RetrogeneDB ID: | retro_cjac_581 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 1:86591592..86592228(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TNNI3 | ||
| Ensembl ID: | ENSCJAG00000017677 | ||
| Aliases: | None | ||
| Description: | troponin I type 3 (cardiac) [Source:HGNC Symbol;Acc:11947] |
Retrocopy-Parental alignment summary:
>retro_cjac_581
ATGGGGGAGGAGAGCAGCCATGCGGCTGGGGAACCTCGCTCCGCACCAGCCCCGGTCAGACGCCGCTCCTCCAACTACCG
CGCGCGTACGCCACGGAGCCTCATGCCAAGAAAAAGTCTAAGATGTCCGTCCGCCTCGAGAAAACTGCAGCTGAAGACCC
TGATGCTGCAGATTGCAAAGCAGGAGCTGGAGCGAGAGGCGGAGGAGCTGCGCGGAGAGAAGGGCGCGCCCTGAGCACCC
GCTGCCAGCCGCTGCAGTTGGCCGGTCTAGCCTTCGCGGAGCTGCAGGACTTGTGCCGACAGCTCCACACCCGTGTGGAC
AAAGTGGATGAAGAGAGATATGACCTAGAGGCAAGAGATACCAAGAACATCACAGAGATTGCAGATCTGACCCAGAAGAT
CTTCGACCTTCGTGGCAAGTTTAAGCGGCCCACCCTGCAGGAGAGTGAGAATCTCTGCGGATGCCATGATGCAGGCGCTG
CTGGGGACCCAGGCTAAGGAGTCCCTGGACCTGCGTGCCCACCTCAAGTAGGTGAAGAAGGAGGACACCGAGAAGGAAAT
CCGGGAGGTGGGAGACTGGCGCAAGAACATCAATGCACTGAGTGGAATGGAAGGCCACAAGAAAAAGTTTGAGGGC
ORF - retro_cjac_581 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.45 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MADESSDAAGEPRPAPAPVRRRSSNYRAYATEPHAKKKSKI--SASRKLQLKTLMLQIAKQELEREAEER |
| M..ESS.AAGEPR.APAPVRRRSSNYRA.........KS....SASRKLQLKTLMLQIAKQELEREAEE. | |
| Retrocopy | MGEESSHAAGEPRSAPAPVRRRSSNYRARTPRSLMPRKSLRCPSASRKLQLKTLMLQIAKQELEREAEEL |
| Parental | RGEKG-RALSTRCQPLELAGLGFAELQDLCRQLHTRVDKVDEERYDIEAKVTKNITEIADLTQKIFDLRG |
| RGEKG.RALSTRCQPL.LAGL.FAELQDLCRQLHTRVDKVDEERYD.EA..TKNITEIADLTQKIFDLRG | |
| Retrocopy | RGEKG<RALSTRCQPLQLAGLAFAELQDLCRQLHTRVDKVDEERYDLEARDTKNITEIADLTQKIFDLRG |
| Parental | KFKRPTL-RRVRISADAMMQALLGTRAKESLDLRAHLKQVKKEDTEKEIREVGDWRKNIDALSGMEGRKK |
| KFKRPTL.RRVRISADAMMQALLGT.AKESLDLRAHLK.VKKEDTEKEIREVGDWRKNI.ALSGMEG.KK | |
| Retrocopy | KFKRPTL>RRVRISADAMMQALLGTQAKESLDLRAHLK*VKKEDTEKEIREVGDWRKNINALSGMEGHKK |
| Parental | KFEG |
| KFEG | |
| Retrocopy | KFEG |
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 | 0 .20 RPM |
| SRP051959_heart | 0 .32 RPM | 415 .51 RPM |
| SRP051959_kidney | 0 .00 RPM | 0 .82 RPM |
| SRP051959_liver | 0 .00 RPM | 0 .11 RPM |
| SRP051959_lung | 0 .00 RPM | 6 .72 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 0 .98 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .92 RPM |
| SRP051959_spleen | 0 .00 RPM | 0 .80 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_581 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_581 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_581 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 | ENSCJAG00000017677 | 1 retrocopy |
retro_cjac_581 ,
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