RetrogeneDB ID: | retro_cjac_2588 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:4559982..4560410(-) | ||
| Located in intron of: | ENSCJAG00000015717 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000032009 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | ENSCJAG00000003896 | ||
| Aliases: | None | ||
| Description: | Glutathione peroxidase [Source:UniProtKB/TrEMBL;Acc:F6T6G6] |
Retrocopy-Parental alignment summary:
>retro_cjac_2588
ATGAACAAGCTGCAGTGGCGCCTTGGGCCCAGTGACCTGGTGGTTCTCGGCTTCCCGTGCAACCAGTTTGGGCATCAGGA
GAACACCAAGAAAGAAGAGATTCTGAATTCCCTAAAGTACGTCCAACCTCGTGGTGGGTTCCAGCCCAACTTCTCGTTCT
TTGAAAAGTGCGAGGTCAACGGTGTAAGGTCGCACCCTCTCTTAGCCTTCCTGTGGAGGCCCTGCCAGTGCCCAGCAATG
ACGCCACGGCACTCATGACCGACCCGGTCTTCAGTGTCTCTAATGTGTGGCAACGATGTTGCCTGGAACTTCAAGAAGTT
CCTGGATGGCCCTGCCGGTGCCCCCGTGCACAGGTACAGCCGCGCTTCCAGACCATTGACATTGAGGCTGACATCCAAGC
CCTGTTGTCCCAACGGTCCAGCCATGCC
ORF - retro_cjac_2588 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 66.44 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MNELQRRLGPRGLVVLGFPCNQFGHQENAKNEEILNSLKYVRPGGGFEPNFMLFEKCEVNSAGSHPLFAF |
| MN.LQ.RLGP..LVVLGFPCNQFGHQEN.K.EEILNSLKYV.P.GGF.PNF..FEKCEVN...SHPL.AF | |
| Retrocopy | MNKLQWRLGPSDLVVLGFPCNQFGHQENTKKEEILNSLKYVQPRGGFQPNFSFFEKCEVNGVRSHPLLAF |
| Parental | LREALPAPSDDATALMTDPKLITWSPVCRNDVAWNFEKFLVGPDGIPVRRYSR-RFQTIDIEPDIEALLS |
| L......P....T.....P.....S..C.NDVAWNF.KFL.GP.G.PV.RYSR.RFQTIDIE.DI.ALLS | |
| Retrocopy | LWRPCQCPA--MTPRHS*PTRSSVSLMCGNDVAWNFKKFLDGPAGAPVHRYSR<RFQTIDIEADIQALLS |
| Parental | QGPSCA |
| Q..S.A | |
| Retrocopy | QRSSHA |
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 .35 RPM | 18 .88 RPM |
| SRP051959_heart | 0 .61 RPM | 18 .19 RPM |
| SRP051959_kidney | 0 .44 RPM | 27 .11 RPM |
| SRP051959_liver | 0 .19 RPM | 33 .79 RPM |
| SRP051959_lung | 0 .44 RPM | 11 .63 RPM |
| SRP051959_lymph_node | 0 .82 RPM | 11 .67 RPM |
| SRP051959_skeletal_muscle | 0 .33 RPM | 14 .00 RPM |
| SRP051959_spleen | 0 .50 RPM | 16 .30 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2588 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2588 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2588 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 6 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000003896 | 6 retrocopies |