RetrogeneDB ID: | retro_mmus_3634 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:70420718..70422454(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000084193 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ythdf2 | ||
| Ensembl ID: | ENSMUSG00000040025 | ||
| Aliases: | Ythdf2, 9430020E02Rik, HGRG8, NY-REN-2 | ||
| Description: | YTH domain family 2 [Source:MGI Symbol;Acc:MGI:2444233] |
Retrocopy-Parental alignment summary:
>retro_mmus_3634
ATGTCAGCCAGCAGCCTCTTGGAGCAGAGACCAAAAGGACAAGTAAACAAAGTACGAAATGGTTCTGTGCATCAAAAGGA
TGGACTAAATGATGATGATTTTGAACGTTACTTGAGCCTACAGGCAAGGCCGAATAATGCATATACTGCCATGTCAGACT
CCTACTTACCCAGTTACTACAGCCCCTCCACTGGCTTTTCCTATTCTTTGGGTTAAGCGGCTTGGTCTACTGAAGGCAAC
ACAGCCATGCCCTATCTAACTTCTTATGGACAACTGAGCAACGGAGAGCCCCACTTTCTACCAGATGCAATGTTTGGGCA
ACCAGGAGCCCTAGGTAGCATCCCATTTCTTGGTCAGCATAGTTTTAATTTTTTTCCCAGTGGGATTGACTTCTCTGCAT
GGGGAAATAACAGTTCTCAGGGACAGTCTACTCAAAGCTCTGGATATAGTAGCAATTATGCTTATGCACCCAGCTCCTTA
GGTGGAGCCATGATTGATGGACAGTCAGCTTTTGCCAATGAGACCCTCAATAAAGCTCCTGGCATGAATACTACAGACCA
AAGGATGGCAGCACTGAAACTAGGTAGCACAGAAGTTTCAAGCAGTGTTCCAAAAGGTGTAGGCTCTGCTGTTGGTAGTG
GGTCCATCACTAGTAACATTGTGGCTTCTAGCAGTTTGCCTCCAGCTACTATTGCTCCTCCAAAACCAGCATCTTGGGCT
GATATTGCTAGCAAGCCTGCAGAATAACAACCTAAACTGAAGACCAAGAATGGCATTGCAGGATCAAGTCTTCCACCACC
CCCAATAAAGCATAACATGGATATTGGAACTTGAGATAACAAGGGTCCCATGTCAAAAGCCCCCTCACAGGCTTTGGTTC
AAAATATAGGCCAGCCAACCCAGGGATCTCCTCAGCCTGTCAGACAGCAGGTCAATAATAGCCCACCAGTGGCTCAGACA
TCAGTAGGGCAACAGACACAGCCTTTGCCTCCACCTCCACCACAGCCTGCTCAGATCTCAGTCCAGCAACAGGCAGCTCA
GCCAACTTGCTGGGTAGCACCTCGGAACCGTGGCAGTGGTTTCGGTCATAATGGGGTGGCTGGTAATGGAGTAGGACAGT
CTCAGGCAGGTTCTGATCTACTCCTTCAGAGCCTCACCCAGTGTTGGAGAAACTTCGGTCCATTAATAACTATAACACTA
AAGATTTCGACTGGAATCTGAAACATGGTCGGGTTTTCATCATTAAGAGCTACTCTGAGGATGATATCCACCTTTCCATT
AAGTATAATATCTGGTGCAGCACAGAGCAAGGTAACAAGATACTGGATGCCACCTATCGGTCCATGAATGGGAAGGGCCC
TGCGTACTTACTTTTCAGTGTCAACGGCAGTGGACACTTCTGTGGAATTTCAGAGATGAAATCTGCTGTGGACTACAACA
CGTGTGCAGGTTTGTGGTCCCAGGACAAATGGAAGGTTCGTTTCAATGTCAGATGGATTTTTGTGAAGGACATTCCCAAT
AGCCAACTGCAACACATTCGTCTAGAGAACAACGAAAATAAACCAGTGACCAACTCTAGGGACACTCAGGAAGTGCCTCT
GGAAAAAGCTAAGCAGGTGTTGAAAATCATAGCCAGCTACAAGCACACCACTTCCATTTTTGATGACTTCTCACACTATG
AGAAATGCCAAGAGGAAGAAGAAAGTGTTAAAAAGGAACGTCAAGGTCGTGGGAAA
ORF - retro_mmus_3634 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 92.93 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSASSLLEQRPKGQGNKVQNGSVHQKDGLNDDDFEPYLSPQARPNNAYTAMSDSYLPSYYSPSIGFSYSL |
| MSASSLLEQRPKGQ.NKV.NGSVHQKDGLNDDDFE.YLS.QARPNNAYTAMSDSYLPSYYSPS.GFSYSL | |
| Retrocopy | MSASSLLEQRPKGQVNKVRNGSVHQKDGLNDDDFERYLSLQARPNNAYTAMSDSYLPSYYSPSTGFSYSL |
