RetrogeneDB ID: | retro_mmus_603 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 10:117594224..117595733(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000043800 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Kifc1 | ||
| Ensembl ID: | ENSMUSG00000079553 | ||
| Aliases: | Kifc1, 100042970, Gm4137, HSET, KNSL2, Kifc5a, Knsl2a, Tctex-7, Tctex-7A, Tctex7, Tctex7a | ||
| Description: | kinesin family member C1 [Source:MGI Symbol;Acc:MGI:109596] |
Retrocopy-Parental alignment summary:
>retro_mmus_603
ATGGACGTGCAGGCGCAGAGGCCACCTTTGTTGGAAGTGAAGAGGAATGTAGAGCTGAAGACAAGCCTGGTCAAGTTCTC
CTCCCGAGTGCCCCGTCAGCAAGCAGGCTCAAGAGAGGTCCTGACCAGATGGAGGATGCCTTGGAGCCCGTAAAGAAACG
GACACGAGGCATGGGTGCAGTGACCAAAGTTGACATATCCCGTCCCAGAGGACCACTCTTCAGCACAGTGTCACAGACCC
AGGGCCACACTGCAGCTCAGAAAGGCCCTAAGAAGGCAGGACCTCGTGGGTGCTCTACTGTTGGTACAGTGCTGAGGAAC
CAGAAGCCAGCTCCCACTGTTCCTGCCCAGAAGCCTGGCACATCCACTGCTCCTGTAGTGGTAAGGAAGAGACCTGGCAA
ACGCCCTTGCCTGGGACCTGAAGGGCCAGTTGTTTGACCTCAGTGAAGAGTTGAAACGCTATCGGGAGAAGACTCAAACG
CTGGAACGGGAGAACCGGGGGCTTCGGAAACATCTCAGAGAGGTCCAGGAGCAGGCCACGACCCTGGGGACAGAGCAGAG
CACCCTGGAAGGGGAGCTGGCCAATGTACGCACCCGAGCTGAGCAGGACCAGCAGAGACTGGAGATGCTGAGTGCCTGTG
TCTTGGAGCTGGAGGAATATCTGGGTACCACGGAAAGGTTGGTTCAGGAGCTTCAGAGAGAGCGGCTGCAATTGAAGGAG
GAGTGGAGCACATTGAGCATCCAACTGGAGGAGCAGGAGAGGAGGTTTCAGGTCGCAGAAGCAGCTCTGTCAAGCAGCCA
AGAAGAGGTGGTGTGTCTTTGGCAGAAGACTGAAGCCCAGGTGACCTTACTGGCTAAGCAAGGAGACCAGCTCTATGGGT
TAGAGATGGAACGGGACGACTCCACAACCAGCTGCAGGAACTGAAGGGCAATATCTGGGTGTTCTGCCACGTGCGCCCTG
TCCTCGCAGGGGAATCCACTCCATCTCCTGGCTTCCTCGTGTTTCTTCCTGGCCCTGCTGGACCCTCTGATCCCCCGACT
CGCCTTAGCCTCTCACTGTCGGCGCTCCACCCTGACTGGGGCCCCGGCACCCACTACCCGCCATGATTTCTCCTTTGATC
GGGTGTTCCCTCCAGGAAGCAAGCAGGAGGAAGTGTTTGAGGGGATCGCCATGCTTGTCCAGTCAGCACTGGATGGCTAC
CCTGTGTGCATTTTTGCCTATGGACAGACAGGCAGTGGCAAGACCTTCACTATGGAAGGTGAACCTAGGGGAGACCCCCA
ATTGGAAGGGCTGATCCCTCAGGCCATGCGGCATCTGTTCTCTGTGGTCCAAAAGATGAGTGGCCAGGGCTGGACATACA
GTTTTGTGGCGAGTTATATAGAGATCTACAATGAGACCGTTTGAGACCTGCTAGCTACTGGGACCCACAAGGGACAAGGG
AGCGAGTGTGAGATTTGTCGGGCAAGCCCAGGGAGTGAGGCGCTAACTGTCACCAATGCATGATATGTG
ORF - retro_mmus_603 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 84.9 % |
| Parental protein coverage: | 75.07 % |
| Number of stop codons detected: | 2 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | MDVQAQRPPLLEVKRNVELKAALVKSSSRVPL-SASRLKRGPDQMEDALEPAKKRTRVMGAVTKVDTSRP |
| MDVQAQRPPLLEVKRNVELK..LVK.SSRVP..SASRLKRGPDQMEDALEP.KKRTR.MGAVTKVD.SRP | |
