RetrogeneDB ID: | retro_mmus_3663 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:94772618..94774034(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082776 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | U2af2 | ||
| Ensembl ID: | ENSMUSG00000030435 | ||
| Aliases: | U2af2, 65kDa | ||
| Description: | U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 2 [Source:MGI Symbol;Acc:MGI:98886] |
Retrocopy-Parental alignment summary:
>retro_mmus_3663
ATGTCGGACTTCTACAAGTTTGAGCAGCAGCTCAAGGGGAACAAAGAAGAACGGGACAAGGAGAACCGGCACCATAAGCG
TAGTCACAGTCGCTCTCGAAGCCGAGATAGAAAGCGCAGGAGCTGGAGCCGAGAGCGGCGCAATCCAGACCAGCGCAGTG
ACTCTCAGGATAGGAGGCGGCGACGACGAAGCCAACATTTGACCAGAGGCGCTAAAGAGGAGCAGGGTGGATGGATTCGT
TCCCCGTGCCATGAGAAGAAGAAGGTGCGTAAATACTGGGACGTGCCGCCACCTGGCTTTGAGCACGTCACCCCAATGCA
GTACAAGGCCATGCAAGCTGCTGGTCAGATTCTAGCCACCGCCCTTCTCCCGACCATGACTCCTGGTGGTCTGGCTGTGA
CCCCGATGCCAGTGCCTGTGGTTGGGAGCCAGATGACCAGACAGGCCAGACGTCTCTACGTGGGCACCATCCCTTTTGGC
ATCACCGAGGAGTCTATGCTGGACTTCTTAAACACCCAGATGCATCTGAGGGGCTTGACTCAGGCCCCTGGCAACCCGAT
CTTGGCTGTGCAGATAAATCTAGACAAAAATTTTGCTTTTTTGGAGTTCCGGTCAGTGGATGAGACGACCCAGGCCTTGG
CCTTTGATGGCATCATCTTCCAGGGCCAGTCATTGAAGATTCGAAGGCCTCATGACTACCAACCACTGCCTGGCATGTCA
GGGAGCCCCTCTGTTTATGTGCCTGGAGTTGTATCCACCATAGTCCCAGACTCTGCCCACAAGCTGTTCATCGGGGGTTT
GCCCAACTACCTAAATGATGACCAGGTAAAAGAGCTGCTGACATCCGTTGGGATTCTCAGGGCCTTCAACTTGGTCAAGG
ATAGTATCACAGGGCTCTCCAAGGGCTATGCCTTCTGTGAGTACATGGACATCAACGTCACCGATCAGGCCATTGCGTGG
CTGAATGGGATGCATCTAGGGGACAAGAAGCTGCTTGTCCAGAGGGCAAGTGTGGGAGCCAAGAATGTCGCTCTGAGCAT
CATCAATCAGACACCTGTGACCCTTCAAGTGCCCGGCCTGACGAGCTCTCAGGTGCAGATGGGCGGTCACCCAACTACGG
TCCTGTGCCTCATGAACATGGTGCTCCCCAAGGAGCTGCTGGACGACGAGGAATATGAAGAGATTGTAGACGACGTACGA
GACGAGTGCAACAAGTATGGACTGGTCAAATCGATTGAAATTCCCCGCCCCATGGATGGTGTTGAGGTGCCTGGCTGTGG
AAAGATCTTTGTGGAGTTCACTTCTGTGATTGACTGCCAGAAAGCTATGCAGGGTCTAACTGGCCGCAAGTTCGCCAACA
GAGTGGTGGTCACCAAATACTGTGACCCTGACTCTTACCACGGTCGGAACTTCTGG
ORF - retro_mmus_3663 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 87.42 % |
| Parental protein coverage: | 100.0 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | MSDFDEFERQLNENKQERDKENRHRKRSHSRSRSRDRKRRSRSRDRRNRDQRSASRDRRRR--SKPLTRG |
| MSDF..FE.QL..NK.ERDKENRH.KRSHSRSRSRDRKRRS.SR.RRN.DQRS.S.DRRRR..S..LTRG | |
| Retrocopy | MSDFYKFEQQLKGNKEERDKENRHHKRSHSRSRSRDRKRRSWSRERRNPDQRSDSQDRRRRRRSQHLTRG |
| Parental | AKEEHGGLIRSPRHEKKKKVRKYWDVPPPGFEHITPMQYKAMQAAGQIPATALLPTMTPDGLAVTPTPVP |
