RetrogeneDB ID: | retro_cjac_2100 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 22:19145904..19146229(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | RARRES2 | ||
| Ensembl ID: | ENSCJAG00000010322 | ||
| Aliases: | None | ||
| Description: | retinoic acid receptor responder (tazarotene induced) 2 [Source:HGNC Symbol;Acc:9868] |
Retrocopy-Parental alignment summary:
>retro_cjac_2100
CACCCTCCCATGCAGTCACCTTTTGGGAGACCAGTGTGGATAGCGCCCGTGGACATGCGCCTCCAAGCAGGAACATTTGT
GAGGCTGGAATTTAAACTCCAGAAGACAAGGGGTCATAAGAAGGACTGAAAGGAACCGGAGTGTAAAGTGAAGCTCAAAG
GGAGGAAGCGGAAATGCCTGGCCTATGTCAAACCGGGCTCTGAAAAGAAGGTTCTGAGCCTGATGGGTCAATGCCCTATA
GAGATGCAGGCTCTGCAGGAGTCTGAGGAGCACCAGGGACCCAGTGTAGCCAAGCCAAGCAGGCGGTGAGGACCCACATC
TGCTT
ORF - retro_cjac_2100 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.45 % |
| Parental protein coverage: | 67.7 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | HPPVQWTFQKICVYSAEDTPFPAGIFVRLEFKLQQTDCRKEDWKKPHCKVKPNGRKRKCLACIKLGSENE |
| HPP.Q..F.........D....AG.FVRLEFKLQ.T...K.D.K.P.CKVK..GRKRKCLA..K.GSE.. | |
| Retrocopy | HPPMQSPFGRPVWIAPVDMRLQAGTFVRLEFKLQKTRGHKKD*KEPECKVKLKGRKRKCLAYVKPGSEKK |
| Parental | VLGRMIHCPTKTQVLREPKEYQ-ENQCIKVQRA-GEDPNSL |
| VL..M..CP...Q.L.E..E.Q...QC.....A.GEDP..L | |
| Retrocopy | VLSLMGQCPIEMQALQESEEHQ<GTQCSQAKQA<GEDPHLL |
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 .26 RPM |
| SRP051959_heart | 0 .00 RPM | 3 .46 RPM |
| SRP051959_kidney | 0 .00 RPM | 2 .06 RPM |
| SRP051959_liver | 0 .00 RPM | 17 .55 RPM |
| SRP051959_lung | 0 .00 RPM | 3 .89 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 2 .44 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 0 .81 RPM |
| SRP051959_spleen | 0 .00 RPM | 2 .58 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2100 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2100 was not experimentally validated.