RetrogeneDB ID:

retro_hsap_3548

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:5066068..5067216(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000220685
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TFB2M
Ensembl ID:ENSG00000162851
Aliases:TFB2M, Hkp1, mtTFB2
Description:transcription factor B2, mitochondrial [Source:HGNC Symbol;Acc:18559]


Retrocopy-Parental alignment summary:






>retro_hsap_3548
ATGTGGATCCCAGTGGCCGGATTTCCTCCTCGGCTGAGGCTCTCCGCCTTGGGGGGCGCTGGTCGCTTTTGCATTTTAGG
GTCTGGAGCGGCGATGCGAAAGCACTTGCCGGCGAGGAACCGCCGTGGCCTGTCTGACTCCTCTCCGCAGCTGTGGCCGG
ATCCGGATTTCAGGAACTCACCAAGGAGGGTGTTAAACTCCATCTTAGACTTTAAGCGTTACGTAACCAATCGGAGATTG
GCTGAGACCCTGGCGCAAATCGTATGGAGAAAACAAAATAGACCTCCACACCTATTGCTGCAGTGCAGTCCAGGTCCTGG
AATCCTGACTCAGGCATTACTTGAAATTGGTGCCAAAGTGGTTGCCCTTGAAAGTGACAAAACTTTTATTCCACATTTGG
AGTCCTTAGGAAAAAATCTGGATGGAAAACTACAAGTGATTCACTGTGACTTCTTTAAAATAGATCCTAGAAGTGGTGGA
GTAATAAAACCACCCGCTATGGCTTCTCAAGGGCTCTTTCAGAATTTGGGAATAGAAGCAGTTCCTTGGACAGCAGGCAG
CCCTTTAAAAGTAACTAGAATGTTCTCAAGTAGAGGTGAAAAAAGGGCCACTTTGGAAACCTGCATATGACGTATTCCTG
TACTTCTAGATATAAATTTGGACGAATAGAACTAAATATGTTTATTGGTAAAAAAGAATTCCAGAAACTAACGGCAGATC
CCCGAAATCCAGACTTGTATCATGTATGAAGTGTTATCTGGCAAGTAGCTTGTGAGATTAAGGTTCTGCACATGGAGGCT
TGGTCGTCATTTGATGTATACACCCAAAATGGGCGGCTGGAAAACCCAAAGTGTAGGGAATTATTGGAGCTATTACAACA
AAATCTGTATCTTACTCGAATGACTCCTCATGGAAATTTATTTACCGAGAACTTAACACCTATTAACTGTAATATATTTT
TTCACATGTGAAAGCACTGTTTTGGGAGGTGCAGTGCCAATCTAATAGACCACTTAAGTTCACTGACTCCACTTGGTGCA
ATGGATATATTGATGCAAATAGGAAAAAAGGAAGAAGAGAAAATAACTAACATGTACCCTCAAGACTTCAAAAAACTTTT
TGAAACTATAGTGTTCCAAAGATTGTGC

