RetrogeneDB ID: | retro_cfam_2022 | ||
Retrocopy location | Organism: | Dog (Canis familiaris) | |
| Coordinates: | JH373239.1:626342..627119(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCAFG00000013199 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
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_2022
GCCACCGGGTCTGTGTCCTCGTCCTCCTACCGCAGGATGTGCGGCGGCCGGCCCGGGAGCCGCCGAGCTCCGCGCGGAGC
TACGCGGCCGCGTCCCCCCGCACCTACAGCCTGGGCGGCGCGCCGCGCCCCGGCACCAGCCGCAGCCTCTAGGCCTCGTC
CCGCGGCGCGTCCGCCACGCGCTCCTCCGCGCTGGCCTGCGGAGCAGTGTGCCTGGCGTGCGTCTGCTGCAGGACTCGGC
GCGCTTCTCGCTGGCCGCCGCCATCAACACCGAGTTCAAGCCCACGCGCACCACGAGAAGCTGCAGCTGCAGGAGCTGAA
TGACTGCTTCGCCAACTGCATCGACAAGGTGCGCTTCCTGGAGCAGCAGAACAGGATCCTGCTGGCCGAGCTCGAGCAGC
TCCGGGGCCAGGGCAAGTCGCGCCTGGGGGACCTCTACGAGGAGGAGCTGCGGGAGCTGCGCCGGCGGGTGGACCAGCTC
ACCAACGACAAGGCCTGCGTCGAGGTGGAGCGCCACGACCCGGTCGAGGACATCATGCGGCTCTGGGAGAAGTTGCAAGA
GGAGATGCTTCAGAGAGAGGAAGCCGAGAGCACCCTGCAGTCTTCCCGACAGGCTGGTGCCAACGCTTCTTTGGCGCGTC
TTGACCTTGAGCGGAAAGTGGAATCCTTGCAAGAAGAGATTGCCTTTTTGAAGAAACTACATGATGAGGAAATCCAGGAG
CTGCAGGCCCAGATTCAGGACCAGCACGTCCAAATCGATATGGATGTTTCCAAGCCA
ORF - retro_cfam_2022 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.64 % |
| Parental protein coverage: | 56.22 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | STRSVSSSSYRRMFGGPGTGSR-PSSTRSYVTTSTRTYSLGSALRPSTSRSLYASSPGGAYATRSSAVR- |
| .T.SVSSSSYRRM.GG...GSR.PSS.RSY...S.RTYSLG.A.RP.TSRSL.ASS.G.A.ATRSSA... | |
| Retrocopy | ATGSVSSSSYRRMCGGR-PGSR<PSSARSYAAASPRTYSLGGAPRPGTSRSL*ASSRG-ASATRSSALA< |
| Parental | LRSSVPGVRLLQDSVDFSLADAINTEFKNTRT-NEKVELQELNDRFANYIDKVRFLEQQNKILLAELEQL |
| LRSSVPGVRLLQDS..FSLA.AINTEFK.TRT..EK..LQELND.FAN.IDKVRFLEQQN.ILLAELEQL | |
| Retrocopy | LRSSVPGVRLLQDSARFSLAAAINTEFKPTRT<HEKLQLQELNDCFANCIDKVRFLEQQNRILLAELEQL |
| Parental | KGQGKSRLGDLYEEEMRELRRQVDQLTNDKARVEVERDNLAEDIMRLREKLQEEMLQREEAESTLQSFRQ |
| .GQGKSRLGDLYEEE.RELRR.VDQLTNDKA.VEVER....EDIMRL.EKLQEEMLQREEAESTLQS.RQ | |
| Retrocopy | RGQGKSRLGDLYEEELRELRRRVDQLTNDKACVEVERHDPVEDIMRLWEKLQEEMLQREEAESTLQSSRQ |
| Parental | DVDNASLARLDLERKVESLQEEIAFLKKLHDEEIQELQAQIQDQHVQIDMDVSKP |
| ...NASLARLDLERKVESLQEEIAFLKKLHDEEIQELQAQIQDQHVQIDMDVSKP | |
| Retrocopy | AGANASLARLDLERKVESLQEEIAFLKKLHDEEIQELQAQIQDQHVQIDMDVSKP |
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 .07 RPM | 104 .42 RPM |
Canis familiaris was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cfam_2022 retrocopy.
Canis familiaris was not studied using FANTOM5 data.
retro_cfam_2022 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cfam_2022 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 |