_syngr1_AAH83255.1    NRPDEVEEFCIFNRNQNACNYAVGMGALDFLCCAAFLALDIYFPQISSVKDRKKAVLADI X.laev_syngr1_BAB79596.1     NSSTEEEEHCIFNRNPSACSYGVTVGVLAFLTCLLYLAVDIYFPQISSVKDRKKTVISDI X.trop_syngr1_NP_001016195.1 NASTEAEEHCIFNRNSSACAYGVTVGVLAFLTCLLYLAVDVYFPQISSVKDRKKTVISDI chick_syngr1_XP_423200.1     NRLDESEEHCIFNRNRNACNYGITVGVLAFLSCLLYLALDAYFPQISSVKDRKKAVLSDI homoSYNGR1a_NP_004702.2      NSASEGEEFCIYNRNPNACSYGVAVGVLAFLTCLLYLALDVYFPQISSVKDRKKAVLSDI T.nigr_CAF89717.1            NIGSE-RLYCVFNKNADACNYGVFVGLVGLLACSFFGLLDYKFSSISSIKDRKKAVMLEI homo_SYNGR3_NP_004200.2      NTDSGPELRCVFNGNAGACRFGVALGLGAFLACAAFLLLDVRFQQISSVRDRRRAVLLDL :*.  *:  *: ::

A.gamb_EAA05258.2            GFSAFWSFLFFIGFCYLTNQWGK---AD--DPPNGEGVNNVQASIVFSFFSIFTWAGCAY bee_XP_624778.1              GFSGFWAFLYFVGFCYLTNAWNK---SE--TPKDNYGVNNVQSAIAFSFFSIFTWAACAW D.mela_NP_610908.1           GFSALWTFMYFVAFLYLWSQWSS---SA--PPPLGIGAGSMKTAIWFCLFSIVSWALCAL E.eleg_NP_509239.1           VVSAIFTAIFLIGFFTFWSKLSAFEVDE--DDENPIKTNNAKFGILSALLSFLAWGGAAF D.rerio_XP_696934.1          AFSGCWTFLWFVCFCLTADQWSK---TSDRS---GIPTDAVHAVIAFSFFSIASWGALTY homo_SYNGR2_AAH00407.1       LFSALWTFLWFVGFCFLTNQWAV---TNPKD--VLVGADSVRAAITFSFFSIFSWGVLAS D.rerio_syngr1_AAH83255.1    GVSAFWSFVWFVGFCFLANQWQV---ANPEDNPLKEGADAARAAITFAFFSIFTWAGQAF X.laev_syngr1_BAB79596.1     AVSALWAFFWFVGFCFLANQWQV---SNPNDNPMNEGADAARAAITFSFFSIFTWAGQAV X.trop_syngr1_NP_001016195.1 AVSGLWAFFWFVGFCFLANQWQV---SNPNDNPMNEGADAARAAIAFSFFSIFTWAGQAV chick_syngr1_XP_423200.1     GVSAFWAFLWFVGFCFLTNQWQA---SKEEDNPMNEGGDAARAAITFSFFSIFTWV homoSYNGR1a_NP_004702.2      GVSAFWAFLWFVGFCYLANQWQV---SKPKDNPLNEGTDAARAAIAFSFFSIFTWAGQAV T.nigr_CAF89717.1            GFSGFWTFLYFVSFCFLANQWSR---TTPDEVPLDQGADAARAAIAFSFFSIITWAGLTV homo_SYNGR3_NP_004200.2      GFSGLWSFLWFVGFCFLTNQWQR---TAPGPATTQAG-DAARAAIAFSFFSILSWVALTV .*. :: .::: *   .                   .  :  *  .::*: :*

