RetrogeneDB ID:

retro_hsap_3784

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:7:128696024..128696821(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230359
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TPI1
Ensembl ID:ENSG00000111669
Aliases:TPI1, HEL-S-49, TIM, TPI, TPID
Description:triosephosphate isomerase 1 [Source:HGNC Symbol;Acc:12009]


Retrocopy-Parental alignment summary:






>retro_hsap_3784
CCCGTTTTAGGCGCTGACACTGACCTACAGCGCCTCAGCTCCAGCGCCATGGCGCCCTCCAGGAAGTTCTTCGTGGGGAG
GAACTGGAAGATGAACGGGCGGAAGAAATGTCTGGGGGAGCTCATCGGCACTCAGAACGCGGCCACTGTGCCTGCCGACA
CCAAGGTGATTTGTGCTCTCGCCACTGCGTATAACGAGTTGGCCCGGCAGAAGCTAGCTCCCAAGATTGCTGTGGCTCCG
CAGAACTGCTACAAAGTGACTAATGGGGCCTTTACTGGGGAGATCAGCCCTGGCATGGTCAAAGACTTAGGAGTCACGTG
GGTGGTGTGGTCCTGGGGCACTCAGAAGGCGTGTCTTTGGGGAGTCAGATGAGCTGATTGGGCAGAAAAGTGGCCCATGC
TCTGGCAGAGAGACTCGGAGTAATCGCCTGCATTGGGGAGAAGCTAGATGAAAGGGAAGCTGGCATCACTGAGAAGGTTG
TTTTTGAGCAGACAAAGGTCATCGCAGATAATGTGAAGGACTGGAGCAAGGTCATCTTGGCCTATGATCCCGTGTGGGCC
ACTGGTACTGGCAAGACTGCAACACCCCAACAGGCCCAGGAGGTACACAAGAAGCTCCGAGGATGGCTTAAGTCCAACAT
CTCTGATGCAGTGGCTCAGAGCACTGGTATCATTTATGGAGGCTCTGTGACCAAGGCAACCTGCAAGGAGCTGGCCAGCC
AGCCTGACGTGGCTGCCTTCCTCATGAGTGGTGTTTCCCTCAAGCCCGAATTCGTAGACATCATCAATGCCAAACAA

ORF - retro_hsap_3784 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.64 %
Parental protein coverage: 92.66 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPRLRADTDLQRLGSSAMAPSRKFFVGGNWKMNGRKQSLGELIGTLNAAKVPADTEVVCAPPTAYIDFARQ
P.L.ADTDLQRL.SSAMAPSRKFFVG.NWKMNGRK..LGELIGT.NAA.VPADT.V.CA..TAY...ARQ
RetrocopyPVLGADTDLQRLSSSAMAPSRKFFVGRNWKMNGRKKCLGELIGTQNAATVPADTKVICALATAYNELARQ
ParentalKLDPKIAVAAQNCYKVTNGAFTGEISPGMIKDCGATWVVLGHSE-RRHVFGESDELIGQK-VAHALAEGL
KL.PKIAVA.QNCYKVTNGAFTGEISPGM.KD.G.TWVV......RR.VFGESDELIGQK.VAHALAE.L
RetrocopyKLAPKIAVAPQNCYKVTNGAFTGEISPGMVKDLGVTWVVWSWGT>RRRVFGESDELIGQK>VAHALAERL
ParentalGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVVLAYEPVWAIGTGKTATPQQAQEVHEKLRGW
GVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKV.LAY.PVWA.GTGKTATPQQAQEVH.KLRGW
RetrocopyGVIACIGEKLDEREAGITEKVVFEQTKVIADNVKDWSKVILAYDPVWATGTGKTATPQQAQEVHKKLRGW
ParentalLKSNVSDAVAQSTRIIYGGSVTGATCKELASQPDVDGFLVGGASLKPEFVDIINAKQ
LKSN.SDAVAQST.IIYGGSVT.ATCKELASQPDV..FL..G.SLKPEFVDIINAKQ
RetrocopyLKSNISDAVAQSTGIIYGGSVTKATCKELASQPDVAAFLMSGVSLKPEFVDIINAKQ

