RetrogeneDB ID: | retro_mmus_2053 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:83744483..83745211(-) | ||
| Located in intron of: | ENSMUSG00000085335 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081801 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Dnmt3l | ||
| Ensembl ID: | ENSMUSG00000000730 | ||
| Aliases: | Dnmt3l, D6Ertd14e, ecat7 | ||
| Description: | DNA (cytosine-5-)-methyltransferase 3-like [Source:MGI Symbol;Acc:MGI:1859287] |
Retrocopy-Parental alignment summary:
>retro_mmus_2053
CTTCCTCTGCCTTTCTCTCAAAGCAGCCTGCTGCAGAGGCGGAGGACATGGCACCACCAGCTAAAGGCCTTCCATCACCT
GGATGGGGCAAACCTCGGGGAGATGTGCAAGGCAGTGCCTATGTGGAAGGATGAGGCAGGGCATGTGCTGACACATGGGA
GGATATTGAACATGAGCTAAAGAGTTTGGGCTTTGGGGAAGTGGATCTGGTTTTGAGGGAGAAAGATGGAAGAACTCAGA
AGCTGTCACAAACATCGCAAGGAGAGACATGGAAGGATGGGGCCCCTTTGACTTCGTGTAAATGGCTCAACACAACCCCT
AGTCTACTGCTGTGACCACTGCCCTGGCTGGTGCCAGTTCCAATTCCACCGGGTCCTACAGTACACATGACCGCACCCAG
GTTGACTGCAGCCCTTCTTCTGGATGTTTGTCAGCAACCCACTGCTGACTAAGAATGACCAAACCTCAGCAGCCTAACTC
GAGATGGAGGCTATGACCTTCAGGATGTCTGCTGCAGATCCTCCAGAATGCTGTATGGGTGTGCAGCGACATGGGGGTGA
GAGGGAGCAAGCATGCACGAGACACTGACACCAGGGAAGGAACAGTTCCTGAAAGCCCAAGTCAGTACAAGAGCCACGCT
GGTACCCAGAGCCTGGAGCTCCTGGAGAACTGCCTTCTCCCCCCTACCAGAATACTTCAGATATTTTTCTCAGAGCTCAC
TTCCTCTT
ORF - retro_mmus_2053 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 50.79 % |
| Parental protein coverage: | 57.96 % |
| Number of stop codons detected: | 4 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | LCLPFSRSGLLQRRKRWRHQLKAFHDQEGAGPMEIYKTVSAWKRQPVRVLS-LFRNIDKVLKSLGFLE-S |
| L.LPFS.S.LLQRR..W.HQLKAFH...GA...E..K.V..WK.....VL......I...LKSLGF.E.S | |
| Retrocopy | LPLPFSQSSLLQRRRTWHHQLKAFHHLDGANLGEMCKAVPMWKDEAGHVLT<TWEDIEHELKSLGFGE<S |
| Parental | GSGSGGGTLKYVEDVTNVVRRDVEKW-GPFDL-VYGSTQPLGSSCDRCPGWYMFQFHRILQYALPRQESQ |
| GSG..G...K..E.VTN..RRD.E.W.GP..L.V.GSTQPL...CD.CPGW..FQFHR.LQY..P..... | |
| Retrocopy | GSGFEGERWKNSEAVTNIARRDMEGW<GPL*LRVNGSTQPLVYCCDHCPGWCQFQFHRVLQYT*PHPG*L |
| Parental | RPFFWIFMDNLLLTEDDQETTTRFLQTEAVT-LQDVRGRD-YQNAMRVWSNIPGLKSKHAPLTPKEEEYL |
| .PFFW.F..N.LLT..DQ.T....L..EA.T.LQDV..R...QNA..V.S......SKHA..T...E... | |
| Retrocopy | QPFFWMFVSNPLLTKNDQ-TSAA*LEMEAMT<LQDVCCRS<LQNAVWVCSDMGVRGSKHARDTDTREGTV |
| Parental | -QAQVRSRSKLDAPKVDLLVKNCLL-PLREYFKYFSQNSLPL |
| ........S........LL..NCLL.PL.EYF.YFSQ.SLPL | |
| Retrocopy | PESPSQYKSHAGTQSLELL-ENCLL>PLPEYFRYFSQSSLPL |
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 | 0 .12 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 0 .09 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .12 RPM |
| SRP007412_kidney | 0 .13 RPM | 0 .33 RPM |
| SRP007412_liver | 0 .05 RPM | 0 .05 RPM |
| SRP007412_testis | 0 .00 RPM | 3 .16 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2053 was not detected
No EST(s) were mapped for retro_mmus_2053 retrocopy.
No TSS is located nearby retro_mmus_2053 retrocopy 5' end.
retro_mmus_2053 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2053 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000000730 | 1 retrocopy |
retro_mmus_2053 ,
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