RetrogeneDB ID: | retro_cfam_1576 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 35:26167586..26169839(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCAFG00000011738 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cfam_1576
CTAGAACGGATCCTGTGCCTGCAGCAGTAGCAGCTGCAGCATATGCAGCTCACCGAACATTGGGCCCTCCACTCTGGTGT
GGCAGGAGTGGACACTCTCAAGACGCTGAGCAGACACATGTCCCAGCAGGTTTCCACAGCTGTGGCCTTGCTCAGCCAGA
AAGCTGGCAGCCAGGGCCTGTCTCTGGATGCCTTGAAACCGGCCAAACTACCTTGCGCAAACATCCCTTCCACCGTCAGC
TCTGTGGCCCAGGGGCTGGCACCTTTCACCCTGAAGCCCATATGACAAGGGTGCTGCTGAACATCATGTCGTGCCTTTCT
GGTGCTTTGCTACCTCAGGCCCCTGGCTCTGTGCTCTTCCAGAGCCCTTTCTCCACCATGGTGTTAGACCCATCCAAGAA
AGGGAAGGGGAAGCCGCCGAACATGTCCCCAGTGGAGGCCAAACCCAAAGATGAGGCCATCCTCTGCAAGCACAGGTGTA
AGTACTGTAGGAAGGTTTTGGGGACCAATAGCTTCCTACAGATCCACCTCACCTCCCATACCAGAGAGAGACCCTTTTTG
TGCTGTCTGTGGCCACTGGTTCACCACCAAGGGCAACCTCAAGGTGCACTTTCATTGACATCATCAGGTGAAGGCCAACC
CCCAGCTCTTTGCAGAGTTCCATGACAAAATGGCAACAGGCAATGACATTCCCTATGCAATCTCTGTACCCAGCCCTGTA
GATGAATTAAGTCTCTCTTTAGACAACAAACCTGTCCTTTTAAGAGGAATCCCCAGTCTAGGGCTATCTCAGAATTCTCT
CTTCAGGGACTAACCCCAAGTACCTAATGCACAACCCACTGCCCAATGACCTGCAGCCTAGGCCTTCCTGGGAAAGTAAG
GACCGACCCCTACTATCGAGGGGTGGTGGTGGAGGGGGTTGCAAACCACACTTCCCCAGCATTGGTGGCTTCCAAGGGAG
TAGGACCCCCAGCCAGGGTCAGAGACCCGAAATTACAAAAGCTGGTGGAGAACATTGACAAGGCCACTACTGATCCCAAC
AAATGTCTCATTTCCCACCATTCTTGAGATTCCAGAGCTCCCTCAAGATGCATTACTGCACCCACACCGGGGAGAGGCCA
TTTCATTGTAAGATCTGTGGTCAGGCCTTCTCCACCAAGGGCAACCTGAAGACACACCTCAGGATTCACCAGACCAACAT
GTCCATAAAGACACAGCAATCATGCGCCATCTGCCAGAAGAAGTTTATGAATGTGGTCCTGCTGCAGCAGCACATCCAGA
TGCACATAGATGGCCAGATTCCCATCACGCCTCTGCCTGAGAACCCCTATGATTTTACGGGTCCAGAGGCTGCGATGGTC
AGCGAAAATGGTAGCGCAGGTGCCACCTGTTATGATGACATCATTGAGAGCATCGATGTTGACTAGCTCAGCCACCCAGT
ACGCTTCTGGCAGCTCCCTGAAGGACCCCGTGCCTCTTCCCAACATCCACTCAGCATCACCCACTCTCCGGTTCTCCGTG
AAAGCTGCCCTAGATGCCCCAGGGAAGGTGGGTCCTGGTCCTCTTGTCTAGCAGCAGCAGAGCAGCAGAGAAAATGGTCC
ATTGGAGAGCGACAGCTTGACCAACAACTCACCGTCCTCGGTGATGGGAGACCAGGAGTACCAGAGCCGAAGTCCAGATG
TGCTGAAGACCACATCCTTCCAGGTCCTGTCCCTGGACAATAGCCACGCAGAGGGCATCCAGTCCGGGTCTCCTGATGCT
