RetrogeneDB ID:

retro_hsap_2102

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:52797785..52799454(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000204993
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CRTC1
Ensembl ID:ENSG00000105662
Aliases:CRTC1, MECT1, TORC-1, TORC1, WAMTP1
Description:CREB regulated transcription coactivator 1 [Source:HGNC Symbol;Acc:16062]


Retrocopy-Parental alignment summary:






>retro_hsap_2102
TTCAGCGAGAAGGTCACACTGCACAATGAGAAACACGCGGGGGAGACAGCGGCCCTCGAGGAGGCCATGAAAGGTCTAAG
CCTGATGCGGCCCCACGGCTCCAGCTCCAGAAATATCAGTATCCGCAACTGGGCCCAAGCGGGGCCAGTACTATGCCGGG
TCCCTGCTCAACGTGAACCAGATCGGGAGTGGCACCGTGGACCTGCCCTTCCAGACCCCCTTCCAATCCTTGGGCCTGGA
CACCAGCCTGACTACCAGGCACCATGGGCTGGTGAACAGGGTGTACCGGGAATGCGGCCGACTAGGCTCCCCGCACTGCC
TGCACCTGTCAAAGGACAAACACGGACAGCAGGCCAACAGCTGCCCATACGGCACCGTGTACCTCTTGCCACCCACGGAC
ACCAGCTGGAGAAGGACCAATTCTGACTCGCCCTGCGCCAGAGCACAATGACGCCCATGCAGCCAGAATCCTTTACTAGT
GGGTCCCAGGACGTGCACCAGAAAAAAGTCTTACTGTTAACAGTCCCAGGAATGGAAGAGACCATATCAGAGGCAGACAA
AAACCTTTCCAAGCAAGCGTGGGGAAACCAAGAAGACGGGATCCAGGACCAAGTCCTGCGCGGAATCAACGAATCAACAT
CTTCCCGTCCGCCGACCAGGAAAACACTACAGCCCTGATCTCCGCCATTCACAATACTGTGGGCTCCCTGCACCGCCTGA
CCAACATCCACTTCCCTTCCCCGCTCGACTCCGAGGAGCCCACCTTCCCCGCACTCAGTAGCTCCAGCAGCACCGACAAC
GTCTCGGCCAACCTGATGCACCTGGGCATCAGCGGCGCCGGCCAAGGGGATGAGTACACTCGGCTCCCCTCCGCAGCACC
GTCCAGCCGGCGTCAGCCCCCTGTCCCGAGCACAGAGACGAGGCATCAGCAGTCATCGCCCACTCTGTCCCCGCTGTCAT
ACATCACTCAGGCCGTGGCCTTGAATGCCCTGTCTCTGGAGCAGCAGGTACCCTACGCCTTCTTCACCCAGACGGACTCC
CAGCAGCCGCTGCCGCAGCCCCAGCCTCCGCCGCCCCCTTAGCCTGGGTCTCAGCAGCCGCCAACCCCACCGCCCCTACA
GGCGCCCGTCCGCCTGCCCCCCGGCAGCCCCTGTTGCCCAGCACCAACCTGAATCGTGGGCCACAGCCGCCCCCGCTCGC
GGTCACGGTACCGTCCTCTCTCTTCCAGTCCCCACGAAGAATCCCGGCCTGCCGTCGATGGGGATCGACATCGCCTCGGC
GCCGCCTCTGCAGCAGTAGCGGCACTAGCCCCGGCTCCTCGGCCAACCAGTCTCCCACCTCGCCAGTCTCCAATCAAGGC
TTCTCCCCAGGGAGCTCCCCGCAACACACTTCCACTCTGGGCAGCGTGTTTGGGGACGCGTACTATGAGCAGCAGATGGC
GTTCAGGCAGGCCAATGCTCTGTCCCACCAGCTGGAGCAGTTCAACACGATGGAGAACGCCATCAGCTCCCTATACAACA
GGGGCTCCACGCTCAACTACTCGCAGGCGGTCATGATAGCCCTCACCCACAGCCACGGGAGCCTGCTGAACTCGCAGCAG
CTGGGCTACACCAGCCACAGTGGCATCCCCAACATCATCCTCATAGTGACAGGACAGTCTCCCCCGGCC

ORF - retro_hsap_2102 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.28 %
Parental protein coverage: 88.8 %
Number of stop codons detected: 2
Number of frameshifts detected 10


Retrocopy - Parental Gene Alignment:

