RetrogeneDB ID: | retro_mmus_2947 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:80507795..80508251(+) | ||
| Located in intron of: | ENSMUSG00000030528 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000091989 | |
| 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_2947
GTCCTCTGCGCCTGTGTCCGCCGCCTGCCCGCGGCCTTCGCGCCGCTGCCCCGGCTTCCCACGTTGGCCTTGGCGTGGCC
GCTCAGCACCACCCTATGCCCTGAGGGAATCCGGAGGAGACCCGGGGCTCTGCAGTCCGCCTTGGCGCTCGCGCAGGTGC
CTGGAACAGTCACACATTTGTGCCGCCAGTACAGTGACGCACCCCCACTGACGTTAGACGGAATCAAGGACCGAGTTCTG
TATGTCTTGAAACTCTATGATAAGATTGATCCAGAAAAGCTCTCCGTAAATTCTTATTTTATGAAGGACCTGGGCTTAGA
CAGTTTGGACCAAGTGGAAATTATTATGGCCATGGAAGACGAATTTGGGTTTGAAATTCCTGATATAGATGCAGAGAAGT
TAATGTGTCCACAAGAAATTGTAGATTACATTGCAGATAAGAAGGATGTGTATGAA
ORF - retro_mmus_2947 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 98.68 % |
| Parental protein coverage: | 97.44 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | VLCACVRRLPAAFAPLPRLPTLALARPLSTTLCPEGIRRRPGALQSALALAQVPGTVTHLCRQYSDAPPL |
| VLCACVRRLPAAFAPLPRLPTLALA.PLSTTLCPEGIRRRPGALQSALALAQVPGTVTHLCRQYSDAPPL | |
| Retrocopy | VLCACVRRLPAAFAPLPRLPTLALAWPLSTTLCPEGIRRRPGALQSALALAQVPGTVTHLCRQYSDAPPL |
| Parental | TLDGIKDRVLYVLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEI |
| TLDGIKDRVLYVLKLYDKIDPEKLSVNS.FMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEI | |
| Retrocopy | TLDGIKDRVLYVLKLYDKIDPEKLSVNSYFMKDLGLDSLDQVEIIMAMEDEFGFEIPDIDAEKLMCPQEI |
| Parental | VDYIADKKDVYE |
| VDYIADKKDVYE | |
| Retrocopy | VDYIADKKDVYE |
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 .04 RPM | 27 .01 RPM |
| SRP007412_heart | 0 .06 RPM | 57 .56 RPM |
| SRP007412_kidney | 0 .00 RPM | 47 .18 RPM |
| SRP007412_liver | 0 .03 RPM | 19 .63 RPM |
| SRP007412_testis | 0 .00 RPM | 6 .68 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2947 was not detected
No EST(s) were mapped for retro_mmus_2947 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_137494 | 141 libraries | 409 libraries | 490 libraries | 23 libraries | 9 libraries |
The graphical summary, for retro_mmus_2947 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_2947 was not experimentally validated.