RetrogeneDB ID: | retro_mmus_2596 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 5:108822226..108823123(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000093756 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Ccdc77 | ||
| Ensembl ID: | ENSMUSG00000030177 | ||
| Aliases: | Ccdc77, 2400002C23Rik, 2700091N06Rik, AV168274 | ||
| Description: | coiled-coil domain containing 77 [Source:MGI Symbol;Acc:MGI:1914450] |
Retrocopy-Parental alignment summary:
>retro_mmus_2596
GCTTCCAAAGTAGATCCTGGAGTAAGCAAAAGATGAGTAAGGATAAAGGACAGAGAAGACTTTTCTGAGCACTACCAGAA
GGACATAGAGACACTCTTCCTGCAAGTGGAAGCACTTCAGACCCAACTGGGAGAGCAGACTAAGTTTTCTAGAGATCATG
TTGAATGACTCATGGAGGACAGACGGAACCCGAATTGAGGAGATCTAAGTTCAGCACCAGAGAAATCAAGAGAAAAATCA
AGGAGCTGACTAAGAATCTCCATCAAACCCAAAAACTGCTCTACCAGAGTACCAAAGACTTTCTATAACTAAAACTTGAA
AACCAAAATAAAGAGAAGGTATTTTTTGCTTGAGAAAGATCACCTGATGTCAAAGATTAAACAGTATGAAGTACTTTGCA
AGAAGAAAGAAGATAAACTTGGAAAAATAGTTCCCATTTTTCATGAAAGTCATCCTTCTCAAAATGAATATATTAAGTCT
CCTAAGGATAAGCTAATACAAGAGAAAAAGCTGTCCAACATATACCAAGAACAGTGCATCTCCCTAGAAGAAGAACTTCC
TCTTCGTAAGGAGGAAGAAGGAGTGAGGAGAGAGATCTTCACGAATCACTCCAACAAGATGGGCAAGTGGTCACATATAA
TGACAAAACACTATCAGGCCTTGGAGCATTGAAAATCCTGGGAGTAGAAGGTTTCAAGATAGACATTAAGGTTCTCTGAC
AGAAGTTGAAAGACCTGGACAAATGTTCTATAAGGCAACCATGAACACTCATGGAAATCAGGACCTGACCATGCTATGTG
AAGTCCAGATAGCAATAGAAGAACCCATAAGATACAAGGAGAACTGAAGAACCTCAACTCTAAAGTGTTTGGTCTGCAGA
ATGAGCTTAGGCTGTGT
ORF - retro_mmus_2596 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 76.14 % |
| Parental protein coverage: | 61.35 % |
| Number of stop codons detected: | 6 |
| Number of frameshifts detected: | 6 |
Retrocopy - Parental Gene Alignment:
| Parental | ASKADPGVSKRQVRIKDKEGISERHQRDTEMLLLQVEALQAQLGEQTKLSREQVEGLMEDRR-IRVEEIQ |
| ASK.DPGVSKR.VRIKD.E..SE..Q.D.E.L.LQVEALQ.QLGEQTK.SR..VE.LMEDRR..R.EEI. | |
| Retrocopy | ASKVDPGVSKR*VRIKDREDFSEHYQKDIETLFLQVEALQTQLGEQTKFSRDHVE*LMEDRR>TRIEEI* |
| Parental | VQHQRNQEK-IMELTKSLHHTQELLYESTKDFLQLKFENQNKEKVW-MLEKDHLMSKITQYRAQCKKKED |
| VQHQRNQEK.I.ELTK.LH.TQ.LLY.STKDFL.LK.ENQNKEKV...LEKDHLMSKI.QY...CKKKED | |
| Retrocopy | VQHQRNQEK>IKELTKNLHQTQKLLYQSTKDFL*LKLENQNKEKVF>LLEKDHLMSKIKQYEVLCKKKED |
| Parental | KLGKVVPILHESHHTQNEYIKSLKDKLIQEKKLSNMYQEQCISLEEELARIREEEGVRREIFKDRSNKMG |
| KLGK.VPI.HESH..QNEYIKS.KDKLIQEKKLSN.YQEQCISLEEEL....EEEGVRREIF...SNKMG | |
| Retrocopy | KLGKIVPIFHESHPSQNEYIKSPKDKLIQEKKLSNIYQEQCISLEEELPLRKEEEGVRREIFTNHSNKMG |
| Parental | KRLQIMTKRYQALEHRRALE-VEGFKTDIKSLRQKLRDLE-QMLYKATMNNTHGDQDLAMLCEVR-DSNR |
| K...IMTK.YQALEH....E.VEGFK.DIK.L.QKL.DL..QM.YKATM.NTHG.QDL.MLCEV..DSNR | |
| Retrocopy | KWSHIMTKHYQALEH*KSWE<VEGFKIDIKVL*QKLKDLD<QMFYKATM-NTHGNQDLTMLCEVQ<DSNR |
| Parental | RAHKIQGELKNLKSKVFGLENALRLC |
| R.HKIQGELKNL.SKVFGL.N.LRLC | |
| Retrocopy | RTHKIQGELKNLNSKVFGLQNELRLC |
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 | 5 .98 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 9 .29 RPM |
| SRP007412_heart | 0 .00 RPM | 6 .13 RPM |
| SRP007412_kidney | 0 .00 RPM | 6 .29 RPM |
| SRP007412_liver | 0 .00 RPM | 4 .10 RPM |
| SRP007412_testis | 0 .05 RPM | 29 .68 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_2596 was not detected
No EST(s) were mapped for retro_mmus_2596 retrocopy.
No TSS is located nearby retro_mmus_2596 retrocopy 5' end.
retro_mmus_2596 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_2596 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 | ENSMUSG00000030177 | 2 retrocopies |
retro_mmus_1581, retro_mmus_2596 ,
|