RetrogeneDB ID: | retro_cjac_4009 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | GL288040.1:3549..4298(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
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_4009
GATGTTGGGATGAGAGTTGGAGCCGAATACCCAGCTCGGATCCCTGAATTTGATCCAGGTGCTACAAAGTACACAGATAA
AGACAGTGGAGGGATGTTTGTATGGTTTCCATATCACAGTATCCCAGATGCCAAACTGGATGAATACACTGCAATTGCAA
AGGAGAAGCATGGCTACGATGTGGAGCAGGCACTTGGCATGTTGTTCTGGCAGAAACGTGACGTTGAGAAGTCCCTTGCC
GGTCTCCCTAATTTCACTCCCTTTCCTGATGAGTGGACAGTGGAAGATAAAGTCCTATTTGAACAAGCCTTTAGCTTTCA
TGGAAACAGCTTTCACAGGATTCAGCAAATGCTTCCAGATAAGACAGTTGCAAGCCTTGCAAAATATTACTATTCCTAGA
AAAAAGCTCACTCTCGGACAAGTCTGATGGATCGCCAGGCTCGTAAACCAGCTAATAGACATACTCAGGGTGACCGTGAT
GATGATGTAGAAGAACCACATCCAACGGATGGGAACGATAGTGATTATGATCCCAAACAAGAGGGTAATACTGAACAACC
TGTTCTAACTAGCAAGATTGGACTCGGAAGAAGAGAGTATCAGAGTTTACAACATCGCCATCATTCTCAGCGTTCTAGTG
CCGTCCCCCTAAGGCCATGTGTTTAACCCAGGAAGATGTGGTAGCGGTTTCCTGTAGTCCCAATGCAGCCAACACCATTC
TGAGGCAACTGGACATGGAGCTGATCTCT
ORF - retro_cjac_4009 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.84 % |
| Parental protein coverage: | 66.67 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DVGMRVGAEYQARIPEFDPGATKYTDKDNGGMLVWSPYHSIPDAKLDEYIAIAKEKHGYNVEQALGMLFW |
| DVGMRVGAEY.ARIPEFDPGATKYTDKD.GGM.VW.PYHSIPDAKLDEY.AIAKEKHGY.VEQALGMLFW | |
| Retrocopy | DVGMRVGAEYPARIPEFDPGATKYTDKDSGGMFVWFPYHSIPDAKLDEYTAIAKEKHGYDVEQALGMLFW |
| Parental | HKHNIEKSLADLPNFTPFPDEWTVEDKVLFEQAFSFHGKSFHRIQQMLPDKTIASLVKYYYSWKKTRSRT |
| .K...EKSLA.LPNFTPFPDEWTVEDKVLFEQAFSFHG.SFHRIQQMLPDKT.ASL.KYYYS.KK..SRT | |
| Retrocopy | QKRDVEKSLAGLPNFTPFPDEWTVEDKVLFEQAFSFHGNSFHRIQQMLPDKTVASLAKYYYS*KKAHSRT |
| Parental | SLMDRQARKLANRHNQGDSDDDVEEPHPMDGNDSDYDPKKEAKKEGNTEQPVQTSKIGLGRREYQSLQHR |
| SLMDRQARK.ANRH.QGD.DDDVEEPHP.DGNDSDYDPK.E....GNTEQPV.TSKIGLGRREYQSLQHR | |
| Retrocopy | SLMDRQARKPANRHTQGDRDDDVEEPHPTDGNDSDYDPKQE----GNTEQPVLTSKIGLGRREYQSLQHR |
| Parental | HHSQRSK-CRPPKGMYLTQEDVVAVSCSPNAANTILRQLDMELIS |
| HHSQRS..CRPPK.M.LTQEDVVAVSCSPNAANTILRQLDMELIS | |
| Retrocopy | HHSQRSS<CRPPKAMCLTQEDVVAVSCSPNAANTILRQLDMELIS |
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 .60 RPM | 5 .92 RPM |
| SRP051959_heart | 0 .47 RPM | 13 .17 RPM |
| SRP051959_kidney | 0 .29 RPM | 14 .29 RPM |
| SRP051959_liver | 0 .43 RPM | 4 .07 RPM |
| SRP051959_lung | 0 .94 RPM | 13 .10 RPM |
| SRP051959_lymph_node | 1 .60 RPM | 13 .79 RPM |
| SRP051959_skeletal_muscle | 0 .50 RPM | 13 .12 RPM |
| SRP051959_spleen | 0 .59 RPM | 12 .61 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_4009 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_4009 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_4009 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 ,
|