RetrogeneDB ID: | retro_cjac_2657 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:116268246..116268877(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000034012 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TAF11 | ||
| Ensembl ID: | ENSCJAG00000015388 | ||
| Aliases: | None | ||
| Description: | TAF11 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 28kDa [Source:HGNC Symbol;Acc:11544] |
Retrocopy-Parental alignment summary:
>retro_cjac_2657
ATGGACGATGCCCGCGAGTCGCCCACAGACTAAGGTGGAGAGACAGGGGAGTCGGATGAGACCATCGCTGCGCCCGGGGA
CCCGGGGGCTACCGACACGGATGGAATCCCAGAGGAAACTGACGGAAGACGCAGATGCGGACTTACAAGAAGCTGCAGCA
GAGGAAGGCGAGCTCAAGAGTCAGGATGTCTCAGATTTAACAGCAGTTGAAAGGGAAGACTCATCATTACTTACTCCTGC
AGCCAAAAAACTGAAAATAGATACCAAAGAAAAGAAAGAGAAGAAGCAGAAGGTAGATGAAGATGAGATTCAGAAGATGG
AAACCCTGGTTTCTTCTTTTTCTGAAGAGCAGCTGAACCATTATGAAATGTATCCTCGCTCAGCTTTCCCTAAGACAGCC
ATCAAAAGACTGATCCAGTCCATCACGGGCACCTCTGTGTCTCAGAATGTTGTTATTGCTATGTCTGGTATTTCCAAGGT
TTTCGTCGGGCAGGTGGTAGAAGAAGCACTGGATGTGTGTGAGAAGTGGGGAGAAATGCCACCACTGCAACCCAAACATA
TGAGGGAAGCCGTTAGAAGGTTAAAGTCAAAAGGACAGATCCCTAACTTGAAGCACAAAAAAATCATCTTC
ORF - retro_cjac_2657 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 94.79 % |
| Parental protein coverage: | 99.53 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MDDARESPTDKGGETGESDETVAAPGDPGATDTDGIPEETDG-DADADLKEAAAEEGELKSQDVSDLTAV |
| MDDARESPTD.GGETGESDET.AAPGDPGATDTDGIPEETDG.DADADL.EAAAEEGELKSQDVSDLTAV | |
| Retrocopy | MDDARESPTD*GGETGESDETIAAPGDPGATDTDGIPEETDG>DADADLQEAAAEEGELKSQDVSDLTAV |
| Parental | EREDSSLLTPAAKKLKIDTKEKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQ |
| EREDSSLLTPAAKKLKIDTKEKKEKKQKVDEDEIQKM..LVSSFSEEQLN.YEMY.RSAFPK.AIKRLIQ | |
| Retrocopy | EREDSSLLTPAAKKLKIDTKEKKEKKQKVDEDEIQKMETLVSSFSEEQLNHYEMYPRSAFPKTAIKRLIQ |
| Parental | SITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIPNSKHKKII |
| SITGTSVSQNVVIAMSGISKVFVG.VVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIPN.KHKKII | |
| Retrocopy | SITGTSVSQNVVIAMSGISKVFVGQVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKGQIPNLKHKKII |
| Parental | F |
| F | |
| Retrocopy | F |
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 | 5 .37 RPM |
| SRP051959_heart | 0 .02 RPM | 5 .67 RPM |
| SRP051959_kidney | 0 .00 RPM | 4 .84 RPM |
| SRP051959_liver | 0 .00 RPM | 5 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 5 .16 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .09 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 7 .47 RPM |
| SRP051959_spleen | 0 .00 RPM | 5 .02 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2657 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2657 was not experimentally validated.