| Retrocopy | MDVQAQRPPLLEVKRNVELKTSLVKFSSRVPR<SASRLKRGPDQMEDALEPVKKRTRGMGAVTKVDISRP |
| Parental | RGPLLSTVSQTQGHTAAQKGPKKTGPRGCSAIGTVLRSQKPVPAAPAQKPGTSTAPVVVGKRAGKRP-AW |
| RGPL.STVSQTQGHTAAQKGPKK.GPRGCS..GTVLR.QKP.P..PAQKPGTSTAPVVV.KR.GKRP.AW | |
| Retrocopy | RGPLFSTVSQTQGHTAAQKGPKKAGPRGCSTVGTVLRNQKPAPTVPAQKPGTSTAPVVVRKRPGKRP>AW |
| Parental | DLKGQLCDLNEELKRYREKTQTLELENRGLREQLREVQEQATTLGTERNTLEGELASVRSRAEQDQQRLE |
| DLKGQL.DL.EELKRYREKTQTLE.ENRGLR..LREVQEQATTLGTE..TLEGELA.VR.RAEQDQQRLE | |
| Retrocopy | DLKGQLFDLSEELKRYREKTQTLERENRGLRKHLREVQEQATTLGTEQSTLEGELANVRTRAEQDQQRLE |
| Parental | TLSARVLELEECLGTRERLLQELQGERLQLQEERSTLSTQLEEQERRFQATEAALSSSQEEVVCLRQKTE |
| .LSA.VLELEE.LGT.ERL.QELQ.ERLQL.EE.STLS.QLEEQERRFQ..EAALSSSQEEVVCL.QKTE | |
| Retrocopy | MLSACVLELEEYLGTTERLVQELQRERLQLKEEWSTLSIQLEEQERRFQVAEAALSSSQEEVVCLWQKTE |
| Parental | AQVTLLAEQGDRLYGLEMERR-RLHNQLQELKGNIRVFCRVRPVLEGESTPSPGFLVFPPGPAGPS-DPP |
| AQVTLLA.QGD.LYGLEMER..RLHNQLQELKGNI.VFC.VRPVL.GESTPSPGFLVF.P...GP..DP. | |
| Retrocopy | AQVTLLAKQGDQLYGLEMERD<RLHNQLQELKGNIWVFCHVRPVLAGESTPSPGFLVFLP---GPA>DPL |
| Parental | TGLSLSRSDDRRSTLTGAPAPTVRHDFSFDRVFPPGSKQEEVFEEIAMLVQSALDGYPVCIFAYGQTGSG |
| .......S..RRSTLTGAPAPT.RHDFSFDRVFPPGSKQEEVFE.IAMLVQSALDGYPVCIFAYGQTGSG | |
| Retrocopy | IPRLALASHCRRSTLTGAPAPTTRHDFSFDRVFPPGSKQEEVFEGIAMLVQSALDGYPVCIFAYGQTGSG |
| Parental | KTFTMEGGPRGDPQLEGLIPRAMRHLFSVAQEMSGQGWTYSFVASYVEIYNETVRDLLATGPRKGQGGEC |
| KTFTMEG.PRGDPQLEGLIP.AMRHLFSV.Q.MSGQGWTYSFVASY.EIYNETV.DLLATG..KGQG.EC | |
| Retrocopy | KTFTMEGEPRGDPQLEGLIPQAMRHLFSVVQKMSGQGWTYSFVASYIEIYNETV*DLLATGTHKGQGSEC |
| Parental | EIRRASPGSEELTVTNARYV |
| EI.RASPGSE.LTVTNA.YV | |
| Retrocopy | EICRASPGSEALTVTNA*YV |
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 .98 RPM |
| SRP007412_cerebellum | 0 .09 RPM | 5 .73 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .62 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .73 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .08 RPM |
| SRP007412_testis | 1 .23 RPM | 5 .81 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_603 was not detected
No EST(s) were mapped for retro_mmus_603 retrocopy.
No TSS is located nearby retro_mmus_603 retrocopy 5' end.
retro_mmus_603 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_603 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000001631 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000079553 | 1 retrocopy |
retro_mmus_603 ,
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