RetrogeneDB ID:

retro_mmus_15

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:12:65225764..65227468(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000035560
Aliases:Wdr20rt, 4921538B03Rik, 4930427E19Rik, Wdr20, Wdr20b
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Wdr20a
Ensembl ID:ENSMUSG00000037957
Aliases:Wdr20, 2310040A13Rik, AI549910, Wdr20a
Description:WD repeat domain 20A [Source:MGI Symbol;Acc:MGI:1916891]


Retrocopy-Parental alignment summary:






>retro_mmus_15
ATGGCGACGGAGGGAAGAGGAAAGGAGACGAACGAGATTAAGACCCATTTCACCACCCGAGAAGGTCTGTACAGGCTGCT
GCCGCACTCGGAGTACAGTCGGCCCAACCGGGTGCCCTTCAACTCACAGGGATCCAATCCTGTCCGCGTCTCCTTCGTAA
ACCTCAACGACCAGACTGGTAATGGCAACCGCCTGTGCTTCAGTGTGGGCCGGGAGCTCTACGTCTATATCTACAAGGGG
GTCCGCAAGGCTGCCGACCTGAGTAAACCAATAGATAAAAGGATATACAAAGGAACGCAGCCCACTTGTCATGATTTCAA
CCACCTAACGGCCACAGCGGAGAGCGTCTCTCTCCTAGTGGGCTTTTCCGCAGGCCAAGTCCAGCTTATAGACCCAATCA
AGAAAGAAACCAGCAAGCTCTTTAACGAGGAAAGACTAATAGACAAGTCACGCGTAACCTGTGTCAAATGGGTCCCTGGT
TCGGACAGCCTTTTCCTAGTAGCCCATTCAAGTGGGAACATGTACTCGTACAATGTGGAGCATACTTACGGCACCACAGC
CCCCCACTACCAGCTCCTGAAGCAGGGAGAGAGCTTTGCCGTGCACAATTGCAAGAGCAAATCCACAAGGGACCTTAAGT
GGACGGTGGGCGAGGGGGCCCTCAACGAGTTTGCTTTCTCCCCAGATGGCAAGTTCTTAGCGTGTGTGAGCCAGGACGGG
TTTCTGCGCGTGTTCAACTTTGACTCAGCGGAGCTGCACGGTACAATGAAAAGCTACTTTGGGGGCTTGCTTTGTCTGTG
CTGGAGCCCAGATGGCAAGTACATTGTGACAGGTGGAGAGGACGACTTGGTGACAGTCTGGTCCTTTCTAGACTGCCGAG
TAATAGCTAGAGGCCGTGGGCACAAATCCTGGGTCAGTGTTGTAGCATTTGATCCCTATACTACTAGTGTAGAAGAAAGT
GACCCTATGGAGTTTAGTGACAGTGACAAGAACTTCCAGGACCTTCTTCATTTTGGCAGAGATCGAGCGAACAGTACACA
GTCTAGACTATCCAAACAGAACTCGACAGACAGCCGCCCTGTAAGTGTTACGTATCGGTTTGGTTCGGTGGGCCAGGATA
CACAGCTGTGTTTATGGGACCTTACAGAAGACATCCTTTTCCCTCACCAGCCCCTCTCAAGAGCAAGGGCACATGCAAAC
GTTATGAATGCCACAGGTCTGCCTGCCGGAAGCAATGGGAGCGCTGTCACTACACCTGGGAACTCTGTGCCCCCTCCATT
GCCACGGTCCAATAGCCTTCCACATTCAGCAGTCTCCAATGCTGCTAGCAAAGGCAGCGTCATGGACGGGGCCATTACCT
CTGGGGTCAGCAAGTTTGCACTTCTGTCGCTACATGACCGGAAGGAGAGACACCACGAGAAAGACCGTAAACGAAATCAT
AGTATGGGACACATTTCCAGCAAGAGCAGTGACAAACTGAACCTAGTTAATAAAGCCAAAACGGACCCAGCTAAAACTTT
GGGGACATCCCTGTGTCCTCGGATGGAAGATGTTCCCTTGTTAGAGCCACTGATCTGTAAAAAGATAGCTCATGAAAGAC
TGACGGTATTGGTTTTTCTTGAAGACTGTATAGTCACTGCTTGTCAGGAGGGATTTATTTGCACATGGGCAAGGCCTGGT
AAAGTTAGTAAGTTTCAACCCTGA

