RetrogeneDB ID: | retro_cjac_1980 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 2:185820246..185820868(-) | ||
| Located in intron of: | ENSCJAG00000033957 | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000011820 | |
| 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_1980
ATGGACTGGATCCGCATCTCAGCCATGGAGACAGGCAGGCAAACAGGTGTGTCTGCTGAGATGTTCACCATGCCTTGAGG
TCTGGAGGCCAGCAACAAGGATGGAATCCCAGAGGATCTAGATGGGAACTTGGAAGAACCCATGGATCAGGAAGGTAAGC
TCAGGAGTCGGGACGTTATGGACCTCACAGCAGATGACAAGGAAGCCTCAGCCTCAGGTCCTCCTGCATCCAAAAGACTG
AAAACAGATACCAAAGGAAAGAAGGAGAGGAAGCCCACGGTGGATGAAGATGAGGCTCAGAGGATGACAAACCTCCTGTC
TGCTATGTCTGAGGAGCAGCTGGCCCGCTATGAGGTGTGTCGCCGGTCAGCTTTCCCAAAAACACGCATTGCAAATCTGA
TGCAGTCTATCACTGGCAGGTCAGTGCCTGAGAATGTGACCATTGCTATGGCTGGAATAGCCAAGGTCTTGGTGGGAGAG
GTGGTGGAAGAGGCCCTGGACGTGTGTGAGATGTGGGGAGAAACGCCCCCGCTGCAGCCCAGGCATTTGAGGGAGGCTGT
TCGCAGGTTAAAGTCCAAGGGCCTCTTCCCCCAACACCAAGTACAAGAAAATCATGTTCTTC
ORF - retro_cjac_1980 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 59.91 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MDDARESPTDKGGETGESDETVAAPGDPGATDTDGIPEETDGDADADLKEAAAEEGELKSQDVSDLTAVE |
| MD..R.S....G..TG.S.E....P....A...DGIPE..DG.....L.E....EG.L.S.DV.DLTA.. | |
| Retrocopy | MDWIRISAMETGRQTGVSAEMFTMP*GLEASNKDGIPEDLDGN----LEEPMDQEGKLRSRDVMDLTADD |
| Parental | REDSSLLTPAAKKLKIDTKEKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYEMYRRSAFPKAAIKRLIQS |
| .E.S....PA.K.LK.DTK.KKE.K..VDEDE.Q.M..L.S..SEEQL.RYE..RRSAFPK..I..L.QS | |
| Retrocopy | KEASASGPPASKRLKTDTKGKKERKPTVDEDEAQRMTNLLSAMSEEQLARYEVCRRSAFPKTRIANLMQS |
| Parental | ITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVRRLKSKG-QIPNSKHKKII |
| ITG.SV..NV.IAM.GI.KV.VGEVVEEALDVCE.WGE.PPLQP.H.REAVRRLKSKG...PN.K.KKI. | |
| Retrocopy | ITGRSVPENVTIAMAGIAKVLVGEVVEEALDVCEMWGETPPLQPRHLREAVRRLKSKG>SSPNTKYKKIM |
| Parental | FF |
| FF | |
| Retrocopy | FF |
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 .00 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_1980 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1980 was not experimentally validated.