ParentalFSEKIALHNQKQAEETAAFEEVMKDLSLTR-AARLQLQKSQYLQLGPS-RGQYYGGSLPNVNQIGSGTMD
FSEK..LHN.K.A.ETAA.EE.MK.LSL.R.A.RLQLQK.QY.QLGPS.RGQYY.GSL.NVNQIGSGT.D
RetrocopyFSEKVTLHNEKHAGETAALEEAMKGLSLMR<APRLQLQKYQYPQLGPS<RGQYYAGSLLNVNQIGSGTVD
ParentalLPFQTPFQSSGLDTSRTTRHHGLVDRVYRERGRLGSPHRRPLSVDKHGRQADSCPYGTMYLSPPADTSWR
LPFQTPFQS.GLDTS.TTRHHGLV.RVYRE.GRLGSPH...LS.DKHG.QA.SCPYGT.YL.PP.DTSWR
RetrocopyLPFQTPFQSLGLDTSLTTRHHGLVNRVYRECGRLGSPHCLHLSKDKHGQQANSCPYGTVYLLPPTDTSWR
ParentalRTNSDS-ALHQSTMTPTQPESFSSGSQDVHQKRVLLLTVPGMEETTSEADKNLSKQAW-DTKKTGSRPKS
RTNSDS.AL.QSTMTP.QPESF.SGSQDVHQK.VLLLTVPGMEET.SEADKNLSKQAW..TKKTGSR.KS
RetrocopyRTNSDS<ALRQSTMTPMQPESFTSGSQDVHQKKVLLLTVPGMEETISEADKNLSKQAW>ETKKTGSRTKS
ParentalCEVPGINIFP-SADQENTTALIPATHNTGGSLPDLTNIHFPSPLPTPLDPEEPTFPALSSSSSTGNLAAN
C........P.SADQENTTALI.A.HNT.GSL..LTNIHFPSPL....D.EEPTFPALSSSSST.N..AN
RetrocopyCAESTNQHLP>SADQENTTALISAIHNTVGSLHRLTNIHFPSPL----DSEEPTFPALSSSSSTDNVSAN
ParentalLTHLGIGGAGQ-GMSTPGSSPQHRPAGVSPLSL-STEARRQQASPTLSPLSPITQAVAMDALSLEQQLPY
L.HLGI.GAGQ.GMST.GS.PQHRPAGVSPLS..STE.R.QQ.SPTLSPLS.ITQAVA..ALSLEQQ.PY
RetrocopyLMHLGISGAGQ>GMSTLGSPPQHRPAGVSPLSR<STETRHQQSSPTLSPLSYITQAVALNALSLEQQVPY
ParentalAFFTQAGSQQPPPQPQPPPPPPPASQQPPPPPPPQAPVRLPPGG-PLLPSASLTRGPQPPPLAVTVPSSL
AFFTQ..SQQP.PQPQPPPPP.P.SQQPP.PPP.QAPVRLPPG..PLLPS..L.RGPQPPPLAVTVPSSL
RetrocopyAFFTQTDSQQPLPQPQPPPPP*PGSQQPPTPPPLQAPVRLPPGS<PLLPSTNLNRGPQPPPLAVTVPSSL
ParentalPQS-PPENPGQPSMGIDIASAPALQQYR-TSAGSPANQSPTSPVSNQGFSPGSSPQHTSTLGSVFGDAYY
.QS.P..NPG.PSMGIDIASAP.LQQ.R.TS.GS.ANQSPTSPVSNQGFSPGSSPQHTSTLGSVFGDAYY
RetrocopyFQS<PTKNPGLPSMGIDIASAPPLQQ*R>TSPGSSANQSPTSPVSNQGFSPGSSPQHTSTLGSVFGDAYY
ParentalEQQMAARQANALSHQLEQFNMMENAISSSSLYSPGSTLNYSQAAMMGLTGSHGSLPDSQQLGYASHSGIP
EQQMA.RQANALSHQLEQFN.MENAI..SSLY..GSTLNYSQA.M..LT.SHGSL..SQQLGY.SHSGIP
RetrocopyEQQMAFRQANALSHQLEQFNTMENAI--SSLYNRGSTLNYSQAVMIALTHSHGSLLNSQQLGYTSHSGIP
ParentalNIILTVTGESPPS
NIIL.VTG.SPP.
RetrocopyNIILIVTGQSPPA

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 12 .48 RPM
bodymap2_adrenal 0 .00 RPM 9 .99 RPM
bodymap2_brain 0 .00 RPM 43 .27 RPM
bodymap2_breast 0 .00 RPM 8 .29 RPM
bodymap2_colon 0 .00 RPM 10 .11 RPM
bodymap2_heart 0 .00 RPM 5 .02 RPM
bodymap2_kidney 0 .00 RPM 8 .73 RPM
bodymap2_liver 0 .00 RPM 1 .92 RPM
bodymap2_lung 0 .00 RPM 4 .40 RPM
bodymap2_lymph_node 0 .00 RPM 10 .96 RPM
bodymap2_ovary 0 .00 RPM 25 .45 RPM
bodymap2_prostate 0 .00 RPM 12 .73 RPM
bodymap2_skeletal_muscle 0 .02 RPM 12 .19 RPM
bodymap2_testis 0 .17 RPM 17 .99 RPM
bodymap2_thyroid 0 .00 RPM 11 .69 RPM
bodymap2_white_blood_cells 0 .00 RPM 10 .59 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2102 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2102 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2102 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2102 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2102 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1542
Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000074213 retrocopies
retro_cjac_2682, retro_cjac_595, retro_cjac_666,
Homo sapiens ENSG00000105662 1 retrocopy
retro_hsap_2102 ,
Pan troglodytes ENSPTRG000000107191 retrocopy
retro_ptro_1542,

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 .05 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 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .05 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .05 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 .00 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 .03 RPM
YRI_NA18870 0 .00 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:

The presence of retro_hsap_2102 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_2102 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. 2:52793394..52798900 100 100 98.97 100 100 100 100 100 100 100 100 100 100 100

Indel #1, located at the genomic coordinates 2:52793394..52798900.

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 100 % Yoruba in Ibadan,Nigeria YRI 100 % 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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