RetrogeneDB ID: | retro_cfam_1058 | ||
Retrocopylocation | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 22:55204970..55205487(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | STUB1 | ||
| Ensembl ID: | ENSCAFG00000031099 | ||
| Aliases: | None | ||
| Description: | STIP1 homology and U-box containing protein 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:11427] |
Retrocopy-Parental alignment summary:
>retro_cfam_1058
CTCAGCTTTGGGGAGGATATCCCTAGTGTTCTGCACATTACCAAGAAGCAGCGTTGGAACAGCATTAAGGAGTGGTGCAT
CCACCAAGAGAATGAGCTGCCCTTCTACCTCGATCCGTTCATTGTGGCCAAGTGGGAGAGCAAGCTAGAATGCCAGCAGA
ACCTTGAGGATGATAAGGATGATGGCTACATCTGCATCCAGCAGGCCTGCGTCGAGGCCAATCATGACAAGTACTTAGTA
GACCTGAATGACCTTTTCTCCCAGGTGGATAAGAGAGAAAGAAGTGAGACATTTCTAACCACCTGTGTGGCAAGATCAGC
TTTGAGTTCATGCAGGAGCCATGCATCATGCCCAGTGGCATTACCTAGGACCACAGGGACATTGAGGATCACCTGCAGTG
TGTGGGTCACATTGACCCTGTCACCTGGAGCCCCCTGATCCAGGAACAGCTCATCCCCAACCTAGCATGAAAGAGGTTGG
TGATGTGTTCATCTCTAAGAACTGCTGGATGGAAGAT
CTCAGCTTTGGGGAGGATATCCCTAGTGTTCTGCACATTACCAAGAAGCAGCGTTGGAACAGCATTAAGGAGTGGTGCAT
CCACCAAGAGAATGAGCTGCCCTTCTACCTCGATCCGTTCATTGTGGCCAAGTGGGAGAGCAAGCTAGAATGCCAGCAGA
ACCTTGAGGATGATAAGGATGATGGCTACATCTGCATCCAGCAGGCCTGCGTCGAGGCCAATCATGACAAGTACTTAGTA
GACCTGAATGACCTTTTCTCCCAGGTGGATAAGAGAGAAAGAAGTGAGACATTTCTAACCACCTGTGTGGCAAGATCAGC
TTTGAGTTCATGCAGGAGCCATGCATCATGCCCAGTGGCATTACCTAGGACCACAGGGACATTGAGGATCACCTGCAGTG
TGTGGGTCACATTGACCCTGTCACCTGGAGCCCCCTGATCCAGGAACAGCTCATCCCCAACCTAGCATGAAAGAGGTTGG
TGATGTGTTCATCTCTAAGAACTGCTGGATGGAAGAT
ORF - retro_cfam_1058 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 67.61 % |
| Parental protein coverage: | 75.32 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | LNFGDDIPSALRIAKKKRWNSIEERRIHQENELHSYLTRLIVAERERELEECQRNHEGDEDDGHVRAQQA |
| L.FG.DIPS.L.I.KK.RWNSI.E..IHQENEL..YL...IVA..E..LE.CQ.N.E.D.DDG....QQA | |
| Retrocopy | LSFGEDIPSVLHITKKQRWNSIKEWCIHQENELPFYLDPFIVAKWESKLE-CQQNLEDDKDDGYICIQQA |
| Parental | CIEAKHDKYLADMDELFSQVDEK-RKKRDIPDYLCGKISFELMREPCITPSGITYDRKDIEEHLQRVGHF |
| C.EA.HDKYL.D...LFSQVD...RKK.DI...LCGKISFE.M.EPCI.PSGIT.D..DIE.HLQ.VGH. | |
| Retrocopy | CVEANHDKYLVDLNDLFSQVDKR<RKK*DISNHLCGKISFEFMQEPCIMPSGIT*DHRDIEDHLQCVGHI |
| Parental | DPVTRSPLTQEQLIPNLA-MKEVIDAFISENGWVED |
| DPVT.SPL.QEQLIPNLA.MKEV.D.FIS.N.W.ED | |
| Retrocopy | DPVTWSPLIQEQLIPNLA<MKEVGDVFISKNCWMED |
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 .00 RPM | 33 .35 RPM |
| SRP017611_brain | 0 .00 RPM | 25 .41 RPM |
| SRP017611_kidney | 0 .00 RPM | 42 .13 RPM |
| SRP017611_liver | 0 .00 RPM | 12 .47 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1058 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1058 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1058 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 | ENSCAFG00000031099 | 1 retrocopy |
retro_cfam_1058 ,
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