A.gamb_EAA05258.2            FAFLRFKAGVDPSFSSTYESDPSAAQQ--YAAYP-ASNE-ND-Q bee_XP_624778.1              FAFQRFKQGTDAAFAPSYEADPVGGTG--YTSYP-DATD-TG-- D.mela_NP_610908.1           MAYKRFLIGAGDEFTSAFETDPANVVH--QQ--AYGYS-MDND-ND-Q E.eleg_NP_509239.1           FAWRRYEEGNQATHEPNYDEHFGQVSTDVQD--GYGYGGDSTG-IG-H D.rerio_XP_696934.1          FAVVRFRQGVEEV--TQSYTDPPPDLSSPYPS--TYTPPTYP-SFQNT-GAD---I homo_SYNGR2_AAH00407.1       LAYQRYKAGVDDF--IQNYVDPTPDPNTAYASYPGA-SVD---N D.rerio_syngr1_AAH83255.1    FGFQRYKLGSSSSLFSQDYTDPSQDPAAAPSEGT-EYT-G X.laev_syngr1_BAB79596.1     LAYQQYRLGSDSALFSQDYMDPSQDQGPPYPPYA-SNEDLDPSA---G X.trop_syngr1_NP_001016195.1 LAYQRYRLGSDSALFSQDYMDPSQDQGPPYPPYA-SNEDLDPSA---G chick_syngr1_XP_423200.1 homoSYNGR1a_NP_004702.2      LAFQRYQIGADSALFSQDYMDPSQDSSMPYAPYV-EPTGPDPAGMGGT T.nigr_CAF89717.1            RAVQKYLLGTDMSLFTTEHLDGAAPTQRLPLQLTCRRHRRDHGGLP-EPPLHREQR---S homo_SYNGR3_NP_004200.2      KALQRFRLGTDMSLFATEQLSTGASQA--YPGYP-VGSGVEGTE---T

A.gamb_EAA05258.2            FQEAPF-- bee_XP_624778.1              YQEPPFGQQQQQQQQQQQQQQQQRMPDFRAPA-Y-- D.mela_NP_610908.1           YSASPFGQPQQGGMEQQQSGM-EYQQPT-Y-- E.eleg_NP_509239.1           VGAPPPQSSYQSGAAPQTMQQPPSNPYTQSEG-YGY D.rerio_XP_696934.1          YQQPPFTPNPDPSGQ--TSFQPPV-Y-- homo_SYNGR2_AAH00407.1       YQQPPFTQNAETTEGYQPPPVY-- D.rerio_syngr1_AAH83255.1    YNADM-EANYD-GS---GGYQNQD-Y-- X.laev_syngr1_BAB79596.1     YQQPP-TEAYDAGS---HGYQTQD-Y-- X.trop_syngr1_NP_001016195.1 YQQPP-SDAYDAGS---QGYQTQD-Y-- chick_syngr1_XP_423200.1 homoSYNGR1a_NP_004702.2      YQQP--ANTFDTEP---QGYQSQG-Y-- T.nigr_CAF89717.1            THLPGSHLLDQGSP---RRARSSA-K-- homo_SYNGR3_NP_004200.2      YQSPPFTETLDTSP---KGYQVPA-Y--

