RetrogeneDB ID: | retro_cjac_4068 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | X:56160890..56161429(+) | ||
| Located in intron of: | None | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | TMEM82 | ||
| Ensembl ID: | ENSCJAG00000008582 | ||
| Aliases: | None | ||
| Description: | transmembrane protein 82 [Source:HGNC Symbol;Acc:32350] |
Retrocopy-Parental alignment summary:
>retro_cjac_4068
CTGGGCGCCCGGCGCCTCCACCGCCACGTCTGCCGCCTCTACAAGCTGCACAGCAGCCAGCGCTACTGTGGGGTATGCCT
GGGCCTGCTGGCCGGCGCGCACGATCTCCCCCGTCTGCTGGGCCGTGCCCTGGCCGTGGTCTTTGCTGTGGGTGACCTGG
CAGCAGTGGCCCTCATCAATCGGGACTTTCTGACTACCTCGGAGGCCGTGCGGTTCTGGACGCCGCTCACCATCTGCTAC
ACGCTGCTGGTCATCTACATGCAGGAGGAGCAGCGGCAGCACCCTGGCCTGCAGAGTCAGGTGCAGACGGTGCTGGTGTG
CATGGGCGGTCTCTTTGTGCTGCTGCTGACTGTGGGCCGCTGGCTGGACCTGCTGGGCATCCTCGTTTCCCTGCTGGGCG
AGCTCTGGTGTCTGGTGGGCGTCCGCACCCTACTTGACCTCTGCCAGATACAGGACATTCCAACCCAGAGGCCTTCGGTG
TCAACGCCAAGGCCCAGCCCCTGCCCTCTACACCCCAGCCCCAGAGTTCAGCCTCCTCC
CTGGGCGCCCGGCGCCTCCACCGCCACGTCTGCCGCCTCTACAAGCTGCACAGCAGCCAGCGCTACTGTGGGGTATGCCT
GGGCCTGCTGGCCGGCGCGCACGATCTCCCCCGTCTGCTGGGCCGTGCCCTGGCCGTGGTCTTTGCTGTGGGTGACCTGG
CAGCAGTGGCCCTCATCAATCGGGACTTTCTGACTACCTCGGAGGCCGTGCGGTTCTGGACGCCGCTCACCATCTGCTAC
ACGCTGCTGGTCATCTACATGCAGGAGGAGCAGCGGCAGCACCCTGGCCTGCAGAGTCAGGTGCAGACGGTGCTGGTGTG
CATGGGCGGTCTCTTTGTGCTGCTGCTGACTGTGGGCCGCTGGCTGGACCTGCTGGGCATCCTCGTTTCCCTGCTGGGCG
AGCTCTGGTGTCTGGTGGGCGTCCGCACCCTACTTGACCTCTGCCAGATACAGGACATTCCAACCCAGAGGCCTTCGGTG
TCAACGCCAAGGCCCAGCCCCTGCCCTCTACACCCCAGCCCCAGAGTTCAGCCTCCTCC
ORF - retro_cjac_4068 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.48 % |
| Parental protein coverage: | 52.34 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | LGARRLHRHVCRLYELHSSQRYCGVCLGLLAGAHDLPRLLGRALAVAFAVGDLAAVALINRDFLTTSEAV |
| LGARRLHRHVCRLY.LHSSQRYCGVCLGLLAGAHDLPRLLGRALAV.FAVGDLAAVALINRDFLTTSEAV | |
| Retrocopy | LGARRLHRHVCRLYKLHSSQRYCGVCLGLLAGAHDLPRLLGRALAVVFAVGDLAAVALINRDFLTTSEAV |
| Parental | QFWTPLTICYTLLVIYMQEEQRQHPGLQSQVQTVLVRMGGLFVLLLTVGRWLDLLGILVSLLGELWCLVG |
| .FWTPLTICYTLLVIYMQEEQRQHPGLQSQVQTVLV.MGGLFVLLLTVGRWLDLLGILVSLLGELWCLVG | |
| Retrocopy | RFWTPLTICYTLLVIYMQEEQRQHPGLQSQVQTVLVCMGGLFVLLLTVGRWLDLLGILVSLLGELWCLVG |
| Parental | VRTLLDLCQIQDIPTQRPSVSTP-SQPLP-STPQSQSSASS |
| VRTLLDLCQIQDIPTQRPSVSTP...P.P.STPQ.QSSASS | |
| Retrocopy | VRTLLDLCQIQDIPTQRPSVSTPRPSPCP<STPQPQSSASS |
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 | 0 .09 RPM |
| SRP051959_heart | 0 .04 RPM | 0 .98 RPM |
| SRP051959_kidney | 0 .02 RPM | 0 .13 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .47 RPM |
| SRP051959_lung | 0 .15 RPM | 0 .11 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .07 RPM | 0 .52 RPM |
| SRP051959_spleen | 0 .06 RPM | 0 .04 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4068 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4068 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4068 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000008582 | 1 retrocopy |
retro_cjac_4068 ,
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