RetrogeneDB ID: | retro_cjac_2919 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 7:98953135..98953438(+) | ||
| Located in intron of: | ENSCJAG00000016555 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | CSRP2 | ||
| Ensembl ID: | ENSCJAG00000019153 | ||
| Aliases: | None | ||
| Description: | cysteine and glycine-rich protein 2 [Source:HGNC Symbol;Acc:2470] |
Retrocopy-Parental alignment summary:
>retro_cjac_2919
CAGAGTGTTCAGCCTCACAGGCCTACAACAAATCCAAACATTTCTAAATTTGCTCAGAAATATGGAGGTGCTGAGACGTG
TTCCAGATGTGGGGATTTTGTATATACTGCCGAGAAGATAATTGGAGCTGGAAAGCCCTGGCACAAAAACTGTTTCCGAT
GTGCAAAGTGTAAGAAGAGTCTTGAATCAGCAAATCTAACTGAAAAAGAAGGTGAAATCTATCATAAAGGATGCTATGAA
AAGAACTTTGGGCCCAAGGGATTTGGCTATGGCTAAGGAGCAGGGGCTCTTGTTCATTCCCAG
CAGAGTGTTCAGCCTCACAGGCCTACAACAAATCCAAACATTTCTAAATTTGCTCAGAAATATGGAGGTGCTGAGACGTG
TTCCAGATGTGGGGATTTTGTATATACTGCCGAGAAGATAATTGGAGCTGGAAAGCCCTGGCACAAAAACTGTTTCCGAT
GTGCAAAGTGTAAGAAGAGTCTTGAATCAGCAAATCTAACTGAAAAAGAAGGTGAAATCTATCATAAAGGATGCTATGAA
AAGAACTTTGGGCCCAAGGGATTTGGCTATGGCTAAGGAGCAGGGGCTCTTGTTCATTCCCAG
ORF - retro_cjac_2919 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.12 % |
| Parental protein coverage: | 52.33 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ESVQPHRPTTNPNTSKFAQKYGGAEKCSRCGDSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLTEKE |
| .SVQPHRPTTNPN.SKFAQKYGGAE.CSRCGD.VY.AEKIIGAGKPWHKNCFRCAKC.KSLES..LTEKE | |
| Retrocopy | QSVQPHRPTTNPNISKFAQKYGGAETCSRCGDFVYTAEKIIGAGKPWHKNCFRCAKCKKSLESANLTEKE |
| Parental | GEIYCKGCYAKNFGPKGFGYGQGAGALVHAQ |
| GEIY.KGCY.KNFGPKGFGYG.GAGALVH.Q | |
| Retrocopy | GEIYHKGCYEKNFGPKGFGYG*GAGALVHSQ |
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 .02 RPM | 2 .24 RPM |
| SRP051959_heart | 0 .05 RPM | 9 .93 RPM |
| SRP051959_kidney | 0 .00 RPM | 18 .66 RPM |
| SRP051959_liver | 0 .00 RPM | 2 .34 RPM |
| SRP051959_lung | 0 .00 RPM | 7 .58 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 3 .33 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 2 .27 RPM |
| SRP051959_spleen | 0 .04 RPM | 2 .92 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2919 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2919 was not experimentally validated.