RetrogeneDB ID: | retro_cjac_2944 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:127589258..127590251(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000034623 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | PHF11 | ||
| Ensembl ID: | ENSCJAG00000008839 | ||
| Aliases: | None | ||
| Description: | PHD finger protein 11 [Source:HGNC Symbol;Acc:17024] |
Retrocopy-Parental alignment summary:
>retro_cjac_2944
ATGGCCCAGGCGTCACCACCTCTGCCGGAGTCAATGCACAGCACTGGCAGCTGGGAGGCCCAGCCGGAGCAGGAGGCGCT
CCTCCTTCCCACCGGTGTCTTTCAGGTTGCAGAAAAGATGGAAAAAAGGACATGTGCACTTTGCCCCAAAGATGTCGAGT
ATAATATCCTGTACTTTGCACAATCAGAGAATATAGCTGCCCATGAAAATTGTTTGCTGTATTCTTCAGGACTTGTGGAA
TGTGAGGATCATGATCCACTTAATCTTGATAGAAATTTTGATGTGGAATCGGTAAAGAAAGAAATCCAGAGAGGAAGGAA
GTTGAAATGCACATTTTGTCGTAAAAGAGGAGCCACCGTGGGATGTGATTTAAAAGCCTATAACAAGAATTACCACTTTT
TCTGTGCCAAGAAGGACCATGCAGTTCCAAAGTCTGATGGAGCTCGAGGAATTTATAAATTGTTTTGCCAACAACATGCT
CAATTCCCGATCATCACTCAAAGTGCTAAATTTTCAGGAGTTAAAGGAAAAAGAGGAAGGAAGAAACACTTCACAGTCAA
TCACATACAGCCACCCGAAACAATGACACATAATAGATTCGTAAGACACGTGAAAGAAGAGCATGGCAAACGCACAGATG
CAACTGTGAAAGTTCCTTTTCTTAAGAAGTGCAAGGAAGCAGGACTTCTTACATACGTACTTGAAGAAATATTAGACAAA
GTTCATTCAATTCCAGAAAAACTCATGGATGAGACTACTTCAGAAGCAGACTATGAAGAAATCGGGAGTGCACTTTTTGA
ATGCAGATTGTTCGAAGACACATTTGAAAATTTTCAAGCAGCAATAGAGAAAAAAATTGACACATCTCAACAAAGGCGGC
AGCAGTTGAAGGAAGAGATTGAGCTACTTCATGACTTAAAACAAACCTTGTGCTCTCTTCAAGAAAGTAGAGAGCCTATG
TCAAGTTCTACATCAATATCGTCCCTGTCATCT
ORF - retro_cjac_2944 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 95.2 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MAQASPPLPESMHSTGSWEAQPEQEALLLPTGVFQVAEKMEKRTCALCPKDVEYNILYFAQSENIAAHEN |
| MAQASPPLPESMHSTGSWEAQPEQEALLLPTGVFQVAEKMEKRTCALCPKDVEYNILYFAQSENIAAHEN | |
| Retrocopy | MAQASPPLPESMHSTGSWEAQPEQEALLLPTGVFQVAEKMEKRTCALCPKDVEYNILYFAQSENIAAHEN |
| Parental | CLLYSSGLVECEDHDPLNLDRNFDVESVKKEIQRGRKLKCTFCRKRGATVGCDLKACNKNYHFFCAKKDH |
| CLLYSSGLVECEDHDPLNLDRNFDVESVKKEIQRGRKLKCTFCRKRGATVGCDLKA.NKNYHFFCAKKDH | |
| Retrocopy | CLLYSSGLVECEDHDPLNLDRNFDVESVKKEIQRGRKLKCTFCRKRGATVGCDLKAYNKNYHFFCAKKDH |
| Parental | AVPKSDGARGIYKLFCQQHAQFPIITQSAKFSGVKGKRGRKKHFTVNHIQPPETMTHNRFVRHVKEEHGK |
| AVPKSDGARGIYKLFCQQHAQFPIITQSAKFSGVKGKRGRKKHFTVNHIQPPETMTHNRFVRHVKEEHGK | |
| Retrocopy | AVPKSDGARGIYKLFCQQHAQFPIITQSAKFSGVKGKRGRKKHFTVNHIQPPETMTHNRFVRHVKEEHGK |
| Parental | RTGNFLKI-LFVANARKQDF-LTIITEEILAKVHSIPRKLMDETTSEADYEEIGSALFECRLFEDTFENF |
| RT....K..LF...ARKQDF.LT...EEIL.KVHSIP.KLMDETTSEADYEEIGSALFECRLFEDTFENF | |
| Retrocopy | RTDATVKV>LFLRSARKQDF<LTYVLEEILDKVHSIPEKLMDETTSEADYEEIGSALFECRLFEDTFENF |
| Parental | QAAIEKKIDTSQQRRQQLKEEIELLHDLKQTLCSLQESREPMSSSTSISSLSS |
| QAAIEKKIDTSQQRRQQLKEEIELLHDLKQTLCSLQESREPMSSSTSISSLSS | |
| Retrocopy | QAAIEKKIDTSQQRRQQLKEEIELLHDLKQTLCSLQESREPMSSSTSISSLSS |
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 | 2 .71 RPM | 6 .37 RPM |
| SRP051959_heart | 2 .60 RPM | 7 .10 RPM |
| SRP051959_kidney | 4 .75 RPM | 11 .58 RPM |
| SRP051959_liver | 3 .44 RPM | 6 .71 RPM |
| SRP051959_lung | 6 .26 RPM | 14 .71 RPM |
| SRP051959_lymph_node | 6 .53 RPM | 15 .25 RPM |
| SRP051959_skeletal_muscle | 1 .75 RPM | 4 .91 RPM |
| SRP051959_spleen | 8 .07 RPM | 17 .69 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2944 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2944 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2944 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000004238 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000008839 | 1 retrocopy |
retro_cjac_2944 ,
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