RetrogeneDB ID: | retro_cfam_2030 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | JH373319.1:12048..12673(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000024953 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | STARD5 | ||
| Ensembl ID: | ENSCAFG00000013792 | ||
| Aliases: | None | ||
| Description: | StAR-related lipid transfer (START) domain containing 5 [Source:HGNC Symbol;Acc:18065] |
Retrocopy-Parental alignment summary:
>retro_cfam_2030
GTGGCCGCGCAGATGAGCGACGCGGTGGCGGAGAAGGTGCTCCGGTCCGGCGGGAGGAGTCAGGATGGAAGATTTGCCGG
GAAGGCAATGGAGTTTCAGTTTCCCGGAGGCCATCTGTGGAGTTTCCAGGGAACCTGTGCCGGGGAGAAGGCATTGTGAA
CTCGACACCAGACAGAGTGTGGGGCTGCATGAAGCCGCTTGCTGGGACCCTGCGAGACAAGTGGGATGAGAATGTGAGCA
GCTTTGAAATTATCGAAAGCATCACTGATATGCTGTGCGTGAGCAGAACCGCCACCCCCTCGGCTGCCACGAAGCTCATT
TCCCCCAGGGACTTTGTGGACTTGGTGCTAGTCAAGAAGTGTGAGGACGGGATGCTCAGTTCCAATGCTGTCCACGTAGA
ACACCTGTTATGTCCTCTGAAGCCAGGTTACGTGAGAGGGTTTAACCACCCTTGTGGGTGCTTCTGTGAGCCTCTGCCAG
GGGAGCCCAACAAGACCAAGCTGGTCACGTTCTTCCAGACTGACCTCAGTGGCTACCTCCGCCGAGTGTGGTGGACTCCT
TCTTCCCCCGCAGCATGGCCGGTCTCTACACCAACCTGGAGAAAGCAGTGAAGAGGCTTTATGAC
ORF - retro_cfam_2030 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.0 % |
| Parental protein coverage: | 98.12 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VAAQMSEAVAEKVLR-YRRDESGWKICREGNGVSVSWRPSMEFPGNLYRGEGIVNSTPEKVWGCIKPLAG |
| VAAQMS.AVAEKVLR..RR.ESGWKICREGNGVSVS.RPS.EFPGNL.RGEGIVNSTP..VWGC.KPLAG | |
| Retrocopy | VAAQMSDAVAEKVLR<VRREESGWKICREGNGVSVSRRPSVEFPGNLCRGEGIVNSTPDRVWGCMKPLAG |
| Parental | TLRDKWDENVSSFEIIESITDMLCVSRTATPSAAMKLISPRDFVDLVLVKKYEDGTLSSNAVNVEHPLCP |
| TLRDKWDENVSSFEIIESITDMLCVSRTATPSAA.KLISPRDFVDLVLVKK.EDG.LSSNAV.VEH.LCP | |
| Retrocopy | TLRDKWDENVSSFEIIESITDMLCVSRTATPSAATKLISPRDFVDLVLVKKCEDGMLSSNAVHVEHLLCP |
| Parental | PKPGYVRGFNHPCGCFCEPLPGEPNKTKLVTFFQTDLSGYL-PQSVVDSFFPRSMAGFYTNLEKAVKRLY |
| .KPGYVRGFNHPCGCFCEPLPGEPNKTKLVTFFQTDLSGYL.P.SVVDSFFPRSMAG.YTNLEKAVKRLY | |
| Retrocopy | LKPGYVRGFNHPCGCFCEPLPGEPNKTKLVTFFQTDLSGYL<PPSVVDSFFPRSMAGLYTNLEKAVKRLY |
| Parental | D |
| D | |
| Retrocopy | D |
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 | 2 .73 RPM | 3 .36 RPM |
| SRP017611_brain | 17 .55 RPM | 5 .72 RPM |
| SRP017611_kidney | 0 .46 RPM | 3 .96 RPM |
| SRP017611_liver | 29 .30 RPM | 55 .04 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2030 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2030 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_2030 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000013792 | 1 retrocopy |
retro_cfam_2030 ,
|
| Canis familiaris | ENSCAFG00000030762 | 1 retrocopy |