RetrogeneDB ID: | retro_cjac_418 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:75632457..75634016(+) | ||
| Located in intron of: | ENSCJAG00000013220 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000013234 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TRIM8 | ||
| Ensembl ID: | ENSCJAG00000018057 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_cjac_418
AACAACTTCTGCCGGGGCTGCATCGGCGAGGCGTGGGCCAAGGACAGCGGCCTTGTGCGCTTTCCAGAGTGCAACCAGGC
CTACAACCAGAAGCCGGGCCTGGAGAAGAACCTGAAGCTCACCAACATCCTGGAGAAGTTCAACGCCCTGCACGTGGAGA
AGCCGCCGCCGGCGCTGCACTGCGTGTTCTGCCGCCGCTGTCCCCCGCTGCCCGCGCAGAAGGTCTGCCTGTGCTGCGAG
GTGCCCTGCTGCCAGTCCCACGTGCAGATGCACCTGCAGCAGCCCTCCACCGCCCGCGGGCACCTCCTGGTGGAGGCGGA
CGACGTGCGGGGCTGGAACTGCCCGCAGCACAACGCCTATCGCCTCTACCACCTCGAGGCCGAGCAGGTGGCAGTTTGCC
AGTACTGCTGCTACTACAGTGGCGCGCATCAGGGACACTCGGTGAGCGACGTGGAGATCCGAAGGAATAAAATCCGGAAG
ATGCTCATGAAGCAGCAGGACCGGCTGGAGGAGCGAGAGCAGGACATTGAGGATCAGCTGTACAAACTCGAGTCAGACAA
GCTACTGGTGGAGGAGAAAGTGAACCAACTGAAGGAGGAAGTTCGACTGCAGTACGAGAAGCTGCACCAGCTGCTAGATG
AGGACCTGCGGCAGACAGTGGAGGTCCTGGACAAGGCCCGGCCAAGTTCTGCAGCGAGAACGCAGCGCAGGCGCTGCACC
TCGGGAAGCACATGCAGGAGGCCAAGAAGCTGCTGGGTTCCCTGCAGCTGCTGTTTGATAAGACGGAGGATGTCAGCTTC
ATGAAGAACCCCAAGTCTGTGAAAATCCTGATGGACAGGACCCAGACCTGCACAGGCAGCAGCCTTTCTCCACCTAAGAT
CGGCCACCTGAACTCCAAGCTCTTTCTGAACCAGGTGGCCAAGAAGGAGAAGCAGCTGCGGAAGATGCTAGAAGGCCCCT
TCAGCACGCTGGTGCCCTTCCTGCAGAGCGTCCCCCTGTACTCTTGCGGCGTCAGCAGCTCTGGGGCAGAAAAGCGCAAG
CACTCAACGGCCTTCCCAGAGGCCAGTTTCCTAGAGATGTTGTCGGGCCCTGTGGGCGGCCAGTACAGGGCGGCGGGCAC
AGCCAGCGGTGAGGGCCAGTCTGGGCAGCCCCTGGGGCCCTGCAGCTCCACACAGCACTTGGTGGCCTTGCCGGGCGGTG
CCCAACCAGTGCACTCAAGCCCCGTGTTCCTCTCATCGCAGTATCCCAATGGCTCTGCCGCCCAGCAGCCCATGCTCCCC
CAGTATGGTGGCCGCAAGACTCTCGTCTGTTCTGTGGACAACTGTTACTGTTTTTCCGTGGCCAACCATGGCGGCCACCA
GCCCTACCCCCGCTCCGGCCACTTTCTCTGGACAGTGCCCTCGCAGGAGTACTCACACCCGCTCCCGCCCACACCCTCCG
TCCCCCAGTCACTTCCCAGCCTGGCGGTCAGAGACTGGCTCGACGCCTCCCAGCAGCCCGACCACCAGGATTTCTACAGG
GTGTATGGGCAGCCGTCCACCAAACACTACGTGACGAGC
ORF - retro_cjac_418 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 93.86 % |
| Parental protein coverage: | 94.37 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | HNFCRGCIGEAWAKDSGLVRCPECNQAYNQKPGLEKNLKLTNIVEKFNALHVEKPPAALHCVFCRRGPPL |
| .NFCRGCIGEAWAKDSGLVR.PECNQAYNQKPGLEKNLKLTNI.EKFNALHVEKPP.ALHCVFCRR.PPL | |
| Retrocopy | NNFCRGCIGEAWAKDSGLVRFPECNQAYNQKPGLEKNLKLTNILEKFNALHVEKPPPALHCVFCRRCPPL |