ORF - retro_hsap_3548 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.34 %
Parental protein coverage: 96.72 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMWIPVVGLPRRLRLSALAGAGRFCILGSEAATRKHLPARNHCGLSDSSPQLWPEPDFRNPPRKASKASLD
MWIPV.G.P.RLRLSAL.GAGRFCILGS.AA.RKHLPARN..GLSDSSPQLWP.PDFRN.PR......LD
RetrocopyMWIPVAGFPPRLRLSALGGAGRFCILGSGAAMRKHLPARNRRGLSDSSPQLWPDPDFRNSPRRVLNSILD
ParentalFKRYVTDRRLAETLAQIYLGKPSRPPHLLLECNPGPGILTQALLEAGAKVVALESDKTFIPHLESLGKNL
FKRYVT.RRLAETLAQI...K..RPPHLLL.C.PGPGILTQALLE.GAKVVALESDKTFIPHLESLGKNL
RetrocopyFKRYVTNRRLAETLAQIVWRKQNRPPHLLLQCSPGPGILTQALLEIGAKVVALESDKTFIPHLESLGKNL
ParentalDGKLRVIHCDFFKLDPRSGGVIKPPAMSSRGLFKNLGIEAVPWTADIPLKVVGMFPSRGEKRALWKLA-Y
DGKL.VIHCDFFK.DPRSGGVIKPPAM.S.GLF.NLGIEAVPWTA..PLKV..MF.SRGEKRA.......
RetrocopyDGKLQVIHCDFFKIDPRSGGVIKPPAMASQGLFQNLGIEAVPWTAGSPLKVTRMFSSRGEKRATLETC<H
ParentalDLYSCTSIYKFGRIEVNMFIGEKEFQKLMADPGNPDLYHVLSVIWQLACEIKVLHMEPWSSFDIYTRKGP
..YSCTS.YKFGRIE.NMFIG.KEFQKL.ADP.NPDLYHV.SVIWQ.ACEIKVLHME.WSSFD.YT..G.
RetrocopyMTYSCTSRYKFGRIELNMFIGKKEFQKLTADPRNPDLYHV*SVIWQVACEIKVLHMEAWSSFDVYTQNGR
ParentalLENPKRRELLDQLQQKLYLIQMIPRQNLFTKNLTPMNYNIFFHLLKHCFGRRSATVIDHLRSLTPLDARD
LENPK.RELL..LQQ.LYL..M.P..NLFT.NLTP.N.NIFFH..KHCFGR.SA..IDHL.SLTPL.A.D
RetrocopyLENPKCRELLELLQQNLYLTRMTPHGNLFTENLTPINCNIFFHM*KHCFGRCSANLIDHLSSLTPLGAMD
ParentalILMQIGKQEDEKVVNMHPQDFKTLFETIERSKDC
ILMQIGK.E.EK..NM.PQDFK.LFETI.....C
RetrocopyILMQIGKKEEEKITNMYPQDFKKLFETIVFQRLC

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 .02 RPM 4 .79 RPM
bodymap2_adrenal 0 .18 RPM 10 .09 RPM
bodymap2_brain 0 .21 RPM 6 .66 RPM
bodymap2_breast 0 .16 RPM 12 .98 RPM
bodymap2_colon 0 .27 RPM 8 .55 RPM
bodymap2_heart 0 .26 RPM 12 .70 RPM
bodymap2_kidney 0 .23 RPM 15 .61 RPM
bodymap2_liver 0 .21 RPM 28 .41 RPM
bodymap2_lung 0 .00 RPM 3 .85 RPM
bodymap2_lymph_node 0 .00 RPM 8 .84 RPM
bodymap2_ovary 0 .17 RPM 8 .06 RPM
bodymap2_prostate 0 .07 RPM 11 .85 RPM
bodymap2_skeletal_muscle 0 .25 RPM 11 .28 RPM
bodymap2_testis 0 .08 RPM 13 .39 RPM
bodymap2_thyroid 0 .15 RPM 19 .15 RPM
bodymap2_white_blood_cells 0 .06 RPM 12 .07 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3548 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3548 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3548 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3548 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3548 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2412
Macaca mulatta retro_mmul_1814
Parental genes homology:
Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Cavia porcellus ENSCPOG000000132251 retrocopy
retro_cpor_451,
Homo sapiens ENSG00000162851 1 retrocopy
retro_hsap_3548 ,
Gorilla gorilla ENSGGOG000000010951 retrocopy
retro_ggor_2396,
Myotis lucifugus ENSMLUG000000039231 retrocopy
retro_mluc_1302,
Macaca mulatta ENSMMUG000000229151 retrocopy
retro_mmul_1814,
Nomascus leucogenys ENSNLEG000000041461 retrocopy
retro_nleu_2323,
Oryctolagus cuniculus ENSOCUG000000137272 retrocopies
retro_ocun_1557, retro_ocun_236,
Otolemur garnettii ENSOGAG000000078232 retrocopies
retro_ogar_1444, retro_ogar_2187,
Pongo abelii ENSPPYG000000000461 retrocopy
retro_pabe_3039,
Pan troglodytes ENSPTRG000000021881 retrocopy
retro_ptro_2412,

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 = 0.2 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .20 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .14 RPM
CEU_NA12873 0 .13 RPM
FIN_HG00183 0 .14 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .14 RPM
FIN_HG00338 0 .17 RPM
FIN_HG00349 0 .14 RPM
FIN_HG00375 0 .10 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .13 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .17 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .10 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .10 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .18 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .17 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .16 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .13 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .10 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .14 RPM

Indel association:

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



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