RetrogeneDB ID:

retro_mmus_132

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:16:36041512..36042499(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000034379
Aliases:Wdr5b, 2310009C03Rik, AI606931
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Wdr5
Ensembl ID:ENSMUSG00000026917
Aliases:Wdr5, 2410008O07Rik, AA408785, AA960360, Big, Big-3
Description:WD repeat domain 5 [Source:MGI Symbol;Acc:MGI:2155884]


Retrocopy-Parental alignment summary:






>retro_mmus_132
ATGGCGACCGAGCATCTGCCAGCAGAGAGAGCACAGTCACTTCTCTCTGCCCCCCGGCGCGAGGAAGAGCCGCAGAAACC
CAACTATGCTCTCAGACTTACTCTTGCGGGGCACTCGGCGGCCATATCATCAGTTAAATTTAGTCCTAATGGCGAATGGC
TAGCGAGTTCTGCAGCTGATGCACTAATTATAATTTGGGGAGCATACGATGGGAATTGTAAGAAAACACTCTATGGTCAC
AGTCTGGAAATATCAGATGTTGCCTGGTCTTCAGATTCTAGTCGTCTAGTTTCAGCCTCAGATGATAAGACTCTAAAGGT
ATGGGATATGAGATCTGGAAAATGTCTGAAAACACTGAAGGGGCACAGCGATTTCGTCTTCTGTTGTGACTTCAACCCAC
CATCCAACCTCATCGTTTCGGGCTCTTTTGATGAGAGTGTGAAAATATGGGAAGTAAAAACAGGAAAATGCCTCAAGACT
TTGTCTGCACATTCGGACCCCATTTCTGCCGTAAATTTTAATTGTAATGGGTCCTTGATAGTGTCCGGGAGCTATGATGG
GCTTTGTAGAATTTGGGATGCTGCGTCAGGCCAGTGTTTAAGGACACTTGCTGATGAAGGCAACCCTCCAGTGTCTTTTG
TAAAATTTTCTCCAAATGGTAAATACATTCTCACTGCAACTTTGGACAATACTCTTAAACTGTGGGATTACAGCAGGGGC
AGATGCCTGAAGACATACACTGGTCATAAGAATGAGAAATACTGCCTATTTGCCAGTTTCTCGGTTACTGGTAGAAAGTG
GGTTGTGTCTGGTTCAGAGGACAACATGGTTTACATCTGGAATCTTCAGACTAAAGAGATTGTACAGAGGTTGCAAGGTC
ACACAGATGTGGTGATCTCAGCAGCCTGTCACCCTACAAAAAACATCATCGCATCAGCAGCACTAGAAAATGACAAGACA
ATTAAAGTGTGGTCGAGTGACTGCTGA

ORF - retro_mmus_132 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.79 %
Parental protein coverage: 93.71 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTISGHKLGIS
SA......P.KPNYAL..TLAGH..A.SSVKFSPNGEWLASS.AD.LI.IWGAYDG...KT..GH.L.IS
RetrocopySAPRREEEPQKPNYALRLTLAGHSAAISSVKFSPNGEWLASSAADALIIIWGAYDGNCKKTLYGHSLEIS
ParentalDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTG
DVAWSSDS..LVSASDDKTLK.WD..SGKCLKTLKGHS..VFCC.FNP.SNLIVSGSFDESV.IW.VKTG
RetrocopyDVAWSSDSSRLVSASDDKTLKVWDMRSGKCLKTLKGHSDFVFCCDFNPPSNLIVSGSFDESVKIWEVKTG
ParentalKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILA
KCLKTL.AHSDP.SAV.FN..GSLIVS.SYDGLCRIWD.ASGQCL.TL.D..NPPVSFVKFSPNGKYIL.
RetrocopyKCLKTLSAHSDPISAVNFNCNGSLIVSGSYDGLCRIWDAASGQCLRTLADEGNPPVSFVKFSPNGKYILT
ParentalATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHT
ATLDNTLKLWDYS.G.CLKTYTGHKNEKYC.FA.FSVTG.KW.VSGSEDN.VYIWNLQTKEIVQ.LQGHT
RetrocopyATLDNTLKLWDYSRGRCLKTYTGHKNEKYCLFASFSVTGRKWVVSGSEDNMVYIWNLQTKEIVQRLQGHT
ParentalDVVISTACHPTENIIASAALENDKTIKLWKSDC
DVVIS.ACHPT.NIIASAALENDKTIK.W.SDC
RetrocopyDVVISAACHPTKNIIASAALENDKTIKVWSSDC