GGTGGCAAAGCAGACAGCTCCAAGAACAGCCACACTGAGATGGAAGGTCTAGAAGTCTGCCATCAACATTTATCCAAGCC
CAGCCAACCTATGTCAAAGTTGAAGTCCCTGGTGCGTTTGTTGGACTTGCGCCCATATCCGCAGGCATGACACCTTTGCT
AGTGGCCCAGCCATGCTAACAGGCCAAACAACACAGGTATACACGGTGTGAGAAGAATTTATCTAGGGGAGCGCTCTTCA
AATTCATGAGCAGACTCACACTGGGGAGAAGCCTTTTGTGTGTAACATATATGGGTGAGCTTTTACCACCAAAAGCAACT
TGAAGGTCCACTATATGACACATGGGGCGAACAATAGCTCAGCTCTCTGTGGGAGGAAACTGGCCATCAAGAACACCATG
GCTCTGTTAGGAACTGATGGGAAGAGAGTCCCTGAGATGTTTCCAAAGGAAATCCTGGCCCCTTTGGTGAACATGGACCC
TGTGGTATGGAAT
ORF - retro_cfam_1576 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 77.88 % |
| Parental protein coverage: | 70.78 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 11 |
Retrocopy - Parental Gene Alignment:
| Parental | LQQIQLTEQIRVQVNMWASH-ALHSGVAGADTLKTLGSHMSQQVSAAVALLSQKAGSQGLSLDALKPAKL |
| L..I....Q...Q......H.ALHSGVAG.DTLKTL..HMSQQVS.AVALLSQKAGSQGLSLDALKPAKL | |
| Retrocopy | LERILCLQQ*QLQHMQLTEHWALHSGVAGVDTLKTLSRHMSQQVSTAVALLSQKAGSQGLSLDALKPAKL |
| Parental | PHANIPSTASS--QGLASFALKP-DGTRVLPNVMSRLPGALLPQAPGSVLFQSPFSTVALDPSKKGKGKP |
| P.ANIPST.SS..QGLA.F.LKP...TRVL.N.MS.L.GALLPQAPGSVLFQSPFST..LDPSKKGKGKP | |
| Retrocopy | PCANIPSTVSSVAQGLAPFTLKP<HMTRVLLNIMSCLSGALLPQAPGSVLFQSPFSTMVLDPSKKGKGKP |
| Parental | PNVSPVEAKPKDEAILCKHKCKYCSKVFGTDSSLQIHLRSHTGER-PFVCSVCGHRFTTKGNLKVHFHRH |
| PN.SPVEAKPKDEAILCKH.CKYC.KV.GT.S.LQIHL.SHT.ER.PF.C.VCGH.FTTKGNLKVHFH.H | |
| Retrocopy | PNMSPVEAKPKDEAILCKHRCKYCRKVLGTNSFLQIHLTSHTRER>PF-CAVCGHWFTTKGNLKVHFH*H |
| Parental | PQVKANPQLFAEFHDKMTAGNGIPYALSVPVPVDESSLSLDSKPVLVTGTPGLGLPQN-LSSGTNPKDLL |
| .QVKANPQLFAEFHDKM..GN.IPYA.SVP.PVDE.SLSLD.KPVL..G.P.LGL.QN.LSSGTNPK.L. | |
| Retrocopy | HQVKANPQLFAEFHDKMATGNDIPYAISVPSPVDELSLSLDNKPVLLRGIPSLGLSQN>LSSGTNPKYLM |
| Parental | GGPLPNDLQPGPSPESEDGSLLS----GGG-PNHTSPR-VGGFQGSGTP-EPGSETL-KLQQLVENIDKA |
| ..PLPNDLQP.PS.ES.D..LLS....GGG..NHTSP...GGFQGS.TP..PGSET..KLQ.LVENIDKA | |
| Retrocopy | HNPLPNDLQPRPSWESKDRPLLSRGGGGGG>ANHTSPA<IGGFQGSRTP<QPGSETR<KLQKLVENIDKA |
