RetrogeneDB ID:

retro_hsap_1892

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:57863786..57865406(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000267620
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GTF2H1
Ensembl ID:ENSG00000110768
Aliases:GTF2H1, BTF2, P62, TFB1, TFIIH
Description:general transcription factor IIH, polypeptide 1, 62kDa [Source:HGNC Symbol;Acc:4655]


Retrocopy-Parental alignment summary:






>retro_hsap_1892
ATGGCAACCTCCTCTGAAGAAGTTTTGCTGATTGTAAAGAAAGTGCGTCAAAAGAAGCAGGATGGAGCTCTATACCTCAT
GGCAGAAAGAATTGCTTGGGCACCTGAAGGCAAAAATAGATTTACAGTCAGCCGTATGTATGTAGATGTTAAATGTCAGA
AAATTAGTCCAGAAGGCAAAGCTACAATTCAGCATCAGCTGGACCTACATGAAGGAGATACAATTAACTTCCGTTTTCCC
AGTGAAAACACAGCAGTGAAAGAGCAAGATGCAGTAAAGGACCTTCAGCAGCTGCTTCCCAAATTCAAGAGGAAAGCAAA
TAAAGAACTGGAAGAGAAGAACAGAATGCTGCAAGAAGATCCTGTTTTGTTTCAGCTTTATAAAGATCTTGTTGTGAGCC
AAGTGATGAGTGCTGAGGAATTCTGGGCCAATCATTTAAATGGGAATGCAACAGAAAATTCTTCCACATCCAATCATAAG
CAGGATGTTGGCATTTCTGCTGCATATCTGGCTGATGTCTGGCCCGAAACCGATGGCTGTAACGGTCTGAAATATAATTT
AACTTCTGATATCATTGAGTTCATATTTAGGACCTATCCAGCAGTGAAAATGAAATATGCAGAAAGTGTTCCCCACAACA
TGACAGAGAAGGGATTCTGGACACGTTTTTTCCAGTCCCATTATTTTCACAGGGATTGGCTGAATACAGGGTCAAAGGAT
CTCTCTGCAGAATGTGCCAAAATAGATGAAAAAGGCCTTAAAACAATGGTTTCATTAGGAGTGAAAAACCCACTACTAGA
ATTAACAGCTTTGGGAAATAAGCCATTAGATGAGGGCTATGGCATTTCCTCTGTGCCATCTGCTTCCAATTCTAAATCCA
TAGAAGAGAATAGTAATGCTGCCATCAAGAGATTTAACCATCACAGTGCCATGGTCCTGGCAGCTGGACTCAGGAAACAA
GAAGCAGAAAATGAGCAAAATAGCCCAGCAGCATGGATGGAAATTCCAGAGATGCAGACTGCTTTCAGCCAGTAGTCAAA
AGGGCGAAATCGCAAGAGTCCAGTGAATATGAAGACTTGGGGAAAGATAATTCTATAAAAATGATTGCACTAAACCTCAA
GAAGTCAGGTAGGTATTATCATGGTCTAACTCCAGTCTAGTCACTACAGTATGCAACAATAAGGACATTATTCTTTTCAA
AGTATTGGGCAAGAAATGGAAGCTTATATACCCAAGTTAATTGAGGTTCTCTTGAGTAGTGCTGCCAGTAGTACCATCAT
AGCACTGTCACCTGCAGGGGACCTTATGCAGGGAGGAACACAGCAAACCATAAACCAGATGGTGCCAAGTGATATTCAGT
CTGAATTGAAACACTTGTATGTAGCTGTTGGAGAACTTCTATGGCATTTCTGGTCCTACTTTCCTGTTAATACACCATTC
CTAGAAGAAAGGGTAGTGAAAATGAAAAGTAATTTGGAACGATTCCAAGTTAAGAAGATCTGCCCATTCCAAGAAAAGAT
TCGGAGGCAGTATTTAAGCACACATTTGGTAAGTCACATAGAGATACTCCAGGCAGCCTACAAGCTCCACACATGGCAAT
TATGGTGTCTGATGAAAGAA