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 2 .03 RPM 27 .15 RPM
SRP007412_cerebellum 2 .26 RPM 32 .61 RPM
SRP007412_heart 1 .62 RPM 29 .76 RPM
SRP007412_kidney 1 .73 RPM 41 .69 RPM
SRP007412_liver 0 .71 RPM 32 .91 RPM
SRP007412_testis 0 .87 RPM 44 .23 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_132 in 4 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 16:36040809..36041673
ENCFF001YIJ POLR2A 16:36040263..36042051
ENCFF001YJZ POLR2A 16:36040275..36045345
ENCFF001YKA POLR2A 16:36039216..36045422

EST - click to see more details

1 EST(s) were mapped to retro_mmus_132 retrocopy
EST ID Start End Identity Match Mis-match Score
AA510402 36041631 36041878 99.6 246 1 245

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_46955519 libraries477 libraries74 libraries1 library1 library
TSS #2 TSS_46956222 libraries336 libraries512 libraries1 library1 library
TSS #3 TSS_4695793 libraries119 libraries729 libraries126 libraries5 libraries

The graphical summary, for retro_mmus_132 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_132 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_132 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_11
Pan troglodytes retro_ptro_18
Gorilla gorilla retro_ggor_171
Macaca mulatta retro_mmul_190
Callithrix jacchus retro_cjac_1
Rattus norvegicus retro_rnor_258
Bos taurus retro_btau_299
Sus scrofa retro_sscr_1
Canis familiaris retro_cfam_128
Equus caballus retro_ecab_82
Parental genes homology:
Parental genes homology involve 27 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000111791 retrocopy
retro_amel_29,
Bos taurus ENSBTAG000000470311 retrocopy
retro_btau_299,
Canis familiaris ENSCAFG000000198301 retrocopy
retro_cfam_128,
Callithrix jacchus ENSCJAG000000101231 retrocopy
retro_cjac_1,
Cavia porcellus ENSCPOG000000147901 retrocopy
retro_cpor_12,
Dipodomys ordii ENSDORG000000150101 retrocopy
retro_dord_7,
Equus caballus ENSECAG000000173891 retrocopy
retro_ecab_82,
Echinops telfairi ENSETEG000000157311 retrocopy
retro_etel_15,
Felis catus ENSFCAG000000057121 retrocopy
retro_fcat_119,
Homo sapiens ENSG000001963631 retrocopy
retro_hsap_11,
Gorilla gorilla ENSGGOG000000049972 retrocopies
retro_ggor_171, retro_ggor_2023,
Loxodonta africana ENSLAFG000000111921 retrocopy
retro_lafr_55,
Microcebus murinus ENSMICG000000080851 retrocopy
retro_mmur_34,
Myotis lucifugus ENSMLUG000000022361 retrocopy
retro_mluc_11,
Macaca mulatta ENSMMUG000000141591 retrocopy
retro_mmul_190,
Mustela putorius furoENSMPUG000000121841 retrocopy
retro_mputfur_2,
Mus musculus ENSMUSG000000207451 retrocopy
retro_mmus_2988,
Mus musculus ENSMUSG00000026917 1 retrocopy
retro_mmus_132 ,
Nomascus leucogenys ENSNLEG000000134721 retrocopy
retro_nleu_63,
Otolemur garnettii ENSOGAG000000089601 retrocopy
retro_ogar_86,
Procavia capensis ENSPCAG000000134761 retrocopy
retro_pcap_43,
Pan troglodytes ENSPTRG000000236532 retrocopies
retro_ptro_18, retro_ptro_1975,
Pteropus vampyrus ENSPVAG000000016661 retrocopy
retro_pvam_112,
Rattus norvegicus ENSRNOG000000082121 retrocopy
retro_rnor_258,
Sus scrofa ENSSSCG000000249121 retrocopy
retro_sscr_1,
Ictidomys tridecemlineatus ENSSTOG000000158991 retrocopy
retro_itri_117,
Drosophila melanogaster FBgn00400661 retrocopy
retro_dmel_69,


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