RetrogeneDB ID:

retro_hsap_2970

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:113377079..113378942(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000248697
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TOX4
Ensembl ID:ENSG00000092203
Aliases:TOX4, C14orf92, KIAA0737, LCP1, MIG7
Description:TOX high mobility group box family member 4 [Source:HGNC Symbol;Acc:20161]


Retrocopy-Parental alignment summary:






>retro_hsap_2970
ATGGAGTCTCCCGGAGGAAATGACAATTACCTGACAATCACAGGGCCGTCACACCTCTTCCTGTCAGGGGCCGAGACATT
CCATACACCAAGCTTAGGTGATGAAGAATTTGAAATCCCACCTATCTCTTTGGATTCTGATCCCTCATTGGCTGTCTCAG
ATGTGGTTGACCACTTTGATGACCTGGCAGACCCTTCCTCTTCACAGGATGGCAGTGCTTCAGCCCAGTATGGGGTCCAG
ACATTGGACATGCTCTGTGGGCATGACCCATGGCTTGATGGAGCAAGGTGGGGGCTCCTCAGTGGAGGCTTGATCATGGA
CTTAAACCACTCTATAGGAACTCAGTATAGTGCCAACCCACCTGTTACAATTGATGTACTAATGATAGACATGACATCTG
ACTTGATGGGGCATAGCCAGTTGACCACCACTGATCAGTCAGAACTGAGTTTCCAACTGGGTTTGAGCTTACGGGGTGGC
ACCATCCTGCCACCTGCCCAGTCACCTGAAGATCGTATTTCAACCACCCCTTCACCTACTAGTTCACTTCACGAGGTTGG
TGTTGAGGATTTCTGGAGGCAAATTTCCAGCCAGAAGACAGTGGTGGTGGAAGCAGGGAAAAAGCAGAAGTTCCCAAAGA
AGAGAAAAAAGAAAGATCCTAATGAACCTCAGAAACCAGTTTCAGCATATGCTTTATTCTTTCCTGATACACGGGCTGCC
ATCAAGGGACAGAATCCTAATGCCACTTTTGGTGAGGTTTCAAAAATTGTGGCCTCCATGTGGGATAGTCTTGGAGAGGA
GCAAAAACAGATATATAAGAGGAAAACTGAGGCTGCCAAGAAAGAGTATCTGAAGACACTGGCTGCTTACGAAGACAACC
AGGAGTGTCAGGCCACTGTGGAAACAGCGGAATTGGATCCAGCACCACCATCACAAACTCCTTCTCCACCTTCTATGGCT
ACTGTTGACCCAGCGTCTCCAGCACCAGCTTCAACAGAGCCCCCTGTCCTGTCCCCATCCATTGTTGTTAACTCCACCCT
TTCATCCTATGTGGCAAACCAGGCATCTTCAGGAGCTGGGGGTCAGCCCAATATCACCAAGTTGATTATTACCAAACAAA
CGTTGCCCTCTTCCATTACTATGTCTCAGGGAGGGATGGTTACTGCTATCCTAGCCACAGTGGTGACCTCCTGGGGGCTC
CAACTAGACCCAACCAGTACAGCCACTATCCAGCCCAGTCAACAAGCCCAGATTGTCACTCGGTCAGTGTTGCAGGCAGC
AGCAGCAGCTGCTACTGTTGCTTCTATGCAACTGCCTCCACCCCGACTACAGCCCCCTCCATTATAACAGATGCCACAGC
CCCTGACTCAGCAGCAAGTTACCATTCTGCAGCAGCCTCCTCCACTCCAGGCCATGCAACAGCCTCCACCTCAGAAAGTT
TGAATCAATTTACAGCAACAGCTACCTCCTCTGCAGATCAAGAGTGTGCCTCCACTCACTTTGAAAATGCAGACTACCTT
AGTCCCACCAACTGTGGAAAGTAGTCCTGAGCGGCCTATGAACAATAGTCCTGAGGCCCATACAGTGGAGGCAACTTCTC
CTGAGACCATCTGTGAGATGATCACAGATGTAGTTCCTGAGGTTGAGTCTTCTTCTCAGATGGATGTTGAATTGGTGAGT
GGGTCTCCTGTGGCACTGTCACCCCAGCCTCGATGTGTGATGTCTGGTTGTGAGAATCCTCCCATTGTGAGTAAGGACTG
GGACAATGAATGCTGCAGCAATGAGTGTGTGGTGAAGCACTGCAGGGATGTATTCTTGGCCTGGGTAGCCTCTAGAAATT
CAAACACAGTGGTGTTTGTGAAA

