RetrogeneDB ID:

retro_hsap_4123

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:5110913..5112109(+)
Located in intron of:ENSG00000096968
Retrocopy
information
Ensembl ID:ENSG00000236567
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TCF3
Ensembl ID:ENSG00000071564
Aliases:TCF3, E2A, E47, ITF1, TCF-3, VDIR, bHLHb21
Description:transcription factor 3 [Source:HGNC Symbol;Acc:11633]


Retrocopy-Parental alignment summary:






>retro_hsap_4123
ATGAACCAGCCGCAGAGGATGGCATCCGTGGACACGGACAAGGAGCTCAGTAACCTGGACTTCAGCATGATGTTCCCGCT
GCCCGTTGCCAACGGGAAGGGCCGGCCCGCCTCCCTGGCCGGGGCGCAATTCAGAGGTTCAGGTCTTGAGAACTGGCCCA
GCTCAGGCTCCTGGGGCAGCGGCGACCAGAACAGCTCCTCCTTTGACCCCAGCTGGACGTTCAGCGAAGGCGCTCAACTT
GCTGAGTCGCACGGCAGCCACTCTCCATTCACATTCCTGGGACCGGGACTCGGAGGCAAGAGCAGCTAGCGCGGGCCTAT
TCCTCCTTTGGTAGAGACGCAGGCGTGCGCAGCCTGACTCAGGCTGGCTTCCTGCCGGGCAAGCTGGCCCTCAGCAGCCC
CGGACCCCTGTCCCCCTCAGGCATGAAGGGGACCTCCCGGTACTACCCCTCCTACGCCAGCAGCTCTGGCGGACAGAGGC
GGACAGCGGCCTGGACACGCAGCCCACGAAGGTCGGGAAGGTCCCGCCTGGTCTTCCATCCTCGGCGTACCTGCCCAGCT
CAGGTGAGGAGTACGGTAGGGATGCCGCCGCCTATCCATCCGCCAAGACGCCCAGCAGCGCCTGTCCCGCCCCCTTCTAC
ATGGCAGATGGCAGCCTGCACCCCTAAGCCGAGCTCTGGAGTTCCCTGGGCCAGGTGGGCTTTGGCCCCATGCTGGGCGG
GGGCTCATGCCCCTCGTCCCTCCCGCCCAGCAGCGGCCCTGTGGGCAGTGGCGGAGGCAGCAGCACGTTTGGCGGCCTGC
ACCAGCACGAGCGCGTGGGCTACCGGCTGCACGGAGGAGAAGTGAACGGTGGGCTTCCGGCTGCATCCACCTTCTCCTTG
GCCCCCGGAGCCACGTAGGCGGCGTCTCCAGCCACACGCCTGTCGGCGGGGCCGACAACCTCCTGGGCTCCCGAGGGACC
ACAGCCAGCAGCTCTGGGGACGCCCTCGGGAAGGCCTGGCCTCAATCTACTCTCCGGATCACTCAAGCAATAACTTGTGG
TCCAGCCCCTCCACCGCCGTGGGCTCCCCCCAGGGCCTGGGAGGGACGTCGCACTAGCCTGGAGCAGGAGTCCCTGGTGC
CTTATCACCCAGCTACGACGGGGGTCTCCACGGCCTGGAGAGTAAGATAGAAGACCACCTACCTGAACGAGGGCAT