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 .22 RPM 114 .99 RPM
bodymap2_adrenal 0 .27 RPM 166 .21 RPM
bodymap2_brain 0 .38 RPM 183 .44 RPM
bodymap2_breast 0 .35 RPM 100 .37 RPM
bodymap2_colon 0 .00 RPM 201 .02 RPM
bodymap2_heart 0 .13 RPM 249 .39 RPM
bodymap2_kidney 0 .14 RPM 311 .03 RPM
bodymap2_liver 0 .13 RPM 166 .65 RPM
bodymap2_lung 0 .00 RPM 186 .37 RPM
bodymap2_lymph_node 0 .00 RPM 226 .08 RPM
bodymap2_ovary 0 .21 RPM 124 .80 RPM
bodymap2_prostate 0 .07 RPM 229 .77 RPM
bodymap2_skeletal_muscle 0 .02 RPM 191 .45 RPM
bodymap2_testis 0 .58 RPM 137 .27 RPM
bodymap2_thyroid 0 .30 RPM 125 .62 RPM
bodymap2_white_blood_cells 0 .08 RPM 209 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_3784 in 52 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001VKU POLR2A 7:128694725..128695504
ENCFF002CFW POLR2A 7:128694508..128695515
ENCFF002CFX POLR2A 7:128695025..128695493
ENCFF002CFX POLR2A 7:128694533..128695082
ENCFF002CGN POLR2A 7:128695159..128695486
ENCFF002CGN POLR2A 7:128694739..128695045
ENCFF002CHO POLR2A 7:128694317..128695563
ENCFF002CIH POLR2A 7:128694698..128695082
ENCFF002CIO POLR2A 7:128694633..128695109
ENCFF002CIO POLR2A 7:128695090..128695508
ENCFF002CJE POLR2A 7:128694465..128695556
ENCFF002CJZ POLR2A 7:128694352..128695541
ENCFF002CKX POLR2A 7:128694707..128695490
ENCFF002CLM POLR2A 7:128694655..128695195
ENCFF002CLM POLR2A 7:128695289..128695436
ENCFF002CMI POLR2A 7:128694372..128695582
ENCFF002COJ POLR2A 7:128694712..128695148
ENCFF002COJ POLR2A 7:128694912..128695348
ENCFF002CPG POLR2A 7:128695177..128695498
ENCFF002CPH POLR2A 7:128695146..128695536
ENCFF002CQA POLR2A 7:128694885..128695542
ENCFF002CQC POLR2A 7:128695131..128695491
ENCFF002CQC POLR2A 7:128694712..128695053
ENCFF002CQE POLR2A 7:128695022..128695490
ENCFF002CQE POLR2A 7:128694533..128695067
ENCFF002CQG POLR2A 7:128694703..128695048
ENCFF002CQG POLR2A 7:128695153..128695493
ENCFF002CQI POLR2A 7:128695046..128695480
ENCFF002CQI POLR2A 7:128694704..128695048
ENCFF002CQK POLR2A 7:128694466..128695532
ENCFF002CQM POLR2A 7:128695105..128695494
ENCFF002CQM POLR2A 7:128694708..128695060
ENCFF002CQO POLR2A 7:128694616..128695103
ENCFF002CQO POLR2A 7:128695023..128695520
ENCFF002CRK POLR2A 7:128694703..128695227
ENCFF002CRK POLR2A 7:128694954..128695478
ENCFF002CRO POLR2A 7:128695332..128695437
ENCFF002CSY POLR2A 7:128694456..128695584
ENCFF002CUP POLR2A 7:128695178..128695494
ENCFF002CUP POLR2A 7:128694765..128695081
ENCFF002CUQ POLR2A 7:128694708..128695071
ENCFF002CVJ POLR2A 7:128694684..128695092
ENCFF002CXM POLR2A 7:128695143..128695513
ENCFF002CXN POLR2A 7:128695210..128695525
ENCFF002CXO POLR2A 7:128695174..128695486
ENCFF002CXP POLR2A 7:128694676..128695533
ENCFF002CXQ POLR2A 7:128694432..128695082
ENCFF002CXQ POLR2A 7:128694633..128695283
ENCFF002CXR POLR2A 7:128695047..128695498
ENCFF002CXR POLR2A 7:128694652..128695077
ENCFF002CZC POLR2A 7:128694661..128695537
ENCFF002CZD POLR2A 7:128694695..128695120
ENCFF002CZD POLR2A 7:128695124..128695513
ENCFF002CZQ POLR2A 7:128695161..128695477
ENCFF002CZQ POLR2A 7:128694762..128695042
ENCFF002CZW POLR2A 7:128694588..128695700
ENCFF002CZY POLR2A 7:128694490..128695532
ENCFF002DAE POLR2A 7:128695295..128695442
ENCFF002DAE POLR2A 7:128694720..128695030
ENCFF002DAH POLR2A 7:128695252..128695401
ENCFF002DAK POLR2A 7:128694664..128695164
ENCFF002DAS POLR2A 7:128694683..128695159
ENCFF002DAV POLR2A 7:128695002..128695546
ENCFF002DAY POLR2A 7:128694512..128695148
ENCFF002DAY POLR2A 7:128694713..128695349
ENCFF002DAY POLR2A 7:128694914..128695550
ENCFF002DBB POLR2A 7:128695225..128695425
ENCFF002DBB POLR2A 7:128694831..128695031
ENCFF002DBE POLR2A 7:128694986..128695495
ENCFF002DBE POLR2A 7:128694699..128695079
ENCFF002DBO POLR2A 7:128695155..128695482
ENCFF002DBO POLR2A 7:128694679..128695041
ENCFF002DBP POLR2A 7:128695200..128695458
ENCFF002DBQ POLR2A 7:128695206..128695460
ENCFF002DBQ POLR2A 7:128694721..128695091
ENCFF002DBT POLR2A 7:128695261..128695394

