RetrogeneDB ID: | retro_cjac_2402 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:3786387..3786858(-) | ||
| Located in intron of: | ENSCJAG00000006074 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_2402
GCGGAGGAAGGCGAGCTCAAGAGTCAGGATGTCTCAGATTTAACAGAGGTTGAAAGCTAAGACTCATCATTACTTACTCC
TGCAGCCAAAAAACTGAAAATAGATACCAAAGAAAAGAAAGAGAAGCAGCAGAAGGTAGATGAAGATGAGATTCAGAAGG
TGCAAATCCTGGTTTCTTCTTTTTCTGAAGAGCAGCTGAACCGTTATGAAATGTATCGCTGCTCAGCTTTCCCTAAGGCA
GCCATCAAAAGGCTGATCCAGTCCATCACTGGCACCTCTGTGTCTCAGAATGTTACTGCTATGTCTGGTATTTCCAAGGT
TTTCGTCGGGGAGGTGGTAGAGGCAGCACTGGATGTGTGTGAGAAGTGGGGAGAAATGCCACCACTGCAACCCAAAGGTA
TGAGGGAAGCCGTTAGAAGGTTAAAGTCAAAAGGACAGATCCATAACTCAAAGCACAAAGAATTCATCTTC
ORF - retro_cjac_2402 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 91.77 % |
| Parental protein coverage: | 74.88 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AEEGELKSQDVSDLTAVEREDSSLLTPAAKKLKIDTKEKKEKKQKVDEDEIQKMQILVSSFSEEQLNRYE |
| AEEGELKSQDVSDLT.VE..DSSLLTPAAKKLKIDTKEKKEK.QKVDEDEIQK.QILVSSFSEEQLNRYE | |
| Retrocopy | AEEGELKSQDVSDLTEVES*DSSLLTPAAKKLKIDTKEKKEKQQKVDEDEIQKVQILVSSFSEEQLNRYE |
| Parental | MYRRSAFPKAAIKRLIQSITGTSVSQNVVIAMSGISKVFVGEVVEEALDVCEKWGEMPPLQPKHMREAVR |
| MYR.SAFPKAAIKRLIQSITGTSVSQNV..AMSGISKVFVGEVVE.ALDVCEKWGEMPPLQPK.MREAVR | |
| Retrocopy | MYRCSAFPKAAIKRLIQSITGTSVSQNVT-AMSGISKVFVGEVVEAALDVCEKWGEMPPLQPKGMREAVR |
| Parental | RLKSKGQIPNSKHKKIIF |
| RLKSKGQI.NSKHK..IF | |
| Retrocopy | RLKSKGQIHNSKHKEFIF |
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 .07 RPM | 4 .84 RPM |
| SRP051959_liver | 0 .02 RPM | 5 .00 RPM |
| SRP051959_lung | 0 .10 RPM | 5 .16 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .09 RPM |
| SRP051959_skeletal_muscle | 0 .04 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_2402 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2402 was not experimentally validated.