Promoter analysis

 * 1) go to



>chromosome:NCBI36:5:173403330:173468885:1 CTCCTGCCTCAGCCTCCCAAGTAGTTAGGATTACAGGCATGCGCCACCATGCCTGGCTAA TTTTTGTATTTTTAGTAGAGACGGGATTTCACCATGTTGGTCAGGCTGGTCTCGAACTCC TGACCTTGTGATCCACCTGCCTTGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCAC TGCTCCCGGCTGCCAATTTTTAAATCAGATTTTTGTTTTTTGGCTGTTGTTTGAGTTTCT TATATATTCTGGGTATTAACCCCTGGTCAGATGCATAGTTTGCAGATATTTTCTTCCATT TTGTAGGTTGTCTCTTTAGTCTGTTAATTATTTCCTTTGCTGTGCAGAAGCTTGGCTTGA AATTATTAAAAGTGTGATTTCTATGTGTGAATCAATCACAAGACATGTCAAAAGGAATTT CTTTTTCCTCTGGAGGAAAAAGATTAAACACAAGGGTTCACAATTGACTCCACGTGGTTA TCCACATTGTGTTGTCACAATGATTGCACCTGAAAACTCATCTAGGTCTTTGGAAAGAAG AGAATGGAGGACTAACATTTACTGGGACACTCCCATATTATGTATCTGCCTACTTCTATT AATATAGCCCTGTGCAGCTCAGATGTGCTAGCTTTTGTTGTCTCAGAAAATGTCTCTCTC TCTGTCTCTCCACACACGTGTCCCCCCCCCCCACACGTTTCATTACTGAACAATATATAT AATACTTACGTTTTCTCCTGACCTTTTAGCTAGCAGAGTGTATGCTCAGCACATGAGCAC TAACTAGGGTGACCTAACAATTTATCACATAAACTAGAATACTTTTGAAAGCAAAAGGGG ACCCTATGACAAATGCCAAGACAGCTGGGCCTCATGAAGTGCATCATAAGCAGCACTGCA GCTGGGAATGAACAACCATCAGTGACTTGAACCACAGCTTGGTGAAGACAGTGGCAACAG CCTTGACCTCAGAGGATTTGAAGAGAATCTGTGAGCAATCCCCGGGGATGAAATAATGCA GCCATTCAGAACCTTGTCCCTGAGCAGTAAGGGGTTTCCTTGAGCACAATCTCTTCTCAT ATTTACAATCGCTCTCCTGAGCAATAAGGGGTTTCCTTGAGCACAATCTCTTCTCATATT TACAATCGCTCTGCAAGAGAGATATTATTATTCTTACGCCAGAGAAAAGGAAATGGAGGT TTAAAGAATAAATGCAAAATGTCCAAAATCCATACAGCCAGAATTTGGTAGAGCAGACAC TAGGACTTTGCCCTGTCTGATTCCAGGCACCAACTTGGAAGCCATGCAATGTCCTGGGCT GGATACAAATTTTGGTGGCCACCGATCAGGGTTCAAATTCCAGCTCTGGTTACCGTGGCT GCCCTGTATGATCACAGTGCAATGTTGAGTGTAGTAGCTCATGTGAATACAGTGCTTGCC ATAGTCCCTGCTCTGTACTACATGCATTCCCTATGCTATCCCATTTCATGCTTTGTACTA ACCCCATCATGTGTGTACTATTAGAAACACCATTTTGCAAATGAGGGAGATAGTCTGAAA GAGGCTGGAAAAGTGCCCACTGCATGAAAGATACACAATAAATATATTTCCCTTCTGTCC TGACCACAGGGTCAGAGCACAGTAGAGGTCTTGAACCATTCTGTGTTTTATGATATTGTT CTGGAAGGTCTTAGGAGGCAATGCCCTCTCCTAATGAATGTGCCTGCTTTTCCAGTTTTT CCAAAGGCTCAAGGATTACTTGTTATATGGTGCATATTAATTATTTTTTTGGTGTGGCCA AAATCCTTCCCACTTTCTTGAAACCATTTTGTCCCGTGCAGTGGTTGTGGCCATGCATAA GAAACAGCAGGTGGTGCCAGATGACAGATGGTGTGGGAGCGCGTTCCCCGGTAGGAGGGG GCGCGAGCGAGCAAGCAGGCAGGCAGCTGCCAGGAGCTCTTCCCTGCTCGCTCACGCCTG CTCTCAGAAGCTCCGATCCAGACACACGCGAGGCGCTGTCCTTTCAGCACCACAAGCTCG GGCTGAGGAGGGAGGACTCCTGGCCGTCCTCCTCCTCTTCAAATTGGCTTGAATCTGCTC TGACCCCCCACGAGTGCAGCACA
 * humNSG2ex1 + 2000bp 5' 


 * humSYNGR3 exon1 + 2000bp 5' 

