RetrogeneDB ID: | retro_mmus_1932 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:72632269..72633426(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083279 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Pex13 | ||
| Ensembl ID: | ENSMUSG00000020283 | ||
| Aliases: | Pex13, 2610008O20Rik | ||
| Description: | peroxisomal biogenesis factor 13 [Source:MGI Symbol;Acc:MGI:1919379] |
Retrocopy-Parental alignment summary:
>retro_mmus_1932
TGGGAGACTCGCCGAATTCCTAGGGCCAGCCCAAGGCCGGGCCCTGGACTCACTTTCCAATCTGCTGATTCGGACCCTAC
TTTATTGACAAGACCTGGACAACCAACACTTACATGTGTGCCCCTGCCTATTCTTCCCAGTCCATCTCAGCAGACAGGGA
GCAACAATGTAAACACTTTCAGACCTGCTTACAGTTCATTTTCTTCTGGACACAGAACCTACGGAAATTCATTTTATGGA
AGCTCTAGCCCTTATAGTTATGGATACAATGGTTTGGGCTTTAACTGCCTCTGTGTAGACGATCTTCCTCCCAGTAGGTT
TGTTCAGCAAGCTGAAGAAAGCAGCAGAGGTGCATTTCAGTCCATTGAAAGCATTGTGCATGCATTTGCCTCTGTCAGCA
CGATGATGGGTGCTACTTTTTCAGCCATCTATAAGAGTTTCAGGGCCGTATTAGATGTAGCAAATCACTTTTCCTGGCTA
AAAATATACTTTACAAAGGTTTTTCAGCCTTTGCATTAGTTAGGACTATAAGATATCTTTATAGACGGTTACAGTGGATG
ATGGGTTTAAGAAGAGGCTCTGAGAATGAGGACTTGTGGGCAGAAAGTGAAGGAACTGTGTCCTGCCTTAGTACCGAGGA
CCAAGCAACTAACTCAGCAAAATCTTGGCCAATATTCCTGTTCTTTACTGTTATCCTTGGTGGTCCTCATCTCATCTGGA
TACTTCTATCTACTCGCAATGATGAAGTAACAGACAACACCAACTGGGCAAGTGATGAGGATCACCAAGTAGTTGCAAGA
GCATAATACGATTTTGTTGCTATGTCTGATGAAGAGATTTCTTTCTGTGCTGGTGAGATGCTAAATTTAGCGCTCAAAGA
ACAACAACCCAATGTTCAAGGTTGGCTTCTGGATAATTTTGATGGCCAAACAACAGGACTTATACCTACAAATTATGTCA
AAATTCTTGGTGAAAGAAGAGGCAGAAAAACAATAGAATTGAGTACAATGCCCAAGTCTTTTACCAATCCAACATTAATT
AAAGGAGTCACTACCACTGATTCTTTGGAAGCTGCCCTTGAATCTGCTTTTGTTGAAACTAATAAGGTTTCCAGTGCACC
TGATTCTATAGGGAAAAATGGAGACAAACAAGGTCTT
ORF - retro_mmus_1932 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.81 % |
| Parental protein coverage: | 97.28 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | WESRRIPGAGPGPGSGPGPTYQSADLGPTLLTRPGQPTLTRVPPPILPRPSQQTGSNNVNTFRPAYSSFS |
| WE.RRIP.A.P.PG..PG.T.QSAD..PTLLTRPGQPTLT.VP.PILP.PSQQTGSNNVNTFRPAYSSFS | |
| Retrocopy | WETRRIPRASPRPG--PGLTFQSADSDPTLLTRPGQPTLTCVPLPILPSPSQQTGSNNVNTFRPAYSSFS |
| Parental | SGYGAYGNSFYGSYSPYSYGYNGLGFNRLRVDDLPPSRFVQQAEESSRGAFQSIESIVHAFASVSMMMDA |
| SG...YGNSFYGS.SPYSYGYNGLGFN.L.VDDLPPSRFVQQAEESSRGAFQSIESIVHAFASVS.MM.A | |
| Retrocopy | SGHRTYGNSFYGSSSPYSYGYNGLGFNCLCVDDLPPSRFVQQAEESSRGAFQSIESIVHAFASVSTMMGA |
| Parental | TFSAVYNSFRAVLDVANHFSRLKIHFTKV-FSAFALVRTIRYLYRRLQWMMGLRRGSENEDLWAESEGTV |
| TFSA.Y.SFRAVLDVANHFS.LKI.FTKV.FSAFALVRTIRYLYRRLQWMMGLRRGSENEDLWAESEGTV | |
| Retrocopy | TFSAIYKSFRAVLDVANHFSWLKIYFTKV<FSAFALVRTIRYLYRRLQWMMGLRRGSENEDLWAESEGTV |
| Parental | ACLSAEDQATNSAKSWPIFLFFAVILGGPYLIWKLLSTHNDEVTDNTNWASGEDDHVVARAEYDFVAVSD |
| .CLS.EDQATNSAKSWPIFLFF.VILGGP.LIW.LLST.NDEVTDNTNWAS.ED..VVARA.YDFVA.SD | |
| Retrocopy | SCLSTEDQATNSAKSWPIFLFFTVILGGPHLIWILLSTRNDEVTDNTNWASDEDHQVVARA*YDFVAMSD |
| Parental | EEISFRAGDMLNLALKEQQPKVRGWLLASLDGQTTGLIPANYVKILGKRRGRKTIESSTMLKQQQSFTNP |
| EEISF.AG.MLNLALKEQQP.V.GWLL...DGQTTGLIP.NYVKILG.RRGRKTIE.STM.K...SFTNP | |
| Retrocopy | EEISFCAGEMLNLALKEQQPNVQGWLLDNFDGQTTGLIPTNYVKILGERRGRKTIELSTMPK---SFTNP |
| Parental | TLIKGVTTTNPLDEQEAAFESVFVETNKVSSAPDSTGKNGDKQDL |
| TLIKGVTTT...D..EAA.ES.FVETNKVSSAPDS.GKNGDKQ.L | |
| Retrocopy | TLIKGVTTT---DSLEAALESAFVETNKVSSAPDSIGKNGDKQGL |
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 .00 RPM | 25 .23 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 24 .06 RPM |
| SRP007412_heart | 0 .00 RPM | 19 .99 RPM |
| SRP007412_kidney | 0 .00 RPM | 29 .66 RPM |
| SRP007412_liver | 0 .03 RPM | 37 .47 RPM |
| SRP007412_testis | 0 .05 RPM | 75 .79 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1932 was not detected
No EST(s) were mapped for retro_mmus_1932 retrocopy.
No TSS is located nearby retro_mmus_1932 retrocopy 5' end.
retro_mmus_1932 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1932 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000012871 | 1 retrocopy | |
| Equus caballus | ENSECAG00000019622 | 1 retrocopy | |
| Felis catus | ENSFCAG00000028969 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000020283 | 1 retrocopy |
retro_mmus_1932 ,
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