ORF - retro_hsap_2970 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.3 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMEFPGGNDNYLTITGPSHPFLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVVGHFDDLADPSSSQD
ME.PGGNDNYLTITGPSH.FLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVV.HFDDLADPSSSQD
RetrocopyMESPGGNDNYLTITGPSHLFLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVVDHFDDLADPSSSQD
ParentalGSFSAQYGVQTLDM-PVGMTHGLMEQGG-GLLSGGLTMDLDHSIGTQYSANPPVTIDVPMTDMTSGLMGH
GS.SAQYGVQTLDM..VGMTHGLMEQGG.GLLSGGL.MDL.HSIGTQYSANPPVTIDV.M.DMTS.LMGH
RetrocopyGSASAQYGVQTLDM>SVGMTHGLMEQGG<GLLSGGLIMDLNHSIGTQYSANPPVTIDVLMIDMTSDLMGH
ParentalSQLTTIDQSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPTSSLHEDGVEDFRRQLPSQKTVVVEAGKK
SQLTT.DQSELS.QLGLSL.GGTILPPAQSPEDR.STTPSPTSSLHE.GVEDF.RQ..SQKTVVVEAGKK
RetrocopySQLTTTDQSELSFQLGLSLRGGTILPPAQSPEDRISTTPSPTSSLHEVGVEDFWRQISSQKTVVVEAGKK
ParentalQKAPKKRKKKDPNEPQKPVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKTEA
QK.PKKRKKKDPNEPQKPVSAYALFF.DT.AAIKGQNPNATFGEVSKIVASMWDSLGEEQKQ.YKRKTEA
RetrocopyQKFPKKRKKKDPNEPQKPVSAYALFFPDTRAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQIYKRKTEA
ParentalAKKEYLKALAAYKDNQECQATVETVELDPAPPSQTPSPPPMATVDPASPAPASIEPPALSPSIVVNSTLS
AKKEYLK.LAAY.DNQECQATVET.ELDPAPPSQTPSPP.MATVDPASPAPAS.EPP.LSPSIVVNSTLS
RetrocopyAKKEYLKTLAAYEDNQECQATVETAELDPAPPSQTPSPPSMATVDPASPAPASTEPPVLSPSIVVNSTLS
ParentalSYVANQASSGAGGQPNITKLIITKQMLPSSITMSQGGMVTVIPATVVTSRGLQLGQTSTATIQPSQQAQI
SYVANQASSGAGGQPNITKLIITKQ.LPSSITMSQGGMVT.I.ATVVTS.GLQL..TSTATIQPSQQAQI
RetrocopySYVANQASSGAGGQPNITKLIITKQTLPSSITMSQGGMVTAILATVVTSWGLQLDPTSTATIQPSQQAQI
ParentalVTRSVLQAAAAAAAAASMQLPPPRLQPPPLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQQQP
VTRSVLQAAAAAA..ASMQLPPPRLQPPPL.QMPQP.TQQQVTILQQPPPLQAMQQPPPQKV.INLQQQ.
RetrocopyVTRSVLQAAAAAATVASMQLPPPRLQPPPL*QMPQPLTQQQVTILQQPPPLQAMQQPPPQKV*INLQQQL
ParentalPPLQIKSVPLPTLKMQTTLVPPTVESSPERPMNNSPEAHTVEAPSPETICEMITDVVPEVESPSQMDVEL
PPLQIKSVP..TLKMQTTLVPPTVESSPERPMNNSPEAHTVEA.SPETICEMITDVVPEVES.SQMDVEL
RetrocopyPPLQIKSVPPLTLKMQTTLVPPTVESSPERPMNNSPEAHTVEATSPETICEMITDVVPEVESSSQMDVEL
ParentalVSGSPVALSPQPRCVRSGCENPPIVSKDWDNEYCSNECVVKHCRDVFLAWVASRNSNTVVFVK
VSGSPVALSPQPRCV.SGCENPPIVSKDWDNE.CSNECVVKHCRDVFLAWVASRNSNTVVFVK
RetrocopyVSGSPVALSPQPRCVMSGCENPPIVSKDWDNECCSNECVVKHCRDVFLAWVASRNSNTVVFVK

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 82 .93 RPM
bodymap2_adrenal 0 .08 RPM 55 .37 RPM
bodymap2_brain 0 .00 RPM 69 .90 RPM
bodymap2_breast 0 .00 RPM 62 .63 RPM
bodymap2_colon 0 .00 RPM 70 .05 RPM
bodymap2_heart 0 .00 RPM 63 .34 RPM
bodymap2_kidney 0 .00 RPM 56 .77 RPM
bodymap2_liver 0 .00 RPM 28 .29 RPM
bodymap2_lung 0 .00 RPM 56 .35 RPM
bodymap2_lymph_node 0 .00 RPM 58 .27 RPM
bodymap2_ovary 0 .00 RPM 70 .19 RPM
bodymap2_prostate 0 .00 RPM 87 .62 RPM
bodymap2_skeletal_muscle 0 .02 RPM 144 .52 RPM
bodymap2_testis 0 .02 RPM 83 .10 RPM
bodymap2_thyroid 0 .00 RPM 90 .69 RPM
bodymap2_white_blood_cells 0 .00 RPM 96 .77 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2970 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2970 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2970 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2970 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2970 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2008
Pongo abelii retro_pabe_2463
Parental genes homology:
Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000062611 retrocopy
retro_amel_858,
Canis familiaris ENSCAFG000000056472 retrocopies
retro_cfam_1625, retro_cfam_1698,
Choloepus hoffmanni ENSCHOG000000007142 retrocopies
retro_chof_2239, retro_chof_631,
Homo sapiens ENSG00000092203 1 retrocopy
retro_hsap_2970 ,
Macropus eugenii ENSMEUG000000105011 retrocopy
retro_meug_1384,
Mustela putorius furoENSMPUG000000001811 retrocopy
retro_mputfur_718,
Mus musculus ENSMUSG000000168311 retrocopy
retro_mmus_11,
Nomascus leucogenys ENSNLEG000000145561 retrocopy
retro_nleu_2027,
Pongo abelii ENSPPYG000000055981 retrocopy
retro_pabe_2463,
Pan troglodytes ENSPTRG000000061261 retrocopy
retro_ptro_2008,
Sus scrofa ENSSSCG000000292031 retrocopy
retro_sscr_361,

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 = 0.1 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .06 RPM

Indel association:

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





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