ORF - retro_hsap_4123 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.3 %
Parental protein coverage: 61.75 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMNQPQRMAPVGTDKELSDLLDFSMMFPLPVTNGKGRPASLAGAQFGGSGLEDRPSSGSWGSGDQSSSSFD
MNQPQRMA.V.TDKELS.L.DFSMMFPLPV.NGKGRPASLAGAQF.GSGLE..PSSGSWGSGDQ.SSSFD
RetrocopyMNQPQRMASVDTDKELSNL-DFSMMFPLPVANGKGRPASLAGAQFRGSGLENWPSSGSWGSGDQNSSSFD
ParentalPSRTFSEGTHFTESHSSLSSSTFLGPGLGGKSGERG-AYASFGRDAGVGGLTQAGFLSGELALNSPGPLS
PS.TFSEG....ESH.S.S..TFLGPGLGGKS..RG.AY.SFGRDAGV..LTQAGFL.G.LAL.SPGPLS
RetrocopyPSWTFSEGAQLAESHGSHSPFTFLGPGLGGKSS*RG<AYSSFGRDAGVRSLTQAGFLPGKLALSSPGPLS
ParentalPSGMKGTSQYYPSYSGSSR-RRAADGSLDTQPKKVRKVPPGLPSSVYPPSSGEDYGRDATAYPSAKTPSS
PSGMKGTS.YYPSY..SS..R..AD..LDTQP.KV.KVPPGLPSS.Y.PSSGE.YGRDA.AYPSAKTPSS
RetrocopyPSGMKGTSRYYPSYASSSG<RTEADSGLDTQPTKVGKVPPGLPSSAYLPSSGEEYGRDAAAYPSAKTPSS
ParentalTYPAPFYVADGSLHPSAELWSPPGQAGFGPMLGGGSSPLPLPPGSGPVGSSGSSSTFGGLHQHERMGYQL
..PAPFY.ADGSLHP.AELWS..GQ.GFGPMLGGGS.P..LPP.SGPVGS.G.SSTFGGLHQHER.GY.L
RetrocopyACPAPFYMADGSLHP*AELWSSLGQVGFGPMLGGGSCPSSLPPSSGPVGSGGGSSTFGGLHQHERVGYRL
ParentalHGAEVNGGLPSASSFSSAPGAT-YGGVSSHTPPVSGADSLLGSRGTTAGSSGDALGKA-LASIYSPDHSS
HG.EVNGGLP.AS.FS.APGAT..GGVSSHT.PV.GAD.LLGSRGTTA.SSGDALGKA.LASIYSPDHSS
RetrocopyHGGEVNGGLPAASTFSLAPGAT<VGGVSSHT-PVGGADNLLGSRGTTASSSGDALGKA<LASIYSPDHSS
ParentalNNFSSSPSTPVGSPQGLAGTSQWPRAGAPGALSPSYDGGLHGLQSKIEDHLDEAIH
NN..SSPST.VGSPQGL.GTS..P.AG.PGALSPSYDGGLHGL.SKIEDHL.E..H
RetrocopyNNLWSSPSTAVGSPQGLGGTSH*PGAGVPGALSPSYDGGLHGLESKIEDHLPERGH

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 23 .10 RPM
bodymap2_adrenal 0 .10 RPM 47 .18 RPM
bodymap2_brain 0 .00 RPM 5 .88 RPM
bodymap2_breast 0 .00 RPM 21 .36 RPM
bodymap2_colon 0 .00 RPM 25 .14 RPM
bodymap2_heart 0 .11 RPM 8 .20 RPM
bodymap2_kidney 0 .04 RPM 14 .72 RPM
bodymap2_liver 0 .00 RPM 4 .96 RPM
bodymap2_lung 0 .04 RPM 21 .48 RPM
bodymap2_lymph_node 0 .00 RPM 76 .49 RPM
bodymap2_ovary 0 .04 RPM 51 .95 RPM
bodymap2_prostate 0 .00 RPM 26 .05 RPM
bodymap2_skeletal_muscle 0 .00 RPM 13 .88 RPM
bodymap2_testis 0 .08 RPM 141 .38 RPM
bodymap2_thyroid 0 .00 RPM 24 .95 RPM
bodymap2_white_blood_cells 0 .00 RPM 35 .75 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4123 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4123 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4123 retrocopy 5' end.

Lab - click to see more details

Experiment type: PCR amplification
Forward primer: CTCTCCGGATCACTCAAGCA (20 nt long)
Reverse primer: GACTCCTGCTCCAGGCTAGT (20 nt long)
Anneling temperature: 60 °C
(Expected) product size: 103
Electrophoresis gel image:
Additional comment: Black arrows indicate PCR products of retrogenes undergoing deletions in various human populations (A-J). Lane 1 –GeneRuler Low Range DNA Ladder (Thermo Scientific); 2 –Heart; 3 –Brain; 4 –Placenta; 5 –Lung; 6 –Liver; 7 –Skeletal Muscle; 8 –Kidney; 9 –Pancreas; 10 –Spleen; 11 –Thymus; 12 –Prostate; 13 –Testis; 14 –Ovary, 15 –Small intestine 16 –Colon; 17 –Leukocyte; NTC—No template control (water instead of cDNA).

Retrocopy orthology:
Retrocopy retro_hsap_4123 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2770
Macaca mulatta retro_mmul_1194
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000071564 1 retrocopy
retro_hsap_4123 ,
Gorilla gorilla ENSGGOG000000036671 retrocopy
retro_ggor_2770,
Macaca mulatta ENSMMUG000000090171 retrocopy
retro_mmul_1194,
Nomascus leucogenys ENSNLEG000000017421 retrocopy
retro_nleu_2472,

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 = 0.12 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .12 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .11 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .10 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .07 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .06 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .12 RPM
YRI_NA19223 0 .08 RPM

Indel association:

The presence of retro_hsap_4123 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_4123 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 9:5106619..5115630 99.18 99.43 98.97 100 100 100 100 100 100 100 100 100 100 100

Indel #1, located at the genomic coordinates 9:5106619..5115630.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 99.18 % Yoruba in Ibadan,Nigeria YRI 99.43 % Luhya in Webuye,Kenya LWK 98.97 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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