RetrogeneDB ID: | retro_mmus_2104 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:150110596..150111620(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000083055 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Rexo4 | ||
| Ensembl ID: | ENSMUSG00000052406 | ||
| Aliases: | Rexo4, Gm111, Xpmc2h | ||
| Description: | REX4, RNA exonuclease 4 homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:2684957] |
Retrocopy-Parental alignment summary:
>retro_mmus_2104
GTCTCTGTGTCTTCCCTGTGGTTCGGACTGTGGAGAGCAGGGAGATGAAAACAAAGGCCTTGGCGTCAGTGCCCCAGCCT
GGGCCTATCAGGAAGAAAGCCAAAAGAAGTTCAGGAAGAGCAAAGCTCTGGCAGGAAGTGGGGCTCCAGGAAGCCGCCCT
GTGGCTGTGGTGGGCGGACCACCGAAGGCCCCAGAGAACTTTTCTCAAAATTGGAAGGCGCTACAAGAGCTGCTGAAACA
AACGTCACAGGCCGTAGAAAAACCTCTTGTCTCTCAGATGGATGACAAAATGCACCCCCAAATAATCCAGCAGAACAGAA
AAAAGGCCTCAGATAAATCAAAGGGAGACAAGCAGAGGACAGAAAAAGCCAAGAGCACTAGGGGTTCTGTTACATCTGCA
CCTAAGGACAGGAAGATACTAGTACCTTCCACAGTTACCTCTGGAACAGAGCAGAAGAAAGGAGCCAAGAAGAGGACATA
TAGTGACATCTCTTCTAATCAAGGGGATCTCAAGCCTAAGTGGAAAGCTACAGAGGCAGCTGTTATCTTGAATCAGCCCA
CGCCCACTGAGGAAGACATCTGGTTTGATGATGTGGATCCAGATGATATTGAGGCTGCCATAGGCCCAGAGGCAGCCATG
CTGGTACGGAAGAGGCTGGGGCAGAAGAAGAGGACCATCTCTCTGGTGAAGGAACAAGCCTTTGGTGGCCTGACAAAAGC
CTTGGCCCTGGATTGTGAGATGGTAGGCGTGGGTCCCAAAGGAGAAGAGAGCATCGCAGCCTGTGTGTCCAATGTGAACC
AGTATGGGAAGTGTGTTTATGACAAGTACATCAAGCCAACTGAGCCAGTGTCTGACTACAGGACAGTCGTCAGTGGGATC
CAGCCTGAGAACCTGAAGCAGGGAGAAGAGTTTGAAGTTGTGAAGAAGGTGGCAGAAGTATTGAAGTGCAGAATCCTGGT
GGGGCATGCACTACACAATGATCTAAAGGTTTTGTCCATCCAAAAAAAGAAAATCAGGGACACT
ORF - retro_mmus_2104 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 88.6 % |
| Parental protein coverage: | 80.79 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 2 |
Retrocopy - Parental Gene Alignment:
| Parental | VAVSSL-VVPTAESGEMKTKATAPVPQPGPIRKLARKKAK-KKFRKSKALAGSGVPGSHPAAVAGRPPKA |
| V.VSSL.VV.T.ES.EMKTKA.A.VPQPGPI....RKKAK.KKFRKSKALAGSG.PGS.P.AV.G.PPKA | |
| Retrocopy | VSVSSL<VVRTVESREMKTKALASVPQPGPI----RKKAK<KKFRKSKALAGSGAPGSRPVAVVGGPPKA |
| Parental | PENFSQNWKALQELLKQKSQAAEKPLVSQMDDKMHPQIIQQNRKKASDKSKGDKQRTEKAKSTRGSVTSA |
| PENFSQNWKALQELLKQ.SQA.EKPLVSQMDDKMHPQIIQQNRKKASDKSKGDKQRTEKAKSTRGSVTSA | |
| Retrocopy | PENFSQNWKALQELLKQTSQAVEKPLVSQMDDKMHPQIIQQNRKKASDKSKGDKQRTEKAKSTRGSVTSA |
| Parental | PTDRKILVPPTDTSGTEQKKGAKKRTYSDISSHQGALKPKWKATEAAVILNQPTPTEEDIWFDDVDPDDI |
| P.DRKILVP.T.TSGTEQKKGAKKRTYSDISS.QG.LKPKWKATEAAVILNQPTPTEEDIWFDDVDPDDI | |
| Retrocopy | PKDRKILVPSTVTSGTEQKKGAKKRTYSDISSNQGDLKPKWKATEAAVILNQPTPTEEDIWFDDVDPDDI |
| Parental | EDAIGPEAAMLVRKRLGQKKRTISLEKEQAFGGLTKALALDCEMVGVGPKGEESIAARVSIVNQYGKCVY |
| E.AIGPEAAMLVRKRLGQKKRTISL.KEQAFGGLTKALALDCEMVGVGPKGEESIAA.VS.VNQYGKCVY | |
| Retrocopy | EAAIGPEAAMLVRKRLGQKKRTISLVKEQAFGGLTKALALDCEMVGVGPKGEESIAACVSNVNQYGKCVY |
| Parental | DKYVKPTEPVTDYRTAVSGIRPENLKQGEEFEVVKKEVAEMLKGRILVGHALHNDLKVLFLDHPKKKIRD |
| DKY.KPTEPV.DYRT.VSGI.PENLKQGEEFEVVKK.VAE.LK.RILVGHALHNDLKVL.....KKKIRD | |
| Retrocopy | DKYIKPTEPVSDYRTVVSGIQPENLKQGEEFEVVKK-VAEVLKCRILVGHALHNDLKVLSIQ--KKKIRD |
| Parental | T |
| T | |
| Retrocopy | T |
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 .05 RPM | 42 .73 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 56 .62 RPM |
| SRP007412_heart | 0 .00 RPM | 15 .10 RPM |
| SRP007412_kidney | 0 .08 RPM | 27 .78 RPM |
| SRP007412_liver | 0 .00 RPM | 27 .72 RPM |
| SRP007412_testis | 0 .00 RPM | 18 .62 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2104 was not detected
No EST(s) were mapped for retro_mmus_2104 retrocopy.
No TSS is located nearby retro_mmus_2104 retrocopy 5' end.
retro_mmus_2104 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2104 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Monodelphis domestica | ENSMODG00000012817 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000052406 | 2 retrocopies |
retro_mmus_1006, retro_mmus_2104 ,
|
| Nomascus leucogenys | ENSNLEG00000013130 | 1 retrocopy | |
| Pongo abelii | ENSPPYG00000019735 | 1 retrocopy |