RetrogeneDB ID: | retro_cjac_490 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:185838315..185838958(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | SRA1 | ||
| Ensembl ID: | ENSCJAG00000016613 | ||
| Aliases: | None | ||
| Description: | steroid receptor RNA activator 1 [Source:HGNC Symbol;Acc:11281] |
Retrocopy-Parental alignment summary:
>retro_cjac_490
GGCAACAAGGAGCGAGGTTGGAACGACCCGCCACAGTTCTCATACGGGCTGCAGAGCCAGGCCGGCAGACCCAGGCACGC
ACTACTCACCAAGAGGGTCGCCACACCCCAGGATAGATCCCCCAGAGTCCCAGCCTCAGAGACTTCTCCTGGGCCTCCCT
CAATGGGGCCTCCAGCTCCTTCAAGTAAGGCTCCCAGGTCCTCACCTGTGGGGAGTGATCCTGCCTCTGGTGTGGAGCCC
ACAAGTTTCCCAGTTGAGTCTGAGGCTCTGATGGAAGATGAGCTGAGACCTTTGGAACAGGCATTGGAAGACTGCCGTGG
CCACACAAAGAAACAAGAATGTGATGACATCAGCCGACGCCTGGCACTGCTGCAGGAACAGTGGGCTGGAGGAAAGTTGT
CAATACCTGTAAAGAATAGAATGGCTCTACTGGTACAAGAGCTTTCAACCCACCAGTGGGATGCAACAGATGGCATCCAC
TGCTCACTCATGGTTGACCATGTGACTGAGGCCAATCAGTGGATGGAGTTAAAAGATTAATTGCGGAAAGAAGAGTCTGT
TTTCAGAGGAGGCAGCCAATGAAGAGAAATCTGCAGCCACAGCTGAGAAGAACCAGACCATACCGGGCTTCCAGCGGGCG
CCA
ORF - retro_cjac_490 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.11 % |
| Parental protein coverage: | 91.49 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | GNKERGWNDPPQFSYGLQTQAGGTRRTLLTKRVAAPQDGSPRVPASETSPGPPPMGPPPPSSKAPRSPPV |
| GNKERGWNDPPQFSYGLQ.QAG..R..LLTKRVA.PQD.SPRVPASETSPGPP.MGPP.PSSKAPRS.PV | |
| Retrocopy | GNKERGWNDPPQFSYGLQSQAGRPRHALLTKRVATPQDRSPRVPASETSPGPPSMGPPAPSSKAPRSSPV |
| Parental | GSDPASGVEP-SFPVESEALMEDVLRPLEQALEDCRGHTKKQVCDDISRRLALLQEQWAGGKLSIPVKKR |
| GSDPASGVEP.SFPVESEALMED.LRPLEQALEDCRGHTKKQ.CDDISRRLALLQEQWAGGKLSIPVK.R | |
| Retrocopy | GSDPASGVEPTSFPVESEALMEDELRPLEQALEDCRGHTKKQECDDISRRLALLQEQWAGGKLSIPVKNR |
| Parental | MTLLVQELSNHQWDAADDIHRSLMVDHVTEVSQWMVGVKRLIAEKRSLF-SEEAANEEKSAATPEKNQTI |
| M.LLVQELS.HQWDA.D.IH.SLMVDHVTE..QWM...K.......S.F..E.A..E.KSAAT.EKNQTI | |
| Retrocopy | MALLVQELSTHQWDATDGIHCSLMVDHVTEANQWM-ELKD*LRKEESVF>EEAANEE-KSAATAEKNQTI |
| Parental | PGFHQAP |
| PGF..AP | |
| Retrocopy | PGFQRAP |
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 | 8 .61 RPM |
| SRP051959_heart | 0 .02 RPM | 7 .84 RPM |
| SRP051959_kidney | 0 .02 RPM | 8 .28 RPM |
| SRP051959_liver | 0 .02 RPM | 7 .43 RPM |
| SRP051959_lung | 0 .02 RPM | 6 .98 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 7 .74 RPM |
| SRP051959_skeletal_muscle | 0 .04 RPM | 16 .18 RPM |
| SRP051959_spleen | 0 .02 RPM | 5 .13 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_490 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_490 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_490 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 | ENSCJAG00000016613 | 1 retrocopy |
retro_cjac_490 ,
|
| Oryctolagus cuniculus | ENSOCUG00000021569 | 1 retrocopy |