RetrogeneDB ID: | retro_cfam_1902 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | 8:18280619..18281313(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | VIM | ||
| Ensembl ID: | ENSCAFG00000004529 | ||
| Aliases: | None | ||
| Description: | vimentin [Source:HGNC Symbol;Acc:12692] |
Retrocopy-Parental alignment summary:
>retro_cfam_1902
AAGGTGAGGAGCAGTGTGCCTGGCATGCGTCTGGTGCAGGACTCAGTATAGTTCTCACTGGCTGAAACTATCAACACCGA
GTTCAAGAACACTTGCACTGGGAAAGTGGAGCTGCAGGAGCTCAATGACCGCTTTGCTAACTACATCAAGGTGTGCTTCC
TGGAGCAGCAGAACAAGATCCTGCTGAGTGAACTCAAGCAGCTCAAGGGCCTGGGCAAATTGGGCCTGGGGGACCTCTAT
GAGAAGAAGATGTGAGGGCTGTGCCAGCAGGTAGGCCAGCTCACCAAGAACAAGGCCTATGTCAAAGGGAGCAGGACACC
TGGCTGAAGGCATCATGTGGCTCTAGGAGAAGTTGCAGGAGGAGATGCTTCAAGGAGAGGAAGCCTAGAGCACCCTGCAG
TCTTTCAGGCAGAATGTTGACAATACTTCTTTGGCATGTCTTGACCTTGAGTGTGAAGTGGAATCCTTGCAAGAAGAGAT
TGCCTTTTTGAAGAAACTATATGATGAGGAAATCCAGGAGCTTCAGGTCCAGATTCAGGACCAGCATGCCCAAATCCGTA
TTGATGTTTCCAAGCCTGACCTCATGGCTGCCCTCCATGATGTGCCCTGGCAGTATGAAAACATGGCTACCAAGAACCTT
CAGGAGGCCAAGGAATGGTACAAGTCCAAATCTGCCAACCTCTCTGAGGCTGCT
ORF - retro_cfam_1902 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.42 % |
| Parental protein coverage: | 50.21 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | RLRSSVPGVRLLQDSVDFSLADAINTEFKNTRTNEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQL |
| ..RSSVPG.RL.QDSV.FSLA..INTEFKNT.T..KVELQELNDRFANYI.KV.FLEQQNKILL.EL.QL | |
| Retrocopy | KVRSSVPGMRLVQDSV*FSLAETINTEFKNTCTG-KVELQELNDRFANYI-KVCFLEQQNKILLSELKQL |
| Parental | KGQGKSRLGDLYEEEMRELRRQVDQLTNDKARV-EVERD-NLAEDIMRLREKLQEEMLQREEAESTLQSF |
| KG.GK..LGDLYE..M..L..QV.QLT..KA.V...E.D..LAE.IM.L.EKLQEEMLQ.EEA.STLQSF | |
| Retrocopy | KGLGKLGLGDLYEKKM*GLCQQVGQLTKNKAYV<QREQD<HLAEGIMWL*EKLQEEMLQGEEA*STLQSF |
| Parental | RQDVDNASLARLDLERKVESLQEEIAFLKKLHDEEIQELQAQIQDQHVQIDMDVSKPDLTAALRDVRQQY |
| RQ.VDN.SLA.LDLE..VESLQEEIAFLKKL.DEEIQELQ.QIQDQH.QI..DVSKPDL.AAL.DV..QY | |
| Retrocopy | RQNVDNTSLACLDLECEVESLQEEIAFLKKLYDEEIQELQVQIQDQHAQIRIDVSKPDLMAALHDVPWQY |
| Parental | ESVAAKNLQEAEEWYKSKFADLSEAA |
| E..A.KNLQEA.EWYKSK.A.LSEAA | |
| Retrocopy | ENMATKNLQEAKEWYKSKSANLSEAA |
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 | 192 .48 RPM |
| SRP017611_brain | 0 .00 RPM | 84 .31 RPM |
| SRP017611_kidney | 0 .07 RPM | 172 .09 RPM |
| SRP017611_liver | 0 .22 RPM | 104 .42 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_1902 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_1902 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_1902 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000004529 | 2 retrocopies |
retro_cfam_1902 , retro_cfam_2022,
|
| Dasypus novemcinctus | ENSDNOG00000011305 | 1 retrocopy |