RetrogeneDB ID: | retro_rnor_540 | ||
Retrocopy location | Organism: | Rat (Rattus norvegicus) | |
| Coordinates: | 1:248564054..248564404(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSRNOG00000023901 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ndufa11 | ||
| Ensembl ID: | ENSRNOG00000048320 | ||
| Aliases: | None | ||
| Description: | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 [Source:UniProtKB/Swiss-Prot;Acc:Q80W89] |
Retrocopy-Parental alignment summary:
>retro_rnor_540
GACGGCACCCAGTGTCATCGCAAGGCCTACATCACTACTGCCTTAGGCAGCCTTTGCGGCCTAATAAGCTCTGCTTACAG
CATCACACACAACCCCGCAGATTCTCCCCTGGAAGCCGTGGCCAGGTCGGCCGGTCCACATTCACTGCAGCTGCTATCGG
AGCTATGTTTGGCCTTACCACCTGTGTCAGTGCCCAGGTCCGAGAGAAGCCAGATGAACCCTTGAACTACTTCACTGGAG
GTTGCGCAGGAGGCCTGATATTGGGAGCACGCACTCACAGCTATGGGACCGCCGCCATTGGCTGTGTCTATAAGCTGGAG
GGCTGGGAACTGTTTGCCACCCCCAAGGTG
ORF - retro_rnor_540 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 86.44 % |
| Parental protein coverage: | 82.98 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | DGTQCHRKAYITTALGGLCGLISSAYSITHNPADSPLEAVAR-VGRFTFTAAAIGAMFGLTTCVSAQVRE |
| DGTQCHRKAYITTALG.LCGLISSAYSITHNPADSPLEAVAR.VGR.TFTAAAIGAMFGLTTCVSAQVRE | |
| Retrocopy | DGTQCHRKAYITTALGSLCGLISSAYSITHNPADSPLEAVAR<VGRSTFTAAAIGAMFGLTTCVSAQVRE |
| Parental | KPDDPLNYFIGGCAGGLTLGARTHSYGTAAIGCVYMGTAAALFKMGKL |
| KPD.PLNYF.GGCAGGL.LGARTHSYGTAAIGCVY......LF...K. | |
| Retrocopy | KPDEPLNYFTGGCAGGLILGARTHSYGTAAIGCVYKLEGWELFATPKV |
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 |
|---|---|---|
| SRP017611_brain | 0 .00 RPM | 27 .97 RPM |
| SRP017611_kidney | 0 .00 RPM | 63 .57 RPM |
| SRP017611_liver | 0 .00 RPM | 45 .79 RPM |
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_540 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_540 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_rnor_540 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000002379 | 1 retrocopy | |
| Rattus norvegicus | ENSRNOG00000048320 | 1 retrocopy |
retro_rnor_540 ,
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