RetrogeneDB ID: | retro_mmus_1305 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 14:101572526..101573016(-) | ||
| Located in intron of: | ENSMUSG00000033083 | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cox4i1 | ||
| Ensembl ID: | ENSMUSG00000031818 | ||
| Aliases: | Cox4i1, AL024441, COXIV, Cox4, Cox4a | ||
| Description: | cytochrome c oxidase subunit IV isoform 1 [Source:MGI Symbol;Acc:MGI:88473] |
Retrocopy-Parental alignment summary:
>retro_mmus_1305
ATGTTGACTACCAGGACACTTAGTCCAGTTGGCAAGGCAGCCATTCTATCTCGGTGTGTGTTTGAGCACATGGGAAAGTT
GTGAAGAGTGAAGACTAAGCTCTCCCTATTTATGACTTTGCCTTACCCGATGTGGCTCACATCAGATTGCTGTCTACCAG
CCACAAGACCCTGAAGGTGGAAAAGGCTGACTGGGGCATCCTATCCAGGATGAGAAATTCCAGTTGTACTGCATTCAGTT
TAGCAAGAGCTCCGCTGAGATAAACAGGGGCACCGATAGGTGGAAGACTGTTGTGAGCATGGCCATGCTCTTCATTGACT
TCATGGCTTCCATTCCGATTTGGGAGATGCACTCTGTGAATGGCCCAATCCCTCAGACTTTTGATCGAGACCGGGTGACC
ATGCAGAGCAATCAGATGCTACGTAGGAAGGTCAACCCCATTTAGGACTTCTCCACCAAGTGGGACCAAGACAAGAATGA
GTGGAAGCAG
ORF - retro_mmus_1305 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 62.57 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | MLASRALSLIGKRAI-STSVCLRAHGSVVKSEDYAFPTYADRRDYPLPDVAHVTMLSASQKALKEKEKAD |
| ML..R.LS..GK.AI.S.SVC..AHG.VVKSED.A.P.Y....D..LPDVAH...LS.S.K.LK..EKAD | |
| Retrocopy | MLTTRTLSPVGKAAI<SISVCV*AHGKVVKSED*ALPIY----DFALPDVAHIRLLSTSHKTLKV-EKAD |
| Parental | WSSLSR-DEKVQLYRIQFNESFAEMNRGTNEWKTVVGMAMFFIGFTALVLIWEKSYVYGPIPHTFDRDWV |
| W..LSR.DEK.QLY.IQF..S.AE.NRGT..WKTVV.MAM.FI.F.A...IWE...V.GPIP.TFDRD.V | |
| Retrocopy | WGILSR<DEKFQLYCIQFSKSSAEINRGTDRWKTVVSMAMLFIDFMASIPIWEMHSVNGPIPQTFDRDRV |
| Parental | AMQTKRMLDMKANPIQGFSAKWDYDKNEWKK |
| .MQ...ML..K.NPI..FS.KWD.DKNEWK. | |
| Retrocopy | TMQSNQMLRRKVNPI*DFSTKWDQDKNEWKQ |
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 | 287 .39 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 312 .11 RPM |
| SRP007412_heart | 0 .00 RPM | 988 .32 RPM |
| SRP007412_kidney | 0 .00 RPM | 664 .69 RPM |
| SRP007412_liver | 0 .00 RPM | 237 .53 RPM |
| SRP007412_testis | 0 .00 RPM | 149 .57 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1305 was not detected
No EST(s) were mapped for retro_mmus_1305 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_32052 | 540 libraries | 450 libraries | 82 libraries | 0 libraries | 0 libraries |
The graphical summary, for retro_mmus_1305 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_1305 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1305 has 1 orthologous retrocopies within eutheria group .| Species | RetrogeneDB ID |
|---|---|
| Rattus norvegicus | retro_rnor_1157 |