RetrogeneDB ID: | retro_mmus_3094 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:139659687..139660155(-) | ||
| Located in intron of: | ENSMUSG00000049571 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083626 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ndufab1 | ||
| Ensembl ID: | ENSMUSG00000030869 | ||
| Aliases: | None | ||
| Description: | NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1 [Source:MGI Symbol;Acc:MGI:1917566] |
Retrocopy-Parental alignment summary:
>retro_mmus_3094
ATGGCGTCTCGTGTCCTCTGCGCCTGTGTCCGCCGCCTGCCCGCGGCCTTCGCGCCGCTGCCCCGGCTTCCCACGTTGGC
CTTGGCGCGGCCGCTCAGCACCACCCTATGCCCTGAGGGAATCCGGAGGAGACCCGAGGCTCTGCAGTCCGCCTTGGCGC
TCGCGCAGGTGCCTGGAACAGTCACACATTTGTGCCGCCAGTACAGTGACGCACCCCCACTGACGTTAGACGGAATCAAG
GACCGAGTTCTGTATGTCTTGAAACTCTATGATAAGATTGATCCAGAAAAGCTCTCCGTAAATTCTCATTTTATGAAGGA
CCTGGGCTTAGACAGTTTGGACCAAGTGGAAATTATTATGGCCATGGAAGACGAATTTGGGTTTGAAATTCCTGATATAG
ATGCAGAGAAGTTAATGTGTCCACAAGAAATTGTAGATTACATTGCAGATAAGAAGGATGTGTATGAA
ORF - retro_mmus_3094 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 99.36 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MASRVLCACVRRLPAAFAPLPRLPTLALARPLSTTLCPEGIRRRPGALQSALALAQVPGTVTHLCRQYSD |
| MASRVLCACVRRLPAAFAPLPRLPTLALARPLSTTLCPEGIRRRP.ALQSALALAQVPGTVTHLCRQYSD | |
| Retrocopy | MASRVLCACVRRLPAAFAPLPRLPTLALARPLSTTLCPEGIRRRPEALQSALALAQVPGTVTHLCRQYSD |
| Parental | APPLTLDGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMC |
| APPLTLDGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMC | |
| Retrocopy | APPLTLDGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMC |
| Parental | PQEIVDYIADKKDVYE |
| PQEIVDYIADKKDVYE | |
| Retrocopy | PQEIVDYIADKKDVYE |
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 |
|---|---|---|
| SRP007412_brain | 0 .02 RPM | 20 .21 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 27 .01 RPM |
| SRP007412_heart | 0 .06 RPM | 57 .56 RPM |
| SRP007412_kidney | 0 .00 RPM | 47 .18 RPM |
| SRP007412_liver | 0 .05 RPM | 19 .63 RPM |
| SRP007412_testis | 0 .05 RPM | 6 .68 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3094 was not detected
No EST(s) were mapped for retro_mmus_3094 retrocopy.
| TSS No. | TSS Name | TSS expression level (Expr) in TPM range: | ||||
|---|---|---|---|---|---|---|
| no expression | 0 < Expr ≤ 1 | 1 < Expr ≤ 5 | 5 < Expr ≤ 10 | Expr > 10 | ||
| TSS #1 | TSS_130239 | 295 libraries | 543 libraries | 230 libraries | 2 libraries | 2 libraries |
The graphical summary, for retro_mmus_3094 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)
retro_mmus_3094 was not experimentally validated.