RetrogeneDB ID: | retro_cjac_402 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:66884828..66885411(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000009344 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NANOG | ||
| Ensembl ID: | ENSCJAG00000018999 | ||
| Aliases: | None | ||
| Description: | Nanog homeobox [Source:HGNC Symbol;Acc:20857] |
Retrocopy-Parental alignment summary:
>retro_cjac_402
ATGAATATGGATCCTTCTTATCCACAAAGCCTGCCTTGCTCCAAAGCATCTGACTGTAAAGAATCTTCACCTATGCCTGT
GATTTCTGGGGCTGAAGAAAATTATCCATCCTTGCAAATGTCTTCTGCTGAGATGCCTCACACAGAGACTGTCTCCCCTC
TTCCTTCCTCCATGGATCTGCTTATTCAGGACAGCCCTGATTCTTCCTCCAGTCCCAAAGGCAAACAACCCACTGCTGCA
GAGAGTAGTGCCACAATAAAGGAAGACAAAGTCCCGGTCAAGAAACAGAAGACCAGAACTGTATTCACTTCCACCCAGCT
GTGTGTACTCAATGACAGTTCAGAGACAGAAATACCTCAGTATCCAGCAGATGCAAGAACGTTCCAACATCCTGAATGTT
AGCTACAAACAGATGAAGACCTGTTTCCAGAACCAGAGAATGAAATCTAAGAGGTGGCAGAAAAACAACTGGCCAAAGAA
TAGCAATGATGTGATGGAGAAGGCCTCAGCGCCCGCCTATCCCAGCCTCTACTCTTCCTACCACCAGGGATGCCTGATGA
ACACAACTGGGAACCTTCCAGTG
ORF - retro_cjac_402 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 68.37 % |
| Parental protein coverage: | 63.93 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSMDPVCSQSLPCSEASDCGESSPTPVICEPEENYPSLQMCSAEMPHTETVSPLPSSMDLLTQDSPDSST |
| M.MDP...QSLPCS.ASDC.ESSP.PVI...EENYPSLQM.SAEMPHTETVSPLPSSMDLL.QDSPDSS. | |
| Retrocopy | MNMDPSYPQSLPCSKASDCKESSPMPVISGAEENYPSLQMSSAEMPHTETVSPLPSSMDLLIQDSPDSSS |
| Parental | SP-KGKRPTAAESSPAVKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQV |
| SP.K...P......P.....K............S....CV.....QRQKYLS.QQMQE.SNILN.SYKQ. | |
| Retrocopy | SP>KANNPLLQRVVPQ*RKTKSRSRNRRPE-LYSLPPSCVYSMTVQRQKYLSIQQMQERSNILNVSYKQM |
| Parental | KTWFQNQRMKSKRWQKNNWPRNTSDVTQKASAPTYPSLYSSYHQGCLVNTAGNLPV |
| KT.FQNQRMKSKRWQKNNWP.N..DV..KASAP.YPSLYSSYHQGCL.NT.GNLPV | |
| Retrocopy | KTCFQNQRMKSKRWQKNNWPKNSNDVMEKASAPAYPSLYSSYHQGCLMNTTGNLPV |
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 .04 RPM | 0 .00 RPM |
| SRP051959_heart | 0 .00 RPM | 0 .02 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .02 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .05 RPM | 0 .18 RPM |
| SRP051959_lymph_node | 0 .09 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .08 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_402 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_402 was not experimentally validated.