ORF - retro_mmus_15 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.5 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMATEGGGKEMNEIKTQFTTREGLYKLLQHSEYSRPNRVPFNSQGSNPVRVSFVNLNDQSGNGDRLCFNVG
MATEG.GKE.NEIKT.FTTREGLY.LL.HSEYSRPNRVPFNSQGSNPVRVSFVNLNDQ.GNG.RLCF.VG
RetrocopyMATEGRGKETNEIKTHFTTREGLYRLLPHSEYSRPNRVPFNSQGSNPVRVSFVNLNDQTGNGNRLCFSVG
ParentalRELYFYIYKGVRKAADLSKPIDKRIYKGTQPTCHDFNLLTATAESVSLLVGFSAGQVQLIDPIKKETSKL
RELY.YIYKGVRKAADLSKPIDKRIYKGTQPTCHDFN.LTATAESVSLLVGFSAGQVQLIDPIKKETSKL
RetrocopyRELYVYIYKGVRKAADLSKPIDKRIYKGTQPTCHDFNHLTATAESVSLLVGFSAGQVQLIDPIKKETSKL
ParentalFNEERLIDKSRVTCVKWVPGSESLFLVAHSSGNMYLYNVEHTCGTTAPHYQLLKQGESFAVHTCKSKSTR
FNEERLIDKSRVTCVKWVPGS.SLFLVAHSSGNMY.YNVEHT.GTTAPHYQLLKQGESFAVH.CKSKSTR
RetrocopyFNEERLIDKSRVTCVKWVPGSDSLFLVAHSSGNMYSYNVEHTYGTTAPHYQLLKQGESFAVHNCKSKSTR
ParentalNPLLKWTVGEGALNEFAFSPDGKFLACVSQDGFLRVFNFDSVELHGTMKSYFGGLLCVCWSPDGKYIVTG
...LKWTVGEGALNEFAFSPDGKFLACVSQDGFLRVFNFDS.ELHGTMKSYFGGLLC.CWSPDGKYIVTG
RetrocopyD--LKWTVGEGALNEFAFSPDGKFLACVSQDGFLRVFNFDSAELHGTMKSYFGGLLCLCWSPDGKYIVTG
ParentalGEDDLVTVWSFLDCRVIARGHGHKSWVSVVAFDPYTTSVEESDPMEFSGSDEDFQDLLHFGRDRANSTQS
GEDDLVTVWSFLDCRVIARG.GHKSWVSVVAFDPYTTSVEESDPMEFS.SD..FQDLLHFGRDRANSTQS
RetrocopyGEDDLVTVWSFLDCRVIARGRGHKSWVSVVAFDPYTTSVEESDPMEFSDSDKNFQDLLHFGRDRANSTQS
ParentalRLSKRNSTDSRPVSVTYRFGSVGQDTQLCLWDLTEDILFPHQPLSRARTHTNVMNATSPPAGSNGNSVTT
RLSK.NSTDSRPVSVTYRFGSVGQDTQLCLWDLTEDILFPHQPLSRAR.H.NVMNAT..PAGSNG..VTT
RetrocopyRLSKQNSTDSRPVSVTYRFGSVGQDTQLCLWDLTEDILFPHQPLSRARAHANVMNATGLPAGSNGSAVTT
ParentalPGNSVPPPLPRSNSLPHSAVSNAASKGSVMDGAIASGVSKFATLSLHDRKERHHEKDHKRNHSMGHISSK
PGNSVPPPLPRSNSLPHSAVSNAASKGSVMDGAI.SGVSKFA.LSLHDRKERHHEKD.KRNHSMGHISSK
RetrocopyPGNSVPPPLPRSNSLPHSAVSNAASKGSVMDGAITSGVSKFALLSLHDRKERHHEKDRKRNHSMGHISSK
ParentalSSDKLNLVTKAKTDPAKTLGTSLCPRMEDVPLLEPLICKKIAHERLTVLVFLEDCIVTACQEGFICTWAR
SSDKLNLV.KAKTDPAKTLGTSLCPRMEDVPLLEPLICKKIAHERLTVLVFLEDCIVTACQEGFICTWAR
RetrocopySSDKLNLVNKAKTDPAKTLGTSLCPRMEDVPLLEPLICKKIAHERLTVLVFLEDCIVTACQEGFICTWAR
ParentalPGKVVSFNP
PGKV..F.P
RetrocopyPGKVSKFQP

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 13 .15 RPM
SRP007412_cerebellum 0 .00 RPM 18 .89 RPM
SRP007412_heart 0 .00 RPM 13 .85 RPM
SRP007412_kidney 0 .04 RPM 19 .96 RPM
SRP007412_liver 0 .00 RPM 13 .49 RPM
SRP007412_testis 86 .31 RPM 18 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_15 was not detected

EST - click to see more details

4 EST(s) were mapped to retro_mmus_15 retrocopy
EST ID Start End Identity Match Mis-match Score
BY714765 65226069 65226710 99.1 634 6 628
CF198005 65227134 65227276 96.5 137 5 132
CF198067 65227134 65227276 99.3 141 1 140
CN843444 65225753 65226350 99.9 586 0 577

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_239311065 libraries2 libraries2 libraries0 libraries3 libraries
TSS #2 TSS_239321057 libraries9 libraries2 libraries0 libraries4 libraries
TSS #3 TSS_23933985 libraries78 libraries5 libraries1 library3 libraries
TSS #4 TSS_23934996 libraries70 libraries3 libraries2 libraries1 library

The graphical summary, for retro_mmus_15 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_15 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_15 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000037957 1 retrocopy
retro_mmus_15 ,


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