RetrogeneDB ID:

retro_hsap_4751

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:122695492..122696823(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000228466
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TUBB4A
Ensembl ID:ENSG00000104833
Aliases:TUBB4A, DYT4, TUBB4, TUBB5, beta-5
Description:tubulin, beta 4A class IVa [Source:HGNC Symbol;Acc:20774]


Retrocopy-Parental alignment summary:






>retro_hsap_4751
ATGCAGGAGATCATGCACCTGCAGGCCGGCCAGTGTGGCAGCCAGATCAGGGCCAAGTTTTGGGAGGTTATCAGTGACAA
ACATGGGCATCGACCCCACAGGCACATACTATAGGGACAGTGACCTGCAACCGGAAAGGATCAACGTGTACTACAATGAG
GCCAGAGGAGGAAATTATGTCCCCAGAGCGGTGCTGGTGGACCTGGAACCCAGCACCATGGACTCTATCCTTTCCGGCCC
CTTCGGTCAGATCTTTCGGCCGGACAACTTCGTGTTTGGCCAGTCCAGAGCCGGCAACAACTGGGTGAAGGGGCACTACA
CGGAGGGCACAGAGCTGGTAGGCACTGTCCTGGACGTGGTCCAGAAGGAGGCCTAGAACTGCGACTGCCTTCAAGGCTTC
CAGCTGACGCACTTGCTGGGGGGTGGCACGGGGTCCGGGATGGGCACACTGCTCATCAGTAAGATCCGTGAGGAGTTCCC
AGACCGCATCATGAACACCTTCAGCATGGTGCCCTCGCCCAAAGTGTCAGATACGGTGTGGAGCCCTACAATGCCACACT
GTCTGTGCACCAGCTGGTGGAGAATACGAATGAGACCTACTGCATCAACAATGGGGCACTCTATGACATCTGCTTCCGCA
CCCTCAAGCTGACCACCTCCACCTACGGGGACCTCAACCACCTGGTGTCAGCCACCATGAGCAGAGTCACCACCTGCCTG
TGCTTCCTGGGCCAGCTGAACACCAACCTGCACAAGCTGGCCGTCAACATGGTCCCCTTTCCTTGCCCGCACTTCTTCAT
GCCTGGCTTCGCACCCCTGACCAGCCGGGGCAGCCAGCAGTACCAGGCCCTGAGGGTGCCTGAGCTCACACAGCAGATGT
TCGATGCCAAGAACATGATGGCCATGTGCAACCCGCGACATGGCCGCTACCTGACCATGGCCACCGTGTTCCGGGCCGCA
TGTCCATGAAGGAGGTGGACAAGCAGATGCTGAGCCTGCAGAGCAAGAACAGCAGCTACTTCGTGCAGTGGATCCCCAAC
AACATGAAGACGGCCGTGTGCGACATCTCGCCCCACGGCCTGAAGATAGCCGCAACTTTCATCAGCAACAACACAGACTT
CCAGGAGCTGTTCAAGTGCATCTCTGCGCAGTTCACGGCCATGTTGTGGTGCAAGGCGTTCCTGCACTGGTACACAGGCG
AGGGCATGGACGAGATGGAGTTCACCGAGACTGACAGCAACATGAATGACCTGGTATCTGAGTACCAGCAGTACCAGGAT
GCCACAGCCGAGGAGGGCGAGTTCAAGCAGGAGGCCGAGGAGGAGGTGGCC

