RetrogeneDB ID: | retro_cjac_2636 | ||
Retrocopylocation | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 5:94069274..94069713(-) | ||
| Located in intron of: | ENSCJAG00000013688 | ||
Retrocopyinformation | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental geneinformation | Parental gene summary: | ||
| Parental gene symbol: | DECR2 | ||
| Ensembl ID: | ENSCJAG00000011883 | ||
| Aliases: | None | ||
| Description: | 2,4-dienoyl CoA reductase 2, peroxisomal [Source:HGNC Symbol;Acc:2754] |
Retrocopy-Parental alignment summary:
>retro_cjac_2636
CCCAGTTCAGGAGGACCCTTCTTGATCCAGAAGGGGACCCTGGTCTCATTGAAGCCAGAGGGAGTCTTGCAGCGGCCTGT
TAGACACGTGATCCAGTGCTTTGGAGGCAGGGTTTCAAGCTGGTGGGGATGAAGATCCTGCAGTCGGCCAGAGAACGTCC
TTGTGAACACTACCAGGACCTGCTGAGGAAGCCCTTCTACCCAGTCCTTCTTAGCTACGTGAGCTCAAGGCTTGTTGATG
GCCATGGTCTGGGAAGGGTACAATGTGGTCCACACCTTGAGGACCATGATAAAATACACTGACAGGGCTGAGGCTGACTC
TGTGACCATGTGGGGAGACTTCAGCAACATCCACATCAGCAGGAACGTCCACACCAGCTATTCAGGATATCAGGGCCAGA
GAGAGATCCAGCTCTGGGTTTGAAAGCAGTGAGCTGGCG
CCCAGTTCAGGAGGACCCTTCTTGATCCAGAAGGGGACCCTGGTCTCATTGAAGCCAGAGGGAGTCTTGCAGCGGCCTGT
TAGACACGTGATCCAGTGCTTTGGAGGCAGGGTTTCAAGCTGGTGGGGATGAAGATCCTGCAGTCGGCCAGAGAACGTCC
TTGTGAACACTACCAGGACCTGCTGAGGAAGCCCTTCTACCCAGTCCTTCTTAGCTACGTGAGCTCAAGGCTTGTTGATG
GCCATGGTCTGGGAAGGGTACAATGTGGTCCACACCTTGAGGACCATGATAAAATACACTGACAGGGCTGAGGCTGACTC
TGTGACCATGTGGGGAGACTTCAGCAACATCCACATCAGCAGGAACGTCCACACCAGCTATTCAGGATATCAGGGCCAGA
GAGAGATCCAGCTCTGGGTTTGAAAGCAGTGAGCTGGCG
ORF - retro_cjac_2636 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 51.68 % |
| Parental protein coverage: | 62.66 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | PGSGGPSWTRERTLVAVKPDGVQRRLVGDVIRRFE-RRGFTLVGMKMLQAPESILAEHYRDLQRKPFYPA |
| P.SGGP......TLV..KP.GV..R.V..VI..F..R.GF.LVGMK.LQ.......EHY.DL.RKPFYP. | |
| Retrocopy | PSSGGPFLIQKGTLVSLKPEGVLQRPVRHVIQCFG<RQGFKLVGMKILQSARERPCEHYQDLLRKPFYPV |
| Parental | LIRYMSS-GPMVAMVWEGYNVVRASRAMIGHTDSAEAAPGTIRGDFSVHISRNVIHASDSVEGAQREIQL |
| L..Y.SS.G...AMVWEGYNVV...R.MI..TD.AEA...T..GD..............S....QREIQL | |
| Retrocopy | LLSYVSS>GLLMAMVWEGYNVVHTLRTMIKYTDRAEADSVTMWGDXXXXXXXXXXXXXYSGYQGQREIQL |
| Parental | W-FQSSELS |
| W.F.SSEL. | |
| Retrocopy | W>FESSELA |
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 | 4 .44 RPM |
| SRP051959_heart | 0 .02 RPM | 7 .19 RPM |
| SRP051959_kidney | 0 .02 RPM | 4 .86 RPM |
| SRP051959_liver | 0 .02 RPM | 6 .74 RPM |
| SRP051959_lung | 0 .02 RPM | 5 .86 RPM |
| SRP051959_lymph_node | 0 .02 RPM | 3 .72 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 6 .60 RPM |
| SRP051959_spleen | 0 .02 RPM | 5 .38 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2636 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2636 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2636 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 | ENSCJAG00000011883 | 1 retrocopy |
retro_cjac_2636 ,
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