RetrogeneDB ID: | retro_cjac_641 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:182898587..182899104(-) | ||
| Located in intron of: | ENSCJAG00000017316 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000017291 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | POLR2G | ||
| Ensembl ID: | ENSCJAG00000018688 | ||
| Aliases: | None | ||
| Description: | polymerase (RNA) II (DNA directed) polypeptide G [Source:HGNC Symbol;Acc:9194] |
Retrocopy-Parental alignment summary:
>retro_cjac_641
GTGTTCTACCATATCTCTCCAGAGCACAAAATCCTGGTGTACCCACGCTACTTCGGCCCCAACTTGCTCAACATGGTGAA
GCAGAAGCTCTTCACCGAGGTGGAGGGGACCTGCACCGGGAAGTATGGTTTTGTAAACGCTATAACCACCATTGACAATA
TCGGTGCTGGTGTGATCCAGCCAGGCCGAGGCTTCCTCCTTTATCCAGTTAAGTACAAGGCTATTGTTTTCCGGCCCTTT
AAAAGCGAAGTGGTGGATGCTATTGTCACTCAGGTCAACAAAGTTGGACTCTTCACAGAAATTGGGCCTATGTCTTGCTT
CATCTCTCGACATTCCATCCCTTCAGAGATGGAGTTTGATCCTAACTCCAACCCACCATGTTACAAGACAACGGATGAGG
ATATTGTGATTCAGCAGGACGATGAGATCCGCTTAAAGACTGTGGGGACCCGTGTGGACAAGAATGACATTTTTGCTATT
GGCTCCCTGATGGATGATTACTTAAGGGCTTGTAAGC
ORF - retro_cjac_641 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.91 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPV |
| .FYHIS.EH.IL..PRYFGPNLLN.VKQKLFTEVEGTCTGKYGFV.A.TTIDNIGAGVIQPGRGF.LYPV | |
| Retrocopy | VFYHISPEHKILVYPRYFGPNLLNMVKQKLFTEVEGTCTGKYGFVNAITTIDNIGAGVIQPGRGFLLYPV |
| Parental | KYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQD |
| KYKAIVFRPFK.EVVDA.VTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKT.DEDIVIQQD | |
| Retrocopy | KYKAIVFRPFKSEVVDAIVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTTDEDIVIQQD |
| Parental | DEIRLKIVGTRVDKNDIFAIGSLMDDYL-GLVS |
| DEIRLK.VGTRVDKNDIFAIGSLMDDYL.GLVS | |
| Retrocopy | DEIRLKTVGTRVDKNDIFAIGSLMDDYL>GLVS |
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 .73 RPM | 9 .19 RPM |
| SRP051959_heart | 0 .32 RPM | 9 .66 RPM |
| SRP051959_kidney | 0 .71 RPM | 9 .32 RPM |
| SRP051959_liver | 0 .32 RPM | 8 .58 RPM |
| SRP051959_lung | 0 .78 RPM | 12 .27 RPM |
| SRP051959_lymph_node | 0 .46 RPM | 17 .62 RPM |
| SRP051959_skeletal_muscle | 0 .94 RPM | 8 .60 RPM |
| SRP051959_spleen | 0 .50 RPM | 16 .05 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_641 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_641 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_641 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000018688 | 1 retrocopy |
retro_cjac_641 ,
|
| Dipodomys ordii | ENSDORG00000015696 | 1 retrocopy | |
| Macropus eugenii | ENSMEUG00000011547 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000011039 | 1 retrocopy | |
| Pteropus vampyrus | ENSPVAG00000003481 | 1 retrocopy |