>chromosome:NCBI36:16:1977969:1984376:1 GTGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCATGAACCACCCACCTCAGCTTCCCAA GGTGCTGAGATTACAAGCGTGAGCCACTGCGCCAGGCCAGAGTCTGTTTTTGAAGGCATC CAGGCCAGTGGAACTCTAGTGCAAGGAAAAGTTCTGGCTTGAGCTGGTGTTCCAGAGCTG TTGACACGCAGACCAAAGGAGTTAGCACAGAGGGAGAGACCTCCCCAGGATCGCGCCCTG GGCTCCTAAGGCTCACAGGTCACAGAGGAAGGACCCATGAGGGAGGAGGACCTCCAGGAG GGGCATAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAAACCAAGGTGGGCAGATCAC TTGAAGTCAGGAGTTCGAGACCAGCCTGGTCAACATGGCGAAACCCCGTCTCTACTAAAA ATACAAAAAAAAAAAAAAAAAAAATTAGCTGGGTGCGGTGGCACACCTGGAATCCCAGCT ACTCCAGTGGCTGAGGTAGGAGAATCACTTGAGCCCCTGAGGCAAAGCTTGCAGTGAGCC AAGATTGCGCCACTGCACTCCAGCCTGGGTAACAGAGTGCGACTGTAACTCAAAAAATAA ATAAATAACTAAAGAAATAAATGAGTCGACAGCAGCATCAGACTTGCCCTTGGGATTGGC ACGGAGAGGTCAGTGGCAACCTTGAGTTTAGGTGGCGGTGGGAGCTGATTCTGCCGGGTC AGAGGGAGAGAGAGGAGGGTGTTGCAGGCAGAGTTTGCTGCTAAAGGAAGCAGTAACGTA AGGCAGCTGGAGGGGAGGTGGGGTCAACAGTGTTTGGCTTTTAGGAGAAAGTGCAGCATG TCTGGGTGCTGATGTTAGTGATGAAGTAGAGAATGAATGACACAGAGGGGAGGTCTGTGG CCAACAGGTGAGAGGGGTTGTGATCGGACGCACAGTGTGATGGACTTGGAACACAGTGAG TAGCGCCTCTGGCAACACCTGCTCTGCCCACCTGTGCCCAGCAAGGCTGAAGAATGAGCT CCAGGGGGGCTGGGCCACGCAGCACCATCTGTGCACCCGGCTCGTGTAGCAGGGACCTGG GTTGCTTATTATCTGAAGTACAGGGTGGTAACAGTCTCCGCCACTACACAGGTCAAGCGC TTGGCGCTGTAAATGTCAGTGCAGACATCTCAGTGCTCTAGACAGAAACCTAGGAGTCAT CTGAACTTCCAGCCTGCTAGGAACATGAGGAGAGGGACCTTGTTGCACCCAAGGCTGGGG TCTGTGGAGGGGACTCAGCGGGACACAGGGCAGCCAGGCACCACCCCCACCCGACTCCTA GTCTCTGATGCCGCTCCCTGCCCTCCATTCCAGACTAGGCGCCGCAAGTACGCTGGGGAG ACCCAGGAGTAGGGAGGGCATTGGGAGCACCACCACCTGGCCACGGGCAAGGAGCGGAGA CACCGAAACCAACACTCCCAGCGGCGCTGGCCACGGTGGCTCTGTCCCCTCCCTCAACAG GTGCTCCTGGGGCCAACGCCTTTCTTCCCACCAGATCCTCCCCGCCAGAGGCTAGAAGCT GTGATAGCAGCTAGAGCACAGTGGGGGGCCATGAGAAAGACCCCAGTTATCCATCTGGTC TTCTTGGGACCAGGGCCAGGGAGCCGGTCCCCTCTCCCGTGGGTTGGGGGAAGATGCTGC AGCCCGTGGACCTCCTACCCCTTTACTCCCTCACCCAAGTGCCCTTCCCAGAGGAGCGGA CTCCTCCTGTCTGTCCTCCCGGCTCTAGCAAAGTCTGCGCCCAGCACCCGAGCCCCACCC TGCCCCCGGGGACCTGGCTGGTGGGTTCCTGAGGATGGTCTCCATCTCGGGACCGGGGCA GGCAGGTGAGGGTGGGGGATGGGAGGTGGGCGCGGCGGAGGGAGAGGAGGGACCCGGCCC CGCGCGCATGGACCCAGTGGGGGGCGCGGGCGCGGCCCCGCCCCGTCCCGCGCGTCCCCG CCGCGGCCGGCGCGCGCTCCCGGGAGGCGGCAGCGGCTGCAGCGTTGGTAGCATCAGCAT CAGCATCAGCGGCAGCGGCAGCGGCCTCGGGCGGGGCCGGCCGGACGGACAGGCGGACAG AAGGCGCCAGGGGCGCGCGTCCCGCCCGGGCCGGCCATGGAGGGCGCCTCCTTCGGCGCG GGCCGCGCAGGGGCCGCCCTGGACCCCGTGAGCTTTGCGCGGCGGCCCCAGACCCTGCTC CGGGTCGCGTCCTGG

