RetrogeneDB ID: | retro_cjac_3168 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 8:115463715..115464215(-) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | ENSCJAG00000016426 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | PTN | ||
| Ensembl ID: | ENSCJAG00000012786 | ||
| Aliases: | None | ||
| Description: | pleiotrophin [Source:HGNC Symbol;Acc:9630] |
Retrocopy-Parental alignment summary:
>retro_cjac_3168
ATGCAGGCTCAACAGTACCAGCAGCAGCGTCGACATTCGCAGCTGTCTTCTTGGCATTCATTTTCATACTGGCAGCTGTG
GATAATGCCGAAGAAGGGAAGAAAGAGAAACCAGAAAAAGAAGTGAAGAAGTCTGACTGTGGAGAATGGCAGTGGAGTGT
GTGTGTGCCCACCAGTGGAGACTGTGGGCTGGGCATGTGGGAGGGCACTTGGACTGGAGCCGAGTGCAAGCAAACCATGA
AGACCCAGAGATGTAAGATCTCCTGCAGCTGGAAAAAGCAATTTGGAGCGGAGTACAAATACCAGTTGCAGGCCTGGGGA
GAGTGTGACCTGAACATGGCCCTAAAGACCAGCACTGGAAGTCTGAAGCGAGTCCTGCACAATGCCAAATGCCAGAAGAC
AGTCACCATCTCCAAGCCCTTTGGCAAACTGACCAAGCCCAAGCCTCAAGTGGAATCTAAGAAGAAAAAGGAAGGCAAGA
AACAGGAGAAGATGTTGGAT
ATGCAGGCTCAACAGTACCAGCAGCAGCGTCGACATTCGCAGCTGTCTTCTTGGCATTCATTTTCATACTGGCAGCTGTG
GATAATGCCGAAGAAGGGAAGAAAGAGAAACCAGAAAAAGAAGTGAAGAAGTCTGACTGTGGAGAATGGCAGTGGAGTGT
GTGTGTGCCCACCAGTGGAGACTGTGGGCTGGGCATGTGGGAGGGCACTTGGACTGGAGCCGAGTGCAAGCAAACCATGA
AGACCCAGAGATGTAAGATCTCCTGCAGCTGGAAAAAGCAATTTGGAGCGGAGTACAAATACCAGTTGCAGGCCTGGGGA
GAGTGTGACCTGAACATGGCCCTAAAGACCAGCACTGGAAGTCTGAAGCGAGTCCTGCACAATGCCAAATGCCAGAAGAC
AGTCACCATCTCCAAGCCCTTTGGCAAACTGACCAAGCCCAAGCCTCAAGTGGAATCTAAGAAGAAAAAGGAAGGCAAGA
AACAGGAGAAGATGTTGGAT
ORF - retro_cjac_3168 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.35 % |
| Parental protein coverage: | 100. % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MQAQQYQQQRRK-FAAVFLAFIFILAAVDNAEAGKKEKPEKKVKKSDCGEWQWSVCVPTSGDCGLGTREG |
| MQAQQYQQQRR..FAAVFLAFIFILAAVDNAE.GKKEKPEK.VKKSDCGEWQWSVCVPTSGDCGLG..EG | |
| Retrocopy | MQAQQYQQQRRH<FAAVFLAFIFILAAVDNAEEGKKEKPEKEVKKSDCGEWQWSVCVPTSGDCGLGMWEG |
| Parental | TRTGAECKQTMKTQRCKIPCNWKKQFGAECKYQFQAWGECDLNTALKTRTGSLKRALHNAECQKTVTISK |
| T.TGAECKQTMKTQRCKI.C.WKKQFGAE.KYQ.QAWGECDLN.ALKT.TGSLKR.LHNA.CQKTVTISK | |
| Retrocopy | TWTGAECKQTMKTQRCKISCSWKKQFGAEYKYQLQAWGECDLNMALKTSTGSLKRVLHNAKCQKTVTISK |
| Parental | PCGKLTKPKPQAESKKKKKEGKKQEKMLD |
| P.GKLTKPKPQ.ES.KKKKEGKKQEKMLD | |
| Retrocopy | PFGKLTKPKPQVES-KKKKEGKKQEKMLD |
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 .00 RPM | 1 .84 RPM |
| SRP051959_heart | 0 .00 RPM | 1 .28 RPM |
| SRP051959_kidney | 0 .04 RPM | 1 .86 RPM |
| SRP051959_liver | 0 .06 RPM | 0 .89 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .89 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .09 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .17 RPM |
| SRP051959_spleen | 0 .04 RPM | 0 .29 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3168 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3168 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3168 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 | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000003369 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000012786 | 1 retrocopy |
retro_cjac_3168 ,
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