| Parental | PAQKVCLRCEAPCCQSHVQTHLQQPSTARGHLLVEADDVRAWSCPQHNAYRLYHCEAEQVAVCQYCCYYS |
| PAQKVCL.CE.PCCQSHVQ.HLQQPSTARGHLLVEADDVR.W.CPQHNAYRLYH.EAEQVAVCQYCCYYS | |
| Retrocopy | PAQKVCLCCEVPCCQSHVQMHLQQPSTARGHLLVEADDVRGWNCPQHNAYRLYHLEAEQVAVCQYCCYYS |
| Parental | GAHQGHSVCDVEIRRNEIRKMLMKQQDRLEEREQDIEDQLYKLESDKRLVEEKVNQLKEEVRLQYEKLHQ |
| GAHQGHSV.DVEIRRN.IRKMLMKQQDRLEEREQDIEDQLYKLESDK.LVEEKVNQLKEEVRLQYEKLHQ | |
| Retrocopy | GAHQGHSVSDVEIRRNKIRKMLMKQQDRLEEREQDIEDQLYKLESDKLLVEEKVNQLKEEVRLQYEKLHQ |
| Parental | LLDEDLRQTVEVLDKAQ-AKFCSENAAQALHLGERMQEAKKLLGSLQLLFDKTEDVSFMKNTKSVKILMD |
| LLDEDLRQTVEVLDKA..AKFCSENAAQALHLG..MQEAKKLLGSLQLLFDKTEDVSFMKN.KSVKILMD | |
| Retrocopy | LLDEDLRQTVEVLDKAR<AKFCSENAAQALHLGKHMQEAKKLLGSLQLLFDKTEDVSFMKNPKSVKILMD |
| Parental | RTQTCTGSSLSPPKIGHLNSKLFLNEVAKKEKQLRKMLEGPFSTPVPFLQSVPLYPCGVSSSGAEKRKHS |
| RTQTCTGSSLSPPKIGHLNSKLFLN.VAKKEKQLRKMLEGPFST.VPFLQSVPLY.CGVSSSGAEKRKHS | |
| Retrocopy | RTQTCTGSSLSPPKIGHLNSKLFLNQVAKKEKQLRKMLEGPFSTLVPFLQSVPLYSCGVSSSGAEKRKHS |
| Parental | TAFPEASFLETSSGPVGGQYGAAGTASSEGQSGQPLGPCSSTQHLVALPGGAQPVHSSPVFPPSQYPNGS |
| TAFPEASFLE..SGPVGGQY.AAGTAS.EGQSGQPLGPCSSTQHLVALPGGAQPVHSSPVF..SQYPNGS | |
| Retrocopy | TAFPEASFLEMLSGPVGGQYRAAGTASGEGQSGQPLGPCSSTQHLVALPGGAQPVHSSPVFLSSQYPNGS |
| Parental | AAQQPMLPQYGGRKILVCSVDNCYCSSVANHGGHQPYPRSGHFPWTVPSQEYSHPLPPTPSVPQSLPSLA |
| AAQQPMLPQYGGRK.LVCSVDNCYC.SVANHGGHQPYPRSGHF.WTVPSQEYSHPLPPTPSVPQSLPSLA | |
| Retrocopy | AAQQPMLPQYGGRKTLVCSVDNCYCFSVANHGGHQPYPRSGHFLWTVPSQEYSHPLPPTPSVPQSLPSLA |
| Parental | VRDWLDASQQPGHQDFYRVYGQPSTKHYVTS |
| VRDWLDASQQP.HQDFYRVYGQPSTKHYVTS | |
| Retrocopy | VRDWLDASQQPDHQDFYRVYGQPSTKHYVTS |
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 |
|---|---|---|
| SRP051959_colon | 0 .11 RPM | 8 .45 RPM |
| SRP051959_heart | 0 .19 RPM | 12 .28 RPM |
| SRP051959_kidney | 0 .11 RPM | 24 .29 RPM |
| SRP051959_liver | 0 .11 RPM | 6 .06 RPM |
| SRP051959_lung | 0 .18 RPM | 19 .46 RPM |
| SRP051959_lymph_node | 0 .18 RPM | 16 .73 RPM |
| SRP051959_skeletal_muscle | 0 .24 RPM | 5 .96 RPM |
| SRP051959_spleen | 0 .36 RPM | 12 .12 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_418 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_418 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_418 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 | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000018057 | 1 retrocopy |
retro_cjac_418 ,
|
| Xenopus tropicalis | ENSXETG00000007381 | 1 retrocopy |