RetrogeneDB ID: | retro_mmus_3570 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | X:8662245..8663840(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000082458 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Cdc6 | ||
| Ensembl ID: | ENSMUSG00000017499 | ||
| Aliases: | Cdc6, CDC18L | ||
| Description: | cell division cycle 6 [Source:MGI Symbol;Acc:MGI:1345150] |
Retrocopy-Parental alignment summary:
>retro_mmus_3570
TGTGTGGCCATCATGCCTCAAACCAGATCCCAGACACAAGCTACCATCGGTTTTTCGAAAAAGAAGTTATCCAATCCCTG
GAAGAAAACCAACTCCTGGGACTGTGAAGTAAAATTTAGAAACGTCCAGCCTGTACCCACCACTCCGTGTGCTGATGTAA
AACTTCTGCCTCTCAGTCCCCGAAAAAGTTTGGGTGATGACAACTTGTGCAACACTCCCCGGTTATCTCCCTGTTCTCCA
CCAAAGCTGGGCAAGAAAGAAAACAGACCCCCCCCCCTCGCTCACATACGTGGAAGGGGTGCAGATTAGTATTTGATGAT
GAGCCGACAGTTAAGGCTTCCCCCCAAAAGAACAAAACAGAGTTCACAAACACCAGATATGTTCCTCCTCTGCTCACAGA
AGTCCAGAGAGCAAAACAGATCCTAAGCAGAAATGTCTGCCTGAGAAGGAGTCTGTGTGTATAAGACTGTTCAAGCAAGA
AGGCACTTGCTATCAGCAAGCAAAGCTCGTTCTGAATACAGCTGTCCAGGATCGGCTGCCTGCCAGAGAGCAGGAGATGG
GTGTCATCAGGAATTTTCTGAAGGAGTACATCTGTGGGAAGAAAGCTGGCAGTCTCTACCTTTCTGGCGCTCCTGGAACT
GGAAAAACTGCCTTTTTAAGCCGGATTCTGCAAGACTTCAAGAAGGAAGTAAAAGGCTTTAAATCTATCCTGCTGAATTG
CCTGTCCCTGAGGAGTGCCCAGGCTGTGTTCCCAGCTATTGCTCAGGAGATTGGTCGGGAGGAGCTGTGCAGACCAACTG
GGAAGGACTTGATGAGAAAACTGGAAAAGCACTTGACGGCGGAGAAAGGCCCCATGATCGTGTTGGTGTTGGACGAGATG
GATCAGCTGGACAGCAAAGGGCAGGATGTATTATACACACTGTTTGAGTGGCCGTGGCTAAGCAACTCCTGATTGGTGCT
CATTGGTATTGCTAATACCCTAGATCTCACAGACAGAATTCTGCCGAGACTTGAAGCTAGAGAAAACTGTAAGCCGCAGT
TATTGAACTTCCCACCTTATACCAGGAATCAGATAGCTGCCATCTTGCAGGATAGACTTAATCAGGTGTCAAAAGACCAG
GTTCCGGACAGTGCTGAAATCCAGTTCTGTGCCCGCAAAGTGTCTTCTGTTTCAGGAGACATCCGTAAAGCGCTGGATGT
TTGCAGGCGAGCTATAGAAATTGTGGAGTCGCGTGTCAGGAGCCAGACAGTCCTCAAACCACTCTCCGAAAGTAAATCAC
CCAGTGAGTCGCCGGTTCCCAAACAGGTTGGTCTTGCTCACATATCCCAAGTCATTTTGGAAGTTGATGGGAACAGGGTG
ACTTTGAGCCAAGAAAACACACAGGATTCCCTTCCTCTCCAGCAGAAGATTCTGGTTTGCTCTTTGCTGCTTTTGACCCG
TGGGCTGAAAATCAAAGAGGTCATCTGGGGAAGTTATATGAAGCCTACAGTAGCATCTGTCCCAAACAGCAGGTGACAGC
CATAGACCAGTCTCAGTTTTGTCCCTTTCAGGACTCCTGGAGTCCAGGGGCCTTGTGGGATTAAAGAAAAATAAG
ORF - retro_mmus_3570 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.69 % |
| Parental protein coverage: | 90.15 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 4 |
Retrocopy - Parental Gene Alignment:
| Parental | CVAIMPQTRSQTQATIGFPKKKLSNTLKKPNSRDCEVKLRNVQPVPTTPCVDVKLLPLSPRKRLGDDNLC |
| CVAIMPQTRSQTQATIGF.KKKLSN..KK.NS.DCEVK.RNVQPVPTTPC.DVKLLPLSPRK.LGDDNLC | |
| Retrocopy | CVAIMPQTRSQTQATIGFSKKKLSNPWKKTNSWDCEVKFRNVQPVPTTPCADVKLLPLSPRKSLGDDNLC |