ORF - retro_hsap_1892 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.45 %
Parental protein coverage: 99.82 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLH
MATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGK.RFT.S.MY.D.KCQKISPEGKA.IQ.QL.LH
RetrocopyMATSSEEVLLIVKKVRQKKQDGALYLMAERIAWAPEGKNRFTVSRMYVDVKCQKISPEGKATIQHQLDLH
ParentalAGDTTNFHFSNESTAVKERDAVKDLLQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVISAE
.GDT.NF.F..E.TAVKE.DAVKD.LQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQV.SAE
RetrocopyEGDTINFRFPSENTAVKEQDAVKD-LQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVMSAE
ParentalEFWANRLNVNATDSSSTSNHKQDVGISAAFLADVRPQTDGCNGLRYNLTSDIIESIFRTYPAVKMKYAEN
EFWAN.LN.NAT..SSTSNHKQDVGISAA.LADV.P.TDGCNGL.YNLTSDIIE.IFRTYPAVKMKYAE.
RetrocopyEFWANHLNGNATENSSTSNHKQDVGISAAYLADVWPETDGCNGLKYNLTSDIIEFIFRTYPAVKMKYAES
ParentalVPHNMTEKEFWTRFFQSHYFHRDRLNTGSKDLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEG
VPHNMTEK.FWTRFFQSHYFHRD.LNTGSKDL.AECAKIDEKGLKTMVSLGVKNPLL.LTAL..KPLDEG
RetrocopyVPHNMTEKGFWTRFFQSHYFHRDWLNTGSKDLSAECAKIDEKGLKTMVSLGVKNPLLELTALGNKPLDEG
ParentalYGISSVPSASNSKSIKENSNAAIIKRFNHHSAMVLAAGLRKQEAQNEQTSEPS-NMDGNSGDADCFQPAV
YGISSVPSASNSKSI.ENSNAA.IKRFNHHSAMVLAAGLRKQEA.NEQ.S.P...MDGNS.DADCFQP.V
RetrocopyYGISSVPSASNSKSIEENSNAA-IKRFNHHSAMVLAAGLRKQEAENEQNS-PA<SMDGNSRDADCFQPVV
ParentalKRAKLQESIEYEDLGKNNSVKTIALNLKKSDRYYHGPTPIQSLQYAT-SQDIINSFQSIRQEMEAYTP-K
KRAK.QES.EYEDLGK.NS.K.IALNLKKS.RYYHG.TP..SLQYAT...DII..F...........P.K
RetrocopyKRAKSQESSEYEDLGKDNSIKMIALNLKKSGRYYHGLTPV*SLQYAT<NKDII-LFKVLGKKWKLIYP<K
ParentalLTQVLSSSAASSTITALSPGGALMQGGTQQAINQMVPNDIQSELKHLYVAVGELLRHFWSCFPVNTPFLE
L..VL.SSAASSTI.ALSP.G.LMQGGTQQ.INQMVP.DIQSELKHLYVAVGELL.HFWS.FPVNTPFLE
RetrocopyLIEVLLSSAASSTIIALSPAGDLMQGGTQQTINQMVPSDIQSELKHLYVAVGELLWHFWSYFPVNTPFLE
ParentalEKVVKMKSNLERFQVTKLCPFQEKIRRQYLSTNLVSHIEEMLQTAYNKLHTWQSRRLMKK
E.VVKMKSNLERFQV.K.CPFQEKIRRQYLST.LVSHI.E.LQ.AY.KLHTWQ...LMK.
RetrocopyERVVKMKSNLERFQVKKICPFQEKIRRQYLSTHLVSHI-EILQAAY-KLHTWQLWCLMKE

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 22 .64 RPM
bodymap2_adrenal 0 .00 RPM 32 .46 RPM
bodymap2_brain 0 .00 RPM 36 .29 RPM
bodymap2_breast 0 .00 RPM 35 .53 RPM
bodymap2_colon 0 .00 RPM 27 .26 RPM
bodymap2_heart 0 .00 RPM 28 .41 RPM
bodymap2_kidney 0 .00 RPM 38 .63 RPM
bodymap2_liver 0 .00 RPM 16 .84 RPM
bodymap2_lung 0 .00 RPM 22 .35 RPM
bodymap2_lymph_node 0 .00 RPM 32 .93 RPM
bodymap2_ovary 0 .00 RPM 44 .30 RPM
bodymap2_prostate 0 .00 RPM 49 .36 RPM
bodymap2_skeletal_muscle 0 .00 RPM 15 .86 RPM
bodymap2_testis 0 .04 RPM 67 .08 RPM
bodymap2_thyroid 0 .00 RPM 42 .54 RPM
bodymap2_white_blood_cells 0 .00 RPM 44 .02 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1892 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1892 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1892 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1892 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1892 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000110768 1 retrocopy
retro_hsap_1892 ,
Gorilla gorilla ENSGGOG000000084051 retrocopy
retro_ggor_1385,
Monodelphis domestica ENSMODG000000065401 retrocopy
retro_mdom_1210,
Nomascus leucogenys ENSNLEG000000177601 retrocopy
retro_nleu_1473,
Otolemur garnettii ENSOGAG000000007101 retrocopy
retro_ogar_338,
Pan troglodytes ENSPTRG000000034201 retrocopy
retro_ptro_1269,

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 = 0.06 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 .00 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 .00 RPM
FIN_HG00349 0 .03 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 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .00 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 .03 RPM
YRI_NA18907 0 .00 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 .00 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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