RetrogeneDB ID: | retro_cjac_3028 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:132608004..132608626(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SHARPIN | ||
| Ensembl ID: | ENSCJAG00000021452 | ||
| Aliases: | None | ||
| Description: | SHANK-associated RH domain interactor [Source:HGNC Symbol;Acc:25321] |
Retrocopy-Parental alignment summary:
>retro_cjac_3028
GCCCGGGCCATTGCAGGTGGGGACAAGAAGGGGGCAGTCCAAGCAGCAGCCGTCCTGGCCCAGCATCGTGAGGCCCTCAG
TGTTCAGCTTCAGGAGGCCTGCTTCCCACCTGGCCCCATCAGACTGCAGGTCACACTTGAAGATGCTGCTTCTGCTGCAT
CCACCGCATCCTCTGCCCACATCACACTGCAGGTCCACGCCCACTGCACCATTGCAGATCTCCAGGAGCAGTGTTATCAG
AGCTTGTTTTCCCACCGGCCGTGCAACGCTGGGTCATTGGGCAGTGCTTGTGTGTGCCTGAGCTCAGTCTTGCCTCCTAT
GGGGTTTGGCAGGATGAGGACCCTGCTTTCCTCTACTTGCTGACAGCTCTTCGAAAAGCCCCAGCCACAGGACCCAGCCC
TCATTGCCCCGAGAAGACGGATGGGGAACTTGGACGCTTGTTTCCCGCATCATTGGGCCAGCTCCCAGGCCCCCAGCCAG
CCACTTCCAGCCTGCCCAGTCCTCTCCAGCCCGGCTGGCCCTGTCCTTCCTGCACCTTCATCAATGCCCAAGCCACCCTG
GCTGTCAGATGTGTAGCACCCAGAGGCCCTGCACTTGGGACCCCCTTGCCACAGCTTCCACC
ORF - retro_cjac_3028 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 89.05 % |
| Parental protein coverage: | 53.61 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | ARAIAGGDEKGAAQAAAVLAQHREALSVQLQEACFPPGPIRLQVTLEDAASAASTASSAHIALQVHPHCT |
| ARAIAGGD.KGA.QAAAVLAQHREALSVQLQEACFPPGPIRLQVTLEDAASAASTASSAHI.LQVH.HCT | |
| Retrocopy | ARAIAGGDKKGAVQAAAVLAQHREALSVQLQEACFPPGPIRLQVTLEDAASAASTASSAHITLQVHAHCT |
| Parental | IAALQEQ-VFSELGFPPAVQRWVIGQCLCVPERSLASYGVRQDGDPAFLYLLTAPQEAPAIGPSPHRPQK |
| IA.LQEQ.V.SEL.FPPAVQRWVIGQCLCVPE.SLASYGV.QD.DPAFLYLLTA...APA.GPSPH.P.K | |
| Retrocopy | IADLQEQ<VLSELVFPPAVQRWVIGQCLCVPELSLASYGVWQDEDPAFLYLLTALRKAPATGPSPHCPEK |
| Parental | TDGELGRLFPASLGLPPGPQPATSSLPSPLQPGWPCPSCTFINA-PSRPGCEMCSTQRPCTWDPLAAAST |
| TDGELGRLFPASLG..PGPQPATSSLPSPLQPGWPCPSCTFINA.PS.PGC.MCSTQRPCTWDPLA.AST | |
| Retrocopy | TDGELGRLFPASLGQLPGPQPATSSLPSPLQPGWPCPSCTFINA<PSHPGCQMCSTQRPCTWDPLATAST |
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 .00 RPM | 2 .86 RPM |
| SRP051959_heart | 0 .00 RPM | 5 .89 RPM |
| SRP051959_kidney | 0 .02 RPM | 6 .68 RPM |
| SRP051959_liver | 0 .00 RPM | 4 .96 RPM |
| SRP051959_lung | 0 .00 RPM | 5 .12 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .70 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 5 .94 RPM |
| SRP051959_spleen | 0 .00 RPM | 4 .05 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3028 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3028 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3028 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000021452 | 1 retrocopy |
retro_cjac_3028 ,
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