| Parental | NTPRLSPCSPP-KLG--KKENGPPRSHTWKGCRLVFDDEPTFKASP-PKEQDRVRQHQIRSSSAQRSPES |
| NTPRLSPCSPP.K.G...K.....RSHTWKGCRLVFDDEPT.KASP.PKEQ.RV..HQI.SSSA.RSPES | |
| Retrocopy | NTPRLSPCSPP<KAGQERKQXXXXRSHTWKGCRLVFDDEPTVKASP<PKEQNRVHKHQICSSSAHRSPES |
| Parental | KADPEQKCPPEKESVCIRLFKQEGTCYQQAKLVLNTAVPDRLPAREQEMGVIRNFLKEHICGKKAGSLYL |
| K.DP.QKC.PEKESVCIRLFKQEGTCYQQAKLVLNTAV.DRLPAREQEMGVIRNFLKE.ICGKKAGSLYL | |
| Retrocopy | KTDPKQKCLPEKESVCIRLFKQEGTCYQQAKLVLNTAVQDRLPAREQEMGVIRNFLKEYICGKKAGSLYL |
| Parental | SGAPGTGKTACLSRILQDFKKEVKGFKSILLNCMSLRSAQAVFPAIAQEIGREELCRPAGKDLMRKLEKH |
| SGAPGTGKTA.LSRILQDFKKEVKGFKSILLNC.SLRSAQAVFPAIAQEIGREELCRP.GKDLMRKLEKH | |
| Retrocopy | SGAPGTGKTAFLSRILQDFKKEVKGFKSILLNCLSLRSAQAVFPAIAQEIGREELCRPTGKDLMRKLEKH |
| Parental | LTAEKGPMIVLVLDEMDQLDSKGQDVLYTLFEWPWLSNSRLVLIGIANTLDLTDRILPRLEARENCKPQL |
| LTAEKGPMIVLVLDEMDQLDSKGQDVLYTLFEWPWLSNS.LVLIGIANTLDLTDRILPRLEARENCKPQL | |
| Retrocopy | LTAEKGPMIVLVLDEMDQLDSKGQDVLYTLFEWPWLSNS*LVLIGIANTLDLTDRILPRLEARENCKPQL |
| Parental | LNFPPYTRNQIAAILQDRLSQVSKDQVLDSAAIQFCARKVSAVSGDIRKALDVCRRAIEIVESDVRSQTV |
| LNFPPYTRNQIAAILQDRL.QVSKDQV.DSA.IQFCARKVS.VSGDIRKALDVCRRAIEIVES.VRSQTV | |
| Retrocopy | LNFPPYTRNQIAAILQDRLNQVSKDQVPDSAEIQFCARKVSSVSGDIRKALDVCRRAIEIVESRVRSQTV |
| Parental | LKPLSECKSPSESPVPKRVGLAHISQVISEVDGNRVTLSQENTQDSLPLQQKILVCSLLLLTRRLKIKEV |
| LKPLSE.KSPSESPVPK.VGLAHISQVI.EVDGNRVTLSQENTQDSLPLQQKILVCSLLLLTR.LKIKEV | |
| Retrocopy | LKPLSESKSPSESPVPKQVGLAHISQVILEVDGNRVTLSQENTQDSLPLQQKILVCSLLLLTRGLKIKEV |
| Parental | T-LGKLYEAYSSICRKQQVTAVDQSE-CLSLSGLLESRGLVGLKKNK |
| ..LGKLYEAYSSIC.KQQVTA.DQS...LSLSGLLESRGLVGLKKNK | |
| Retrocopy | I<LGKLYEAYSSICPKQQVTAIDQSQ<VLSLSGLLESRGLVGLKKNK |
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 | 0 .37 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 0 .74 RPM |
| SRP007412_heart | 0 .00 RPM | 0 .47 RPM |
| SRP007412_kidney | 0 .00 RPM | 0 .85 RPM |
| SRP007412_liver | 0 .00 RPM | 0 .36 RPM |
| SRP007412_testis | 0 .05 RPM | 8 .69 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3570 was not detected
No EST(s) were mapped for retro_mmus_3570 retrocopy.
No TSS is located nearby retro_mmus_3570 retrocopy 5' end.
retro_mmus_3570 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3570 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 | |
|---|---|---|---|
| Dasypus novemcinctus | ENSDNOG00000011590 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000017499 | 1 retrocopy |
retro_mmus_3570 ,
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