RetrogeneDB ID: | retro_cjac_1242 | ||
Retrocopy location | Organism: | Marmoset (Callithrix jacchus) | |
| Coordinates: | 14:5600861..5601281(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSCJAG00000021224 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NDUFS7 | ||
| Ensembl ID: | ENSCJAG00000005587 | ||
| Aliases: | None | ||
| Description: | NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20kDa (NADH-coenzyme Q reductase) [Source:HGNC Symbol;Acc:7714] |
Retrocopy-Parental alignment summary:
>retro_cjac_1242
TCAGCTCCTGGCCTGAGCGGCTTCTGGATCCTTGGTCTGCGCTCCAGCGTGGGCGCAGCTGTGCAGGCACGAGGTGTCCA
TCAGACCGTGGCTACCAAGGGCCCGAGCAGCACCCAGCCTGCCCTGCCGAAGGCCAGAGCTGTGGTTCCCAAACCCAGCA
GCCGGAGGGAGTATGTGGTGGCCAAGCTGGATGACCTCATCAACTGGGTCCATAGGAGCTCCCTGTGGCCCATGACCTTC
GGCCTGGCCTGCTGCGCCGTAGAGATGATGCACATGGCCGCACCCCGCTATGACATGGACCGCTTCGGTGTGGTCTTCCG
TGCCAGCCCACGCCAGTCTGACATGATGATCGTGGCCGGCACACTCACCAACAAGATGGCCCCCGCGCTCCGCAACGTCT
ACGACCAGATAGATGCCCGA
ORF - retro_cjac_1242 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.57 % |
| Parental protein coverage: | 66.67 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | AAPGLRGFWTLGLRSSVGAAVQARGVHQTVATNGPSSTQPALPKARAVVPKPSSRGEYVVAKLDDLINWA |
| .APGL.GFW.LGLRSSVGAAVQARGVHQTVAT.GPSSTQPALPKARAVVPKPSSR.EYVVAKLDDLINW. | |
| Retrocopy | SAPGLSGFWILGLRSSVGAAVQARGVHQTVATKGPSSTQPALPKARAVVPKPSSRREYVVAKLDDLINWV |
| Parental | RRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDVMIVAGTLTNKMAPALRSPWPPLPSR |
| .RSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQSD.MIVAGTLTNKMAPALR........R | |
| Retrocopy | HRSSLWPMTFGLACCAVEMMHMAAPRYDMDRFGVVFRASPRQSDMMIVAGTLTNKMAPALRNVYDQIDAR |
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 .16 RPM | 3 .90 RPM |
| SRP051959_heart | 0 .40 RPM | 9 .84 RPM |
| SRP051959_kidney | 0 .18 RPM | 6 .30 RPM |
| SRP051959_liver | 0 .24 RPM | 5 .94 RPM |
| SRP051959_lung | 0 .05 RPM | 2 .07 RPM |
| SRP051959_lymph_node | 0 .05 RPM | 1 .87 RPM |
| SRP051959_skeletal_muscle | 0 .39 RPM | 14 .22 RPM |
| SRP051959_spleen | 0 .11 RPM | 1 .37 RPM |
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1242 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1242 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_cjac_1242 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Callithrix jacchus | ENSCJAG00000005587 | 1 retrocopy |
retro_cjac_1242 ,
|
| Macaca mulatta | ENSMMUG00000003045 | 1 retrocopy | |
| Xenopus tropicalis | ENSXETG00000003702 | 1 retrocopy |