| AKEE.GG.IRSP.HEKKK.VRKYWDVPPPGFEH.TPMQYKAMQAAGQI.ATALLPTMTP.GLAVTP.PVP | |
| Retrocopy | AKEEQGGWIRSPCHEKKK-VRKYWDVPPPGFEHVTPMQYKAMQAAGQILATALLPTMTPGGLAVTPMPVP |
| Parental | VVGSQMTRQARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDET |
| VVGSQMTRQARRLYVG.IPFGITEE.M.DF.N.QM.L.GLTQAPGNP.LAVQIN.DKNFAFLEFRSVDET | |
| Retrocopy | VVGSQMTRQARRLYVGTIPFGITEESMLDFLNTQMHLRGLTQAPGNPILAVQINLDKNFAFLEFRSVDET |
| Parental | TQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKEL |
| TQA.AFDGIIFQGQSLKIRRPHDYQPLPGMS..PSVYVPGVVST.VPDSAHKLFIGGLPNYLNDDQVKEL | |
| Retrocopy | TQALAFDGIIFQGQSLKIRRPHDYQPLPGMSGSPSVYVPGVVSTIVPDSAHKLFIGGLPNYLNDDQVKEL |
| Parental | LTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLVQRASVGAKNATLVSLP |
| LTS.G.L.AFNLVKDS.TGLSKGYAFCEY.DINVTDQAIA.LNGM.LGDKKLLVQRASVGAKN..L.... | |
| Retrocopy | LTSVGILRAFNLVKDSITGLSKGYAFCEYMDINVTDQAIAWLNGMHLGDKKLLVQRASVGAKNVAL---- |
| Parental | STINQTPVTLQVPGLMSSQVQMGGHPTEVLCLMNMVLPEELLDDEEYEEIVEDVRDECSKYGLVKSIEIP |
| S.INQTPVTLQVPGL.SSQVQMGGHPT.VLCLMNMVLP.ELLDDEEYEEIV.DVRDEC.KYGLVKSIEIP | |
| Retrocopy | SIINQTPVTLQVPGLTSSQVQMGGHPTTVLCLMNMVLPKELLDDEEYEEIVDDVRDECNKYGLVKSIEIP |
| Parental | RPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVVVTKYCDPDSYHRRDFW |
| RP.DGVEVPGCGKIFVEFTSV.DCQKAMQGLTGRKFANRVVVTKYCDPDSYH.R.FW | |
| Retrocopy | RPMDGVEVPGCGKIFVEFTSVIDCQKAMQGLTGRKFANRVVVTKYCDPDSYHGRNFW |
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 | 1 .68 RPM | 72 .96 RPM |
| SRP007412_cerebellum | 0 .35 RPM | 76 .86 RPM |
| SRP007412_heart | 0 .22 RPM | 54 .70 RPM |
| SRP007412_kidney | 0 .37 RPM | 63 .72 RPM |
| SRP007412_liver | 0 .11 RPM | 43 .15 RPM |
| SRP007412_testis | 0 .41 RPM | 51 .69 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3663 was not detected
No EST(s) were mapped for retro_mmus_3663 retrocopy.
No TSS is located nearby retro_mmus_3663 retrocopy 5' end.
retro_mmus_3663 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3663 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 8 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Loxodonta africana | ENSLAFG00000018056 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000011051 | 2 retrocopies | |
| Macaca mulatta | ENSMMUG00000004810 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000030435 | 3 retrocopies |
retro_mmus_2251, retro_mmus_3663 , retro_mmus_991,
|
| Otolemur garnettii | ENSOGAG00000007206 | 1 retrocopy |