RetrogeneDB ID: | retro_cjac_2449 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 4:71725142..71725915(-) | ||
| Located in intron of: | ENSCJAG00000009988 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NECAP2 | ||
| Ensembl ID: | ENSCJAG00000008146 | ||
| Aliases: | None | ||
| Description: | NECAP endocytosis associated 2 [Source:HGNC Symbol;Acc:25528] |
Retrocopy-Parental alignment summary:
>retro_cjac_2449
ATGACAGAGAGCGGGTATGAGTCGGTGCTCTGTGTCAAGCCTGACGTCCACGTCTACCGCATTCCCAACCATGGCTACAG
GGCCCCGAGTGGCAGCTGGACCAGCCATCATGGAGTGGCCGGCTGAGGATCACTGCAAAGCGGCAGATGGCCTGCATCAA
GCTGGGGGACAGGTCTCAGGGGAGCTCTTTGCTGCGGCCCCAGTGGATCAGCTTCCTGGCACAGCTGTGGAGAGCATGAG
GGATCCCAGCAAGTACGTCGTGACCCACATTGAAGGTGGAGACCGGTGACGGACGTTTATTGGAATTGGCCTTGGGGACT
GAGGTGATGCCTTTGACTTCAATGTTGCATTGCAGGATCATTTCAAGTGGGTGAAACAGCAGTGTGAATTTGCAAAAAAA
GCCCAGAACCCAGACCAAGGCCCCAAATTGGACCTGGGCTTCGAGGAGGGCCAGACCATCAGGCTCAACAGCGCAAACAT
GAAGAAGGAGGAAGGAGCGGCCGGGAATCCCTGAGCCCGTCCTGCCAGCACGGGAGGGTTGTGCTTGCTTCCCCCTCCCC
CAGGGGGCAAAACTTTCACCCTCATCCCTCCCCCCAGGGAACAGTTGTCAGTCGGGGGAATCCCTTGTCCAACCAGCAGT
TGCTCCCAGTTCAGGAGGAGGTGCTTCTGTACCCTGGCCACAGCCCAAGCCTGCCACCACTGACATCTGGGGAGACTTTA
CCAAATCTACAGGATCAGCTCCCAGCCAGACCCAACCAGGCTGGGTCCAGTTC
ORF - retro_cjac_2449 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 81.72 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 3 |
Retrocopy - Parental Gene Alignment:
| Parental | MEESGYESVLCVKPDVHVYRIPPRATNRGYRAA-EWQLDQPSWSGRLRITAKGQMAYIKLEDRT-SGELF |
| M.ESGYESVLCVKPDVHVYRIP....N.GYRA..EWQLDQPSWSGRLRITAK.QMA.IKL.DR..SGELF | |
| Retrocopy | MTESGYESVLCVKPDVHVYRIP----NHGYRAP<EWQLDQPSWSGRLRITAKRQMACIKLGDRS<SGELF |
| Parental | AQAPVDQFPGTAVESVTDSSRYFVIRIEDGNGRRAFIGIGFGDRGDAFDFNVALQDHFKWVKQQCEFAKQ |
| A.APVDQ.PGTAVES..D.S.Y.V..IE.G...R.FIGIG.GD.GDAFDFNVALQDHFKWVKQQCEFAK. | |
| Retrocopy | AAAPVDQLPGTAVESMRDPSKYVVTHIEGGDR*RTFIGIGLGD*GDAFDFNVALQDHFKWVKQQCEFAKK |
| Parental | AQNPDQSPKLDLGFKEGQTIKLNIANMKKKEGAAGNPRARPASTGGLSLLPPPPGGRTSTLIPPPGEQLS |
| AQNPDQ.PKLDLGF.EGQTI.LN.ANMKK.EGAAGNP.ARPASTGGL.LLPPPPGG.T.TLIPPP.EQLS | |
| Retrocopy | AQNPDQGPKLDLGFEEGQTIRLNSANMKKEEGAAGNP*ARPASTGGLCLLPPPPGGKTFTLIPPPREQLS |
| Parental | VGG-SLVQPAVAPTS-GGASVPWPQPKPATAATADIWGDFTKSTGSTSSQTQPGWVQF |
| VGG.SLVQPAVAP.S.GGASVPWPQPKPAT....DIWGDFTKSTGS..SQTQPGWVQF | |
| Retrocopy | VGG>SLVQPAVAPSSGGGASVPWPQPKPAT---TDIWGDFTKSTGSAPSQTQPGWVQF |
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 .13 RPM | 12 .20 RPM |
| SRP051959_heart | 0 .04 RPM | 8 .61 RPM |
| SRP051959_kidney | 0 .11 RPM | 15 .51 RPM |
| SRP051959_liver | 0 .06 RPM | 9 .68 RPM |
| SRP051959_lung | 0 .28 RPM | 19 .07 RPM |
| SRP051959_lymph_node | 0 .23 RPM | 32 .94 RPM |
| SRP051959_skeletal_muscle | 0 .17 RPM | 4 .04 RPM |
| SRP051959_spleen | 0 .36 RPM | 34 .52 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2449 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2449 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_2449 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Canis familiaris | ENSCAFG00000015895 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000008146 | 2 retrocopies |
retro_cjac_1447, retro_cjac_2449 ,
|
| Macropus eugenii | ENSMEUG00000006140 | 1 retrocopy |