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:

ParentalMSGGVYGGDEVGALVFDIGSYTVRAGYAGEDCPKVDFPTAIGVVLERDDGSTMMEIDGDKGKQGGPTYYI
M.GGVYGG.EVGALVF...SY.VR.GYAGEDCPKVDFPTAI.VVLERDD.ST.ME.DG.KGKQGGPTYYI
RetrocopyMNGGVYGGNEVGALVFNTESYIVRPGYAGEDCPKVDFPTAISVVLERDD*STTMETDGEKGKQGGPTYYI
ParentalDTNALRVPRENMEAISPLKNGMVEDWDSFQAILDHTYKMHVKSEASLHPVLMSEAPWNTRAKREKLTELM
DT.AL.VPRENMEAISP.KN.MVEDWDSFQ.ILDHTYKMHVKSEASLH.VLMSEAPWNTRAKREKLTELM
RetrocopyDTRALQVPRENMEAISPFKNNMVEDWDSFQTILDHTYKMHVKSEASLHLVLMSEAPWNTRAKREKLTELM
ParentalFEHYSIPAFFLCKTAVLTAFANGRSTGLILDSGATHTTAIPVHDGYVLQQGIVKSPLAGDFITMQCRELF
F.HYSIP.FFLCKT.VL.AFANG.STGLILDSGATHTT.IPVHDGYVLQ.GIVKSPLAG.FITMQ..ELF
RetrocopyFQHYSIPEFFLCKTTVLMAFANGHSTGLILDSGATHTTSIPVHDGYVLQKGIVKSPLAGVFITMQYKELF
ParentalQEMNIELIPPYMIASKEAVREGSPANWKRKEKLPQVTRSWHNYMCNCVIQDFQASVLQVSDSTYDEQVAA
QEMNIELIPPYMIA.KEAV..GSPANWKRKE.LPQVT.SWHNYMCN.V.QDFQASVLQV.DSTYD.QVA.
RetrocopyQEMNIELIPPYMIALKEAV*VGSPANWKRKENLPQVTKSWHNYMCNGVTQDFQASVLQVLDSTYDKQVAS
ParentalQMPTVHYEFPNGYNCDFGAERLKIPEGLFDPSN-VKGLSGNTMLGVSHVVTTSVGMCDIDIRPGLYGSVI
QMPT.HYEFPNGY.C.FGA.RLKIPEGLFDPSN..KGLSGN.MLGVSH.VTTSVGMCDI.IRP.LYGSVI
RetrocopyQMPTIHYEFPNGYSCGFGAKRLKIPEGLFDPSN<LKGLSGNMMLGVSHMVTTSVGMCDINIRPSLYGSVI
ParentalVAGGNTLIQSFTDRLNRELSQKTPPSMRLKLIA
.AGGN.LIQSFTDR.NR.LSQKT.PSM.LKLIA
RetrocopyIAGGNKLIQSFTDRINRDLSQKTSPSM*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 actvity 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 ENSCHOG000000094772 retrocopies
Mus musculus ENSMUSG00000027671 1 retrocopy
retro_mmus_1928 ,
Tursiops truncatus ENSTTRG000000089071 retrocopy



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