RetrogeneDB ID: | retro_cjac_3915 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL286236.1:30521..31269(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000007976 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RCOR3 | ||
| Ensembl ID: | ENSCJAG00000000282 | ||
| Aliases: | None | ||
| Description: | REST corepressor 3 [Source:HGNC Symbol;Acc:25594] |
Retrocopy-Parental alignment summary:
>retro_cjac_3915
GATGTTGAGATGAGAGTTGGAGCTGAATACCAAGCTCGGATCCCTGAATTTGATCCAGGTGCTACAAAGTACACAGATAA
AGACAGTGGAGGGATGTTTGTATGGTCTCCATATCACAGTATCCCGGATGCCAAACTGGATGAATACACTGCAATTGCAA
AGGAGAAGCATGGCTACGATGTGGAGCAGGCACTTGGCATGTTGTTCTGGCAGAAACATGACATTGAGAAGTCCCTTGCC
GGTCTCCCTAATTTCACTCCCTTTCCTGATGAGTGGACAGTGGAAGATAAAGTCCTATTTGAACAAGCCTTTAGCTTTCA
TGGAAAGAGCTTTCACAGGATTCAGCAAATGCTTCCAGGTAAGACAGTTGCAAGCCTTGAAAATATTACTATTCCTGGGA
AAAAGCTCACTCTCGGACAAGTCTGATGGATCGCCAGGCTCGTAAACCAGCTAATAGACATACTCAGGGTGACCGTGATG
ATGATGTAGAAGAACCACATCCAACGGATGGGAACGATAGTGATTATGATCCCAAACAAGAGGGTAATACTGAACAACCT
GTTCTAACTAGCAAGATTGGACTCGGAAGAAGAGAGTATCAGAGTTTACAACATCGCCATCATTCTCAGCGTTCTAGTGC
CGTCCCCCTAAGGGCATGTGTTTAACCCAGGAAGATGTGGTAGCGGTTTCCTGTAGTCCCAATGCAGCCAACACCATTCT
GAGGCAACTAGACGTGGAGCTGATCTCT
ORF - retro_cjac_3915 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.67 % |
| Parental protein coverage: | 66.67 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | DVGMRVGAEYQARIPEFDPGATKYTDKDNGGMLVWSPYHSIPDAKLDEYIAIAKEKHGYNVEQALGMLFW |
| DV.MRVGAEYQARIPEFDPGATKYTDKD.GGM.VWSPYHSIPDAKLDEY.AIAKEKHGY.VEQALGMLFW | |
| Retrocopy | DVEMRVGAEYQARIPEFDPGATKYTDKDSGGMFVWSPYHSIPDAKLDEYTAIAKEKHGYDVEQALGMLFW |
| Parental | HKHNIEKSLADLPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLPDKTIASLV-KYYYSWKKTRSR |
| .KH.IEKSLA.LPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLP.KT.ASL..KYYYSW.K..SR | |
| Retrocopy | QKHDIEKSLAGLPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLPGKTVASLE<KYYYSWEKAHSR |
| Parental | TSLMDRQARKLANRHNQGDSDDDVEEPHPMDGNDSDYDPKKEAKKEGNTEQPVQTSKIGLGRREYQSLQH |
| TSLMDRQARK.ANRH.QGD.DDDVEEPHP.DGNDSDYDPK.E....GNTEQPV.TSKIGLGRREYQSLQH | |
| Retrocopy | TSLMDRQARKPANRHTQGDRDDDVEEPHPTDGNDSDYDPKQE----GNTEQPVLTSKIGLGRREYQSLQH |
| Parental | RHHSQRSK-CRPPKGMYLTQEDVVAVSCSPNAANTILRQLDMELIS |
| RHHSQRS..CRPPKGM.LTQEDVVAVSCSPNAANTILRQLD.ELIS | |
| Retrocopy | RHHSQRSS<CRPPKGMCLTQEDVVAVSCSPNAANTILRQLDVELIS |
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 .38 RPM | 5 .92 RPM |
| SRP051959_heart | 0 .49 RPM | 13 .17 RPM |
| SRP051959_kidney | 0 .33 RPM | 14 .29 RPM |
| SRP051959_liver | 0 .43 RPM | 4 .07 RPM |
| SRP051959_lung | 0 .98 RPM | 13 .10 RPM |
| SRP051959_lymph_node | 1 .39 RPM | 13 .79 RPM |
| SRP051959_skeletal_muscle | 0 .31 RPM | 13 .12 RPM |
| SRP051959_spleen | 0 .44 RPM | 12 .61 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3915 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3915 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3915 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000000282 | 3 retrocopies |
retro_cjac_3349, retro_cjac_3915 , retro_cjac_4009,
|