RetrogeneDB ID: | retro_mmus_1928 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 2:68081642..68082787(+) | ||
| Located in intron of: | ENSMUSG00000034780 | ||
Retrocopy information | Ensembl ID: | ENSMUSG00000081257 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Actl6a | ||
| Ensembl ID: | ENSMUSG00000027671 | ||
| Aliases: | Actl6a, 2810432C06Rik, AI851094, ARP4, Actl6, Baf53a, C79802 | ||
| Description: | actin-like 6A [Source:MGI Symbol;Acc:MGI:1861453] |
Retrocopy-Parental alignment summary:
>retro_mmus_1928
ATGAACGGCGGCGTGTATGGCGGAAATGAAGTTGGTGCTCTTGTTTTTAACACTGAATCGTATATAGTGAGGCCTGGCTA
TGCTGGCGAGGACTGCCCTAAGGTTGATTTCCCCACGGCTATCAGTGTGGTGCTGGAAAGAGATGACTGAAGCACAACGA
TGGAGACTGATGGTGAGAAAGGCAAGCAGGGTGGGCCCACCTACTACATAGACACCAGAGCCCTCCAAGTGCCCAGGGAG
AACATGGAGGCCATCTCACCATTCAAGAACAACATGGTTGAAGACTGGGATAGTTTCCAGACAATTTTGGATCATACATA
CAAGATGCATGTCAAATCTGAAGCCAGCCTGCATCTTGTTCTCATGTCGGAAGCACCATGGAACACCAGGGCAAAGAGAG
AGAAACTGACAGAGTTGATGTTTCAGCACTACAGCATCCCTGAATTCTTCCTTTGCAAAACTACAGTTTTGATGGCGTTT
GCTAATGGTCATTCTACTGGGCTGATTTTGGACAGTGGAGCTACCCACACCACTTCGATTCCAGTCCACGATGGCTATGT
CCTTCAAAAAGGCATTGTGAAATCCCCTCTTGCTGGAGTCTTCATTACCATGCAGTACAAAGAACTCTTCCAGGAAATGA
ACATAGAACTCATTCCTCCTTACATGATTGCATTAAAAGAGGCTGTTTGAGTAGGCTCTCCAGCCAACTGGAAAAGAAAA
GAGAACCTGCCCCAGGTTACAAAGTCTTGGCACAATTACATGTGCAACGGTGTCACTCAGGACTTTCAAGCTTCTGTCCT
TCAGGTATTAGACTCCACCTATGACAAACAAGTGGCTTCACAGATGCCAACTATTCACTACGAATTCCCCAATGGTTACA
GCTGTGGTTTTGGTGCAAAGAGGCTGAAAATTCCTGAAGGATTATTTGACCCTTCCAACTAAAGGGCTTGTCTGGGAACA
TGATGCTGGGAGTCAGTCACATGGTCACAACCAGTGTCGGGATGTGTGACATCAATATCAGACCAAGTCTCTATGGCAGT
GTGATCATAGCAGGAGGAAACAAGCTAATACAGAGTTTCACTGACAGGATAAATAGAGACCTTTCTCAGAAAACTTCACC
AAGTATGTAGTTGAAACTGATTGCA
ORF - retro_mmus_1928 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 85.9 % |
| Parental protein coverage: | 89.04 % |
| Number of stop codons detected: | 3 |
| Number of frameshifts detected: | 1 |
Retrocopy - Parental Gene Alignment:
| Parental | MSGGVYGGDEVGALVFDIGSYTVRAGYAGEDCPKVDFPTAIGVVLERDDGSTMMEIDGDKGKQGGPTYYI |
| M.GGVYGG.EVGALVF...SY.VR.GYAGEDCPKVDFPTAI.VVLERDD.ST.ME.DG.KGKQGGPTYYI | |
| Retrocopy | MNGGVYGGNEVGALVFNTESYIVRPGYAGEDCPKVDFPTAISVVLERDD*STTMETDGEKGKQGGPTYYI |
| Parental | DTNALRVPRENMEAISPLKNGMVEDWDSFQAILDHTYKMHVKSEASLHPVLMSEAPWNTRAKREKLTELM |
| DT.AL.VPRENMEAISP.KN.MVEDWDSFQ.ILDHTYKMHVKSEASLH.VLMSEAPWNTRAKREKLTELM | |
| Retrocopy | DTRALQVPRENMEAISPFKNNMVEDWDSFQTILDHTYKMHVKSEASLHLVLMSEAPWNTRAKREKLTELM |
| Parental | FEHYSIPAFFLCKTAVLTAFANGRSTGLILDSGATHTTAIPVHDGYVLQQGIVKSPLAGDFITMQCRELF |
| F.HYSIP.FFLCKT.VL.AFANG.STGLILDSGATHTT.IPVHDGYVLQ.GIVKSPLAG.FITMQ..ELF | |
| Retrocopy | FQHYSIPEFFLCKTTVLMAFANGHSTGLILDSGATHTTSIPVHDGYVLQKGIVKSPLAGVFITMQYKELF |
| Parental | QEMNIELIPPYMIASKEAVREGSPANWKRKEKLPQVTRSWHNYMCNCVIQDFQASVLQVSDSTYDEQVAA |
| QEMNIELIPPYMIA.KEAV..GSPANWKRKE.LPQVT.SWHNYMCN.V.QDFQASVLQV.DSTYD.QVA. | |
| Retrocopy | QEMNIELIPPYMIALKEAV*VGSPANWKRKENLPQVTKSWHNYMCNGVTQDFQASVLQVLDSTYDKQVAS |
| Parental | QMPTVHYEFPNGYNCDFGAERLKIPEGLFDPSN-VKGLSGNTMLGVSHVVTTSVGMCDIDIRPGLYGSVI |
| QMPT.HYEFPNGY.C.FGA.RLKIPEGLFDPSN..KGLSGN.MLGVSH.VTTSVGMCDI.IRP.LYGSVI | |
| Retrocopy | QMPTIHYEFPNGYSCGFGAKRLKIPEGLFDPSN<LKGLSGNMMLGVSHMVTTSVGMCDINIRPSLYGSVI |
| Parental | VAGGNTLIQSFTDRLNRELSQKTPPSMRLKLIA |
| .AGGN.LIQSFTDR.NR.LSQKT.PSM.LKLIA | |
| Retrocopy | IAGGNKLIQSFTDRINRDLSQKTSPSM*LKLIA |
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 .07 RPM | 7 .76 RPM |
| SRP007412_cerebellum | 0 .04 RPM | 11 .25 RPM |
| SRP007412_heart | 0 .00 RPM | 19 .92 RPM |
| SRP007412_kidney | 0 .00 RPM | 23 .83 RPM |
| SRP007412_liver | 0 .08 RPM | 14 .26 RPM |
| SRP007412_testis | 0 .00 RPM | 92 .21 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_1928 was not detected
No EST(s) were mapped for retro_mmus_1928 retrocopy.
No TSS is located nearby retro_mmus_1928 retrocopy 5' end.
retro_mmus_1928 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_1928 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 3 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Choloepus hoffmanni | ENSCHOG00000009477 | 2 retrocopies | |
| Mus musculus | ENSMUSG00000027671 | 1 retrocopy |
retro_mmus_1928 ,
|
| Tursiops truncatus | ENSTTRG00000008907 | 1 retrocopy |