RetrogeneDB ID: | retro_cfam_1492 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 32:6395055..6395565(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | MED20 | ||
| Ensembl ID: | ENSCAFG00000001613 | ||
| Aliases: | None | ||
| Description: | mediator complex subunit 20 [Source:HGNC Symbol;Acc:16840] |
Retrocopy-Parental alignment summary:
>retro_cfam_1492
GTGACCTGTGTGTCCCAGATGCCTGTGGCTGAGGGCAAGAGTGTCCAGCAGACTGTGGAGCTCCTCACCCAGAAATTGGA
GATGCTTGAGGCAGAGAAGCAAGGAATATTTTGTGTGGATTGTGAAACGTGCCATGCAGCTGCCTCTATTTTTGGCAGCC
AAGGTCAGGCCAGAAAGCTGATGTAAGTGATGCACAACTCAGCGTACCCTTTGAGCTGCTTGGTCCTCTTTGAGAATGGC
CCTCGCCTTATTGCCGACACCAACTCTGATGTGCTCATGGTGAAGCTCAAGGGCTTTTTCCAGAGTGCCAAGGCCATCAA
GACTGAGACCCGGGGTACCTGTTACCAGTACCGTGACTTCCTAGTGAAGGGGGGCACAGTCACCAGGGGACCCAGTTCCT
GAAGCATCTCCATTGCCGTGGAGTATGGCCCCTTTGTGGTAGCTAGCGGCATCTGGAGCTTGCTGCTCAAGTTCCTACAG
AGTTTTCTGGGCAGCAGCTATACACCAGGG
ORF - retro_cfam_1492 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.59 % |
| Parental protein coverage: | 79.72 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VVGVSQMPVAEGKSVQQTVELLTRKLEMLGAEKQGTFCVDCETYHTAASTLGSQGQAGKLMYVMHNSEYP |
| V..VSQMPVAEGKSVQQTVELLT.KLEML.AEKQG.FCVDCET.H.AAS..GSQGQA.KLM.VMHNS.YP | |
| Retrocopy | VTCVSQMPVAEGKSVQQTVELLTQKLEMLEAEKQGIFCVDCETCHAAASIFGSQGQARKLM*VMHNSAYP |
| Parental | LSCFALFENGPCLIADTNFDVLMVKLKGFFQSAKASKIETRGTRYQYCDFLVKVGTVTMGPSARGISVEV |
| LSC..LFENGP.LIADTN.DVLMVKLKGFFQSAKA.K.ETRGT.YQY.DFLVK.GTVT.GPS...IS..V | |
| Retrocopy | LSCLVLFENGPRLIADTNSDVLMVKLKGFFQSAKAIKTETRGTCYQYRDFLVKGGTVTRGPSS*SISIAV |
| Parental | EYGPCVVASDCWSLLLEFLQSFLG-SHTPG |
| EYGP.VVAS..WSLLL.FLQSFLG.S.TPG | |
| Retrocopy | EYGPFVVASGIWSLLLKFLQSFLGSSYTPG |
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 .08 RPM | 6 .64 RPM |
| SRP017611_brain | 0 .00 RPM | 1 .83 RPM |
| SRP017611_kidney | 0 .00 RPM | 6 .47 RPM |
| SRP017611_liver | 0 .00 RPM | 2 .90 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1492 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1492 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1492 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000001613 | 1 retrocopy |
retro_cfam_1492 ,
|
| Dasypus novemcinctus | ENSDNOG00000016666 | 1 retrocopy | |
| Microcebus murinus | ENSMICG00000011326 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000014024 | 1 retrocopy |