RetrogeneDB ID: | retro_cjac_2645 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:99021242..99021567(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | ZSWIM7 | ||
| Ensembl ID: | ENSCJAG00000012208 | ||
| Aliases: | None | ||
| Description: | zinc finger, SWIM-type containing 7 [Source:HGNC Symbol;Acc:26993] |
Retrocopy-Parental alignment summary:
>retro_cjac_2645
GAATATCAGTTATCGCTGAAGCTTCTCTTTGGCTCATCAGCCACTCAGGCCTTGGACCTAGTTGATCGACAATCCATAAC
CTTAATCTCATCGCCCAGTGGAAGGCATGTTTACCAGGTACTTGGAAGTTATAGGAAAACATACACGTTTGGCTTCTTGT
TCATGTCCTGTATTTGCCTTCCCAGTGCTACGGAAGAGTGACAGCATCCTGTGCAGGCATCTCTTGGCAGTTTACCTTAG
TTAGGTTTTGAGCGCCTGTCAGCAGCTAAGTGTCTCCAACAAGCAGTTGACTGACATATTATTGATGGAGAAGAAACAAG
AACCA
ORF - retro_cjac_2645 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 82.3 % |
| Parental protein coverage: | 97.39 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EYLLSLKFLFGSSATQALDLVDRQSITLIASPSGRRVYQVLGSS-GKTYTCLASCHYCSCPAFAFKVLRK |
| EY.LSLK.LFGSSATQALDLVDRQSITLI.SPSGR.VYQVLGS..GK..T.LAS...CSCP.FAF.VLRK | |
| Retrocopy | EYQLSLKLLFGSSATQALDLVDRQSITLISSPSGRHVYQVLGSY>GK-HTRLAS---CSCPVFAFPVLRK |
| Parental | SDSILCKHLLAVYLSQVMRTCQQLSVSDKQLTDILLMEKKQEP |
| SDSILC.HLLAVYLS.V...CQQLSVS.KQLTDILLMEKKQEP | |
| Retrocopy | SDSILCRHLLAVYLS*VLSACQQLSVSNKQLTDILLMEKKQEP |
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 .18 RPM | 5 .57 RPM |
| SRP051959_heart | 0 .05 RPM | 6 .54 RPM |
| SRP051959_kidney | 0 .04 RPM | 6 .37 RPM |
| SRP051959_liver | 0 .02 RPM | 7 .41 RPM |
| SRP051959_lung | 0 .13 RPM | 3 .89 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 4 .04 RPM |
| SRP051959_skeletal_muscle | 0 .02 RPM | 6 .62 RPM |
| SRP051959_spleen | 0 .06 RPM | 4 .54 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2645 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2645 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2645 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 | ENSCJAG00000012208 | 1 retrocopy |
retro_cjac_2645 ,
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