RetrogeneDB ID: | retro_cjac_3326 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 9:92593367..92593612(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NDUFA2 | ||
| Ensembl ID: | ENSCJAG00000016525 | ||
| Aliases: | None | ||
| Description: | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa [Source:HGNC Symbol;Acc:7685] |
Retrocopy-Parental alignment summary:
>retro_cjac_3326
GAAACCCTCATCCACAGCACACTCTCAGCATCACTCTCTCTAGCTCACAGGGACTGCATAGAGAAATATGATGTGAATCT
GAAAAGGCAAACCCTGACCTGCCCATCCTAACCCGTGAATACCCCAACATGCAGCCAGAGCTCTAGAACTACCACACATT
TGTCAAAGAAAAGAATGTCTCTTTGTACAGTTTCAGTGCTGATTGGGAAACTAGATCCCTGGAGAATATATGGAGTGGCA
AAGCC
ORF - retro_cjac_3326 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 54.22 % |
| Parental protein coverage: | 82.83 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | EIRIHLCQRSPGSQGVRDFIEKRYVELK-KANPDLPILIRECSDVHPKLWARYAFGQEKNVSLNNFSADE |
| E..IH.......S...RD.IEK..V.LK.KANPDLPIL.RE.....P.L.....F..EKNVSL..FSAD. | |
| Retrocopy | ETLIHSTLSASLSLAHRDCIEKYDVNLK<KANPDLPILTREYPNMQPEL*NYHTFVKEKNVSLYSFSADW |
| Parental | VTRALENVLSGKA |
| .TR.LEN..SGKA | |
| Retrocopy | ETRSLENIWSGKA |
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 | 4 .53 RPM |
| SRP051959_heart | 0 .00 RPM | 9 .54 RPM |
| SRP051959_kidney | 0 .00 RPM | 9 .03 RPM |
| SRP051959_liver | 0 .22 RPM | 10 .31 RPM |
| SRP051959_lung | 0 .00 RPM | 4 .47 RPM |
| SRP051959_lymph_node | 0 .00 RPM | 5 .43 RPM |
| SRP051959_skeletal_muscle | 0 .00 RPM | 16 .55 RPM |
| SRP051959_spleen | 0 .00 RPM | 5 .50 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3326 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3326 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_3326 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 9 parental genes, and 11 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000015041 | 2 retrocopies | |
| Callithrix jacchus | ENSCJAG00000016525 | 1 retrocopy |
retro_cjac_3326 ,
|
| Cavia porcellus | ENSCPOG00000009178 | 2 retrocopies | |
| Latimeria chalumnae | ENSLACG00000005796 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000014294 | 1 retrocopy | |
| Nomascus leucogenys | ENSNLEG00000009325 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000017571 | 1 retrocopy | |
| Sus scrofa | ENSSSCG00000014371 | 1 retrocopy | |
| Tupaia belangeri | ENSTBEG00000005978 | 1 retrocopy |