>chromosome:NCBIM35:17:22866087:22874033:-1 CTGTGGAAAGCTGGTTTTCACTCTTTCAGCAATTCCTAATCGCGGGCACCTTCTGTGATT CCTGGCCAGGAGCAACCCTGTCTCAAAAAATCAAAACAAAATAAACAAACAAACAAAAAA ACCCGACAATAACTTTATTCACTTACTTTTGGTTTTTTGAGACACAGTTTCTCTGCCTAC ATCTGCCTCCAAAGTGCTGGGATTAAAGGCATGCGTTACCACTGCCCAGCCAATAAATTT ATTTTTAGAAAGTAAATCAAGCCAGGCGTGGTGACACATGCCTATAATCCCAGCACTTGG GAGGCAGAAGCCAGTGAATTTCTGAGTTAGAGGCCAGCCTAGTCTACAGAGTTAGTTCCA GGACAGCCACGGCTACACAGAGAAGAGAAACCCTGTCTTGAAAACCCAAAAAAAAAAAAA AAAAAAAAAAAAGCTTCATTTTGTCCCTGTTCACAGAGCATCTGGGTCAAGACAAGCAGA ACTTGTGTGAAGGAAGGTTATGGTTTGAGCTGGCATTTGAGAGCGGTCAGCACAGACAGA GGGATAAGTACTCAGCAATGAAAAAAGGTAAACAGCAGAAGTGTAAGCTCATGGGTGAAC CGGAAGCAAACATTTCCAAAATGCAGGGTAGGGGCTTGGTTATACTGGGTTTTGAGGGAA TGGAGGAAGAGGCACTAGAAATAGATGGGCAACAGCTTGAGTTTGCTGCTAAGGGAGACA GAAGTATGAGCACGAACTGTTTGTTTTGGTGATAATTGGGAATTTAAAACCCCATGCATG CTACTAGCTAAGCAGGCATTCTACCACTGAGCTCAATACTCAGCCCAGGAATGGTGTTTT TCAAAGAATATGCTGCATTGTTTGGGTGTTGATGAAAATGACGGAGGAGAAGGACAAAAT GGGTGATCACACAGATCTGTTAATAGCTAAAGGAGATGGGATGGGATGCTCACCTGCATC CAACTAGACTGAAACAAGACAGACCAGAGCCAGTGGTTCCTCCAGCTACACTTTCCTCTG AAGAATGAACAACAGATCACACAAAGTAAAGTGTGTAGTCTCTATATGTGGGAGCTTTCC TTATACCCAGCTCTGGTCCCAGGAAGACAGAGATAGGTAACTGGGGCCTTACCCATGATC AACTACACCCTAGCTTCTGTGACCATGAAGGTGAAGCCATTCAGTCTCTTACCAGCCTGG CACTGAAAGAGCATCAAGTGGCTCTGTTAGTCAGGCTGTGGGGCAGAGGAATCCCAGCAG AGGTCAGGATAATTAGGCAACAGCTGGGACAAGATCTTATCTCTGGTAATTCTCCCCTCC CAGAACTCAGGATTAATTAGCTACAGATCAACCCAGACCAGAGATGGAAAGGGCTTTTGG AAGAAATGACTTGGCCTGAGGAGAACAGGCATGCTCAACCTTAACTTCTGCTGGCCACAG TGGACTCTGCTTCCCAGACAGTACCCCTGACAGTGACAGAACTGCCACTCTCCCCACCTG ACCCTGTTAGGAAGGTACAACCTATGAAGAAAAAGCCAGAATACAGGGGACATGTGAGCC ACAGACAACACAAGTGTGCACAACACCTCTGAGCTGAGCTTTTCTTGATTCAAGGGCTAG TGAGAACGCCCCGCCAGAGATTTACCTCTGGTCTTCTGAGGTTGAGGGCTCGTTCTCTCT TCCTGAATGTAAAGGTCAAGATGCTGGGCCTCAGTTTCCTCTTACATACTCACCAAAAGG CTCTCCTGATCAGAGAAGCAGGATGCTGCACTTGTCCTCCTGTCGATGCTCTTGGCTATG ACAAAATCTGAGCTTACCTTCTCTTGCCCACCTCTAAACCCCATAAGGGCTTCGTTCTGT GTCTCTTGAGAATGTCCCTATCTCCAACTCTGTCATACGGGGGAGAGCGAGTGGGAAGGA TCCAGGGCAGGGCTCAGACCCCGGCGCATGGACCTAGTCGGGGGCGCTGGCTCAGCCCCG CCCCGCGCGCCCCCGTCGCAGCCGACGCGCGCTCCCGGGAGGCGGCGGCAGAGGCAGCAT CCACAGCATCAGCAGCCTCAGCTTCATCCCCGGGCGGTCTCCGGCGGGGAAGGCCGGTGG GACAAACGGACAGAAGGCAAAGTGCCCGCAATGGAGGGAGCATCCTTTGGCGCGGGCCGT GCGGGAGCTGCCTTTGATCCCGTGAGCTTTGCGCGGCGGCCCCAGACCCTGTTGCGGGTC GTGTCCTGG
 * mus Syngr3 exon1 + 2000bp 5' 

Batch Entrez Acc nos
AAA40104 AAH05595 AAH12710 AAH14854 AAH24644 AAH28901 AAH31452 AAH46616 AAH49971 AAH50927