RetrogeneDB ID: | retro_cjac_2234 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 3:54660461..54661204(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_2234
ATAAGTGTGGATCCAGCTTGTCCACAAAGCCTGCCTTGCTCCAAAGCACCTGACTATAAAGACTCTTCACTTACACCTGT
GATTTGTGGGTCTGAAGAAAACTATCTACCCTTGAAAATGTCTTCTGCTGAGATGCCTCACACAGAGACTGTCTCTCCTC
TTCCTTATTCCATGGATCTGCTTATTCAGGACAACCCTGATTCTTCTACCAGTCCCAAAGGCAAACAACCCACTTCTGCA
GAGAAGACTGCCACAAAAAAGGAAGATAATGTCCCCATTAAGAAACAGAAGACCAGAACTGTTTTCTCTTCTACCCATCT
GTGTGTACTCAATGACAGATTTCAGAGACAGAAAACCCTCAGCCTCCAGCAGATGCAAGAATTTTCCAACATCTTGAACC
TCAGCTACACACAGGTTAAGACCTGGTTCCAGAACCAGAAAATGAAATATAAGAAGTGGTAGAAAACAACTGGCCAAAGA
ATAGCAATGGTGTGACTCAGGCCTCAGTACCTATCTACCCCAGCCTCTACTCTTCCTACCACCAGGAATGCCTGGTGAAC
ATGACTGGGAATCTTCCAATGTGGAACAAACAGACCTGGAGCAATTCAACCTGGAGCAACCAAATCTGGAACATCCAGTC
CTGCAGCAACCTCTCCTGGAATGCTGAGACCTGGTGCACCCAGTCCTGAAACAATCAGGCCTGGAACAGTCCCTTCTATA
ACTGTAACTGCATGCAGTTACAG
ORF - retro_cjac_2234 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 75.2 % |
| Parental protein coverage: | 81.64 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSMDPVCSQSLPCSEASDCGESSPTPVICEPEENYPSLQMCSAEMPHTETVSPLPSSMDLLTQDSPDSST |
| .S.DP.C.QSLPCS.A.D...SS.TPVIC..EENY..L.M.SAEMPHTETVSPLP.SMDLL.QD.PDSST | |
| Retrocopy | ISVDPACPQSLPCSKAPDYKDSSLTPVICGSEENYLPLKMSSAEMPHTETVSPLPYSMDLLIQDNPDSST |
| Parental | SPKGKRPTAAESSPAVKEDKVPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVK |
| SPKGK.PT.AE.....KED.VP.KKQKTRTVFSST.LCVLNDRFQRQK.LSLQQMQE.SNILNLSY.QVK | |
| Retrocopy | SPKGKQPTSAEKTATKKEDNVPIKKQKTRTVFSSTHLCVLNDRFQRQKTLSLQQMQEFSNILNLSYTQVK |
| Parental | TWFQNQRMKSKRWQK-NNWPRNTSDVTQKASAPTYPSLYSSYHQGCLVNTAGNLPVWNNQTWSNSTWSNQ |
| TWFQNQ.MK.K.W.K.NNWP.N...VTQ.AS.P.YPSLYSSYHQ.CLVN..GNLP.WN.QTWSNSTWSNQ | |
| Retrocopy | TWFQNQKMKYKKW*K<NNWPKNSNGVTQ-ASVPIYPSLYSSYHQECLVNMTGNLPMWNKQTWSNSTWSNQ |
| Parental | TRNIQSWSNHSWNTQTWCTQSWNTQAWSSPFYNCGEEPLQ |
| ..NIQS.SN.SWN..TWCTQS.N.QAW.SPFYNC....LQ | |
| Retrocopy | IWNIQSCSNLSWNAETWCTQS*NNQAWNSPFYNCNCMQLQ |
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 .02 RPM | 0 .00 RPM |
| SRP051959_heart | 0 .04 RPM | 0 .02 RPM |
| SRP051959_kidney | 0 .07 RPM | 0 .02 RPM |
| SRP051959_liver | 0 .48 RPM | 0 .00 RPM |
| SRP051959_lung | 0 .00 RPM | 0 .18 RPM |
| SRP051959_lymph_node | 0 .11 RPM | 0 .00 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .00 RPM |
| SRP051959_spleen | 0 .02 RPM | 0 .00 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2234 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2234 was not experimentally validated.