RetrogeneDB ID: | retro_cfam_1891 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 7:75596062..75596752(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000018723 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | AAGAB | ||
| Ensembl ID: | ENSCAFG00000017414 | ||
| Aliases: | None | ||
| Description: | alpha- and gamma-adaptin binding protein [Source:HGNC Symbol;Acc:25662] |
Retrocopy-Parental alignment summary:
>retro_cfam_1891
TTTGACAGCACACAAAAATCTGGTCTTGATAGTGTTTCTTCATGGCTTCTGCTGGCAGAAGCATGGTTACCTGTAGTCAT
GATCTTGGTCTGTGACAGAGTGTGTGGAAATGGTGTAAACCGGCAAAAAGCTCAAGAATGGTGTATCAAACATGGCTTTG
AATTGGTAGCACTCAGTCCAGACGAGTTGCCTGAGGAGGAGGATGACCTCCCAGAATCTACAGGCATAAAGAGAATCGTT
CAAGCCTTGAATGCATACGTGTGGTCCAATGTAGCGATGAAGAATGACAGGAACCAAGGCTTTAGCCCTCTTAGCTCATT
GGCTGGAGCAAACCATAGCATTGGGTCAGCAGAGACGTATCATTCAGAGCAGCCCCATTTGCCAGCACCTGCTAGGACTG
AACCCCTCTTGGAGCATCGGGGTGGTGCATCTAACACAACAGACGCTCAGGCTGATAGCATCGTGGATCCCATGTTAGAT
CTGGATATTCAAGAATTAGCCAGGCTTACTACTGGTGGAGGAGATTTGGAGAATTTTGAAAGACTCTTCACAAAGTTAAA
GGAAATGAAAGACAAGGGTGCGATGCTCCCTCATGAGCAAAGACAGTTGCATGCAGGAAAGGTGGCCGAAGCCTTCTGGG
TGGCAGTTGGGGGAGACAGAGAGGAAATTGAAGGTCTTTCATCTGATGAA
ORF - retro_cfam_1891 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.26 % |
| Parental protein coverage: | 60.85 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | FDSTQKSGLDSVSSWLPLAEAWLPEVMILVCDRVCENGVNRQKAQEWCIKHGFELVELSPEELPEEDDDF |
| FDSTQKSGLDSVSSWL.LAEAWLP.VMILVCDRVC.NGVNRQKAQEWCIKHGFELV.LSP.ELPEE.DD. | |
| Retrocopy | FDSTQKSGLDSVSSWLLLAEAWLPVVMILVCDRVCGNGVNRQKAQEWCIKHGFELVALSPDELPEEEDDL |
| Parental | PESTGVKRIIQALNANVWSNVVMKNDRNQGFSLLSSLAGANHSIGSAETCHSEQPRLPAAARTESLLEHR |
| PESTG.KRI.QALNA.VWSNV.MKNDRNQGFS.LSSLAGANHSIGSAET.HSEQP.LPA.ARTE.LLEHR | |
| Retrocopy | PESTGIKRIVQALNAYVWSNVAMKNDRNQGFSPLSSLAGANHSIGSAETYHSEQPHLPAPARTEPLLEHR |
| Parental | GGASNTTDAQPDSIVDPMLDLDIQELASLTTGGGDLENFERLFSKLKEMKDKAATLPHEQRKLHAEKVAK |
| GGASNTTDAQ.DSIVDPMLDLDIQELA.LTTGGGDLENFERLF.KLKEMKDK.A.LPHEQR.LHA.KVA. | |
| Retrocopy | GGASNTTDAQADSIVDPMLDLDIQELARLTTGGGDLENFERLFTKLKEMKDKGAMLPHEQRQLHAGKVAE |
| Parental | AFWMAIGGDRDEIEGLSSDE |
| AFW.A.GGDR.EIEGLSSDE | |
| Retrocopy | AFWVAVGGDREEIEGLSSDE |
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 | 38 .39 RPM |
| SRP017611_brain | 0 .00 RPM | 65 .90 RPM |
| SRP017611_kidney | 0 .00 RPM | 44 .71 RPM |
| SRP017611_liver | 0 .00 RPM | 10 .08 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1891 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1891 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1891 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000040368 | 1 retrocopy | |
| Canis familiaris | ENSCAFG00000017414 | 1 retrocopy |
retro_cfam_1891 ,
|
| Monodelphis domestica | ENSMODG00000009585 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000008424 | 2 retrocopies |