| Parental | GEAAWSTGGDTAMPYLTSYGQLSNGEPHFLPDAMFGQPGALGSTPFLGQHGFNFFPSGIDFSAWGNNSSQ |
| G.AAWST.G.TAMPYLTSYGQLSNGEPHFLPDAMFGQPGALGS.PFLGQH.FNFFPSGIDFSAWGNNSSQ | |
| Retrocopy | G*AAWSTEGNTAMPYLTSYGQLSNGEPHFLPDAMFGQPGALGSIPFLGQHSFNFFPSGIDFSAWGNNSSQ |
| Parental | GQSTQSSGYSSNYAYAPSSLGGAMIDGQSAFANETLNKAPGMNTIDQGMAALKLGSTEVASSVPKVVGSA |
| GQSTQSSGYSSNYAYAPSSLGGAMIDGQSAFANETLNKAPGMNT.DQ.MAALKLGSTEV.SSVPK.VGSA | |
| Retrocopy | GQSTQSSGYSSNYAYAPSSLGGAMIDGQSAFANETLNKAPGMNTTDQRMAALKLGSTEVSSSVPKGVGSA |
| Parental | VGSGSITSNIVASSSLPPATIAPPKPASWADIASKPAKQQPKLKTKNGIAGSSLPPPPIKHNMDIGTWDN |
| VGSGSITSNIVASSSLPPATIAPPKPASWADIASKPA..QPKLKTKNGIAGSSLPPPPIKHNMDIGT.DN | |
| Retrocopy | VGSGSITSNIVASSSLPPATIAPPKPASWADIASKPAE*QPKLKTKNGIAGSSLPPPPIKHNMDIGT*DN |
| Parental | KGPVAKAPSQALVQNIGQPTQGSPQPVGQQANNSPPVAQASVGQQTQPLPPPPPQPAQLSVQQQAAQPTR |
| KGP..KAPSQALVQNIGQPTQGSPQPV.QQ.NNSPPVAQ.SVGQQTQPLPPPPPQPAQ.SVQQQAAQPT. | |
| Retrocopy | KGPMSKAPSQALVQNIGQPTQGSPQPVRQQVNNSPPVAQTSVGQQTQPLPPPPPQPAQISVQQQAAQPTC |
| Parental | WVAPRNRGSGFGHNGVDGNGVGQSQAGSG-STPSEPHPVLEKLRSINNYNPKDFDWNLKHGRVFIIKSYS |
| WVAPRNRGSGFGHNGV.GNGVGQSQAGS..STPSEPHPVLEKLRSINNYN.KDFDWNLKHGRVFIIKSYS | |
| Retrocopy | WVAPRNRGSGFGHNGVAGNGVGQSQAGSD<STPSEPHPVLEKLRSINNYNTKDFDWNLKHGRVFIIKSYS |
| Parental | EDDIHRSIKYNIWCSTEHGNKRLDAAYRSMNGKGPVYLLFSVNGSGHFCGVAEMKSAVDYNTCAGVWSQD |
| EDDIH.SIKYNIWCSTE.GNK.LDA.YRSMNGKGP.YLLFSVNGSGHFCG..EMKSAVDYNTCAG.WSQD | |
| Retrocopy | EDDIHLSIKYNIWCSTEQGNKILDATYRSMNGKGPAYLLFSVNGSGHFCGISEMKSAVDYNTCAGLWSQD |
| Parental | KWKGRFDVRWIFVKDVPNSQLRHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTSIFDDFSH |
| KWK.RF.VRWIFVKD.PNSQL.HIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTSIFDDFSH | |
| Retrocopy | KWKVRFNVRWIFVKDIPNSQLQHIRLENNENKPVTNSRDTQEVPLEKAKQVLKIIASYKHTTSIFDDFSH |
| Parental | YEKRQEEEESVKKERQGRGK |
| YEK.QEEEESVKKERQGRGK | |
| Retrocopy | YEKCQEEEESVKKERQGRGK |
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 | 31 .80 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 25 .01 RPM |
| SRP007412_heart | 0 .00 RPM | 17 .99 RPM |
| SRP007412_kidney | 0 .00 RPM | 25 .31 RPM |
| SRP007412_liver | 0 .00 RPM | 21 .52 RPM |
| SRP007412_testis | 0 .00 RPM | 26 .85 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3634 was not detected
No EST(s) were mapped for retro_mmus_3634 retrocopy.
No TSS is located nearby retro_mmus_3634 retrocopy 5' end.
retro_mmus_3634 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3634 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000040025 | 2 retrocopies |
retro_mmus_3463, retro_mmus_3634 ,
|