ORF - retro_hsap_4751 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.91 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMREIVHLQAGQCGNQIGAKFWEVISDEHG-IDPTGTYHGDSDLQLERINVYYNEATGGNYVPRAVLVDLE
M.EI.HLQAGQCG.QI.AKFWEVISD.HG.IDPTGTY..DSDLQ.ERINVYYNEA.GGNYVPRAVLVDLE
RetrocopyMQEIMHLQAGQCGSQIRAKFWEVISDKHG>IDPTGTYYRDSDLQPERINVYYNEARGGNYVPRAVLVDLE
ParentalPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVVRKEAESCDCLQGFQLTHSL
P.TMDS..SGPFGQIFRPDNFVFGQS.AGNNW.KGHYTEG.ELV..VLDVV.KEA..CDCLQGFQLTH.L
RetrocopyPSTMDSILSGPFGQIFRPDNFVFGQSRAGNNWVKGHYTEGTELVGTVLDVVQKEA*NCDCLQGFQLTHLL
ParentalGGGTGSGMGTLLISKIREEFPDRIMNTFSVVPSPKVSDTV-VEPYNATLSVHQLVENTDETYCIDNEALY
GGGTGSGMGTLLISKIREEFPDRIMNTFS.VPSPKVSDTV.VEPYNATLSVHQLVENT.ETYCI.N.ALY
RetrocopyGGGTGSGMGTLLISKIREEFPDRIMNTFSMVPSPKVSDTV<VEPYNATLSVHQLVENTNETYCINNGALY
ParentalDICFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGS
DICFRTLKLTT.TYGDLNHLVSATMS.VTTCL.F.GQLN..L.KLAVNMVPFP..HFFMPGFAPLTSRGS
RetrocopyDICFRTLKLTTSTYGDLNHLVSATMSRVTTCLCFLGQLNTNLHKLAVNMVPFPCPHFFMPGFAPLTSRGS
ParentalQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVAAVFR-GRMSMKEVDEQMLSVQSKNSSYFVEWIPN
QQY.AL.VPELTQQMFDAKNMMA.C.PRHGRYLT.A.VFR.GRMSMKEVD.QMLS.QSKNSSYFV.WIPN
RetrocopyQQYQALRVPELTQQMFDAKNMMAMCNPRHGRYLTMATVFR<GRMSMKEVDKQMLSLQSKNSSYFVQWIPN
ParentalNVKTAVCDIPPRGLKMAATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMND
N.KTAVCDI.P.GLK.AATFI.N.T..QELFK.IS.QFTAM...KAFLHWYTGEGMDEMEFTE..SNMND
RetrocopyNMKTAVCDISPHGLKIAATFISNNTDFQELFKCISAQFTAMLWCKAFLHWYTGEGMDEMEFTETDSNMND
ParentalLVSEYQQYQDATAEEGEFEEEAEEEVA
LVSEYQQYQDATAEEGEF..EAEEEVA
RetrocopyLVSEYQQYQDATAEEGEFKQEAEEEVA

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
bodymap2_adipose 0 .00 RPM 0 .99 RPM
bodymap2_adrenal 0 .06 RPM 0 .55 RPM
bodymap2_brain 0 .00 RPM 765 .39 RPM
bodymap2_breast 0 .04 RPM 0 .33 RPM
bodymap2_colon 0 .00 RPM 8 .88 RPM
bodymap2_heart 0 .00 RPM 1 .51 RPM
bodymap2_kidney 0 .00 RPM 2 .63 RPM
bodymap2_liver 0 .00 RPM 0 .97 RPM
bodymap2_lung 0 .00 RPM 0 .37 RPM
bodymap2_lymph_node 0 .00 RPM 3 .36 RPM
bodymap2_ovary 0 .00 RPM 1 .47 RPM
bodymap2_prostate 0 .00 RPM 2 .42 RPM
bodymap2_skeletal_muscle 0 .00 RPM 4 .29 RPM
bodymap2_testis 0 .00 RPM 44 .53 RPM
bodymap2_thyroid 0 .00 RPM 0 .83 RPM
bodymap2_white_blood_cells 0 .00 RPM 1 .12 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4751 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4751 retrocopy.

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_1968971676 libraries103 libraries34 libraries12 libraries4 libraries

The graphical summary, for retro_hsap_4751 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 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_hsap_4751 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4751 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3166
Pongo abelii retro_pabe_3698
Macaca mulatta retro_mmul_2533
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000104833 1 retrocopy
retro_hsap_4751 ,
Homo sapiens ENSG000001732131 retrocopy
retro_hsap_3733,
Homo sapiens ENSG000001738761 retrocopy
retro_hsap_3944,
Homo sapiens ENSG000002589471 retrocopy
retro_hsap_155,
Myotis lucifugus ENSMLUG000000156071 retrocopy
retro_mluc_754,
Mustela putorius furoENSMPUG000000069581 retrocopy
retro_mputfur_1255,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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