| Parental | TTDPNECLICHR-VLSCQSSLKMHYRTHTGERPFQCKICGRAFSTKGNLKTHLGVHRTNTSIKTQHSCPI |
| TTDPN.CLI.H...L..QSSLKMHY.THTGERPF.CKICG.AFSTKGNLKTHL..H.TN.SIKTQ.SC.I | |
| Retrocopy | TTDPNKCLISHH<FLRFQSSLKMHYCTHTGERPFHCKICGQAFSTKGNLKTHLRIHQTNMSIKTQQSCAI |
| Parental | CQKKFTNAVLLQQHIRMHMGGQIPNTPLPENPCDFAGPEAAMVSENGSAGATCHDDVIESIDVDEL-GPQ |
| CQKKF.N.VLLQQHI.MH..GQIP.TPLPENP.DF.GPEAAMVSENGSAGATC.DD.IESIDVD.L...Q | |
| Retrocopy | CQKKFMNVVLLQQHIQMHIDGQIPITPLPENPYDFTGPEAAMVSENGSAGATCYDDIIESIDVD*L>ATQ |
| Parental | DASGSSLKVPVPLPSVHSASPTLGFAVTAALDAPGKVGPAPLVLQRQSSRENGSVESDGLTNDSSSSVMG |
| .ASGSSLK.PVPLP..HSASPTL.F.V.AALDAPGKVGP.PLV.Q.QSSRENG..ESD.LTN.S.SSVMG | |
| Retrocopy | YASGSSLKDPVPLPNIHSASPTLRFSVKAALDAPGKVGPGPLV*QQQSSRENGPLESDSLTNNSPSSVMG |
| Parental | DQEYQSRSPDVLETASFQALSPANSQAESIKSRSPDAGGKADSSENSRTEMEG-RSSLPSTFIRTQPTYV |
| DQEYQSRSPDVL.T.SFQ.LS..NS.AE.I.S.SPDAGGKADSS.NS.TEMEG...SLPSTFI..QPTYV | |
| Retrocopy | DQEYQSRSPDVLKTTSFQVLSLDNSHAEGIQSGSPDAGGKADSSKNSHTEMEG<SRSLPSTFIQAQPTYV |
| Parental | KVEVPGAFVGPATMSPGMTPLLTAQPRRQAKQHGCTRCGKNFSS-ASALQIHERTHTGEKPFVCNICGRA |
| KVEVPGAFVG.A..S.GMTPLL.AQP..QAKQH..TRC.KN.S...SALQIHE.THTGEKPFVCNI.G.A | |
| Retrocopy | KVEVPGAFVGLAPISAGMTPLLVAQPC*QAKQHRYTRCEKNLSR<GSALQIHEQTHTGEKPFVCNIYG*A |
| Parental | FTTKGNLKVHYMTHGANNSSARRGRKLAIENTMALLGTDGKRVPEMFPKEILAPSVNMDPVVWN |
| FTTK.NLKVHYMTHGANNSSA..GRKLAI.NTMALLGTDGKRVPEMFPKEILAP.VNMDPVVWN | |
| Retrocopy | FTTKSNLKVHYMTHGANNSSALCGRKLAIKNTMALLGTDGKRVPEMFPKEILAPLVNMDPVVWN |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP012049_cerebellum | 0 .17 RPM | 0 .00 RPM |
| SRP017611_brain | 0 .08 RPM | 0 .08 RPM |
| SRP017611_kidney | 0 .00 RPM | 1 .06 RPM |
| SRP017611_liver | 0 .00 RPM | 0 .51 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1576 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1576 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1576 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000011738 | 1 retrocopy |
retro_cfam_1576 ,
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