EST - click to see more details

No EST(s) were mapped for retro_hsap_3784 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3784 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3784 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3784 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 13 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000073482 retrocopies
retro_cjac_2190, retro_cjac_2370,
Homo sapiens ENSG00000111669 3 retrocopies
retro_hsap_3038, retro_hsap_3510, retro_hsap_3784 ,
Gorilla gorilla ENSGGOG000000026231 retrocopy
retro_ggor_151,
Macropus eugenii ENSMEUG000000069775 retrocopies
retro_meug_1348, retro_meug_1520, retro_meug_1934, retro_meug_267, retro_meug_512,
Myotis lucifugus ENSMLUG000000249894 retrocopies
retro_mluc_1090, retro_mluc_1311, retro_mluc_1777, retro_mluc_1807,
Macaca mulatta ENSMMUG000000051942 retrocopies
retro_mmul_1864, retro_mmul_250,
Mustela putorius furoENSMPUG000000167741 retrocopy
retro_mputfur_136,
Mus musculus ENSMUSG000000234564 retrocopies
retro_mmus_1180, retro_mmus_3260, retro_mmus_532, retro_mmus_558,
Nomascus leucogenys ENSNLEG000000048212 retrocopies
retro_nleu_1120, retro_nleu_847,
Otolemur garnettii ENSOGAG000000312541 retrocopy
retro_ogar_109,
Pan troglodytes ENSPTRG000000045954 retrocopies
retro_ptro_160, retro_ptro_1999, retro_ptro_2382, retro_ptro_2565,
Rattus norvegicus ENSRNOG000000152901 retrocopy
retro_rnor_1304,
Rattus norvegicus ENSRNOG000000506692 retrocopies
retro_rnor_2615, retro_rnor_787,

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 = 1.25 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .51 RPM
CEU_NA11843 0 .11 RPM
CEU_NA11930 0 .49 RPM
CEU_NA12004 0 .46 RPM
CEU_NA12400 0 .32 RPM
CEU_NA12751 0 .78 RPM
CEU_NA12760 0 .63 RPM
CEU_NA12827 0 .85 RPM
CEU_NA12872 0 .65 RPM
CEU_NA12873 0 .32 RPM
FIN_HG00183 0 .38 RPM
FIN_HG00277 0 .26 RPM
FIN_HG00315 0 .47 RPM
FIN_HG00321 0 .57 RPM
FIN_HG00328 0 .52 RPM
FIN_HG00338 0 .55 RPM
FIN_HG00349 0 .51 RPM
FIN_HG00375 0 .88 RPM
FIN_HG00377 0 .55 RPM
FIN_HG00378 0 .68 RPM
GBR_HG00099 0 .52 RPM
GBR_HG00111 0 .45 RPM
GBR_HG00114 0 .66 RPM
GBR_HG00119 0 .62 RPM
GBR_HG00131 0 .43 RPM
GBR_HG00133 0 .43 RPM
GBR_HG00134 0 .68 RPM
GBR_HG00137 0 .74 RPM
GBR_HG00142 0 .58 RPM
GBR_HG00143 0 .96 RPM
TSI_NA20512 0 .57 RPM
TSI_NA20513 1 .06 RPM
TSI_NA20518 0 .36 RPM
TSI_NA20532 0 .51 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .49 RPM
TSI_NA20765 0 .91 RPM
TSI_NA20771 0 .88 RPM
TSI_NA20786 0 .89 RPM
TSI_NA20798 0 .65 RPM
YRI_NA18870 0 .58 RPM
YRI_NA18907 0 .94 RPM
YRI_NA18916 0 .67 RPM
YRI_NA19093 0 .52 RPM
YRI_NA19099 0 .69 RPM
YRI_NA19114 0 .55 RPM
YRI_NA19118 0 .60 RPM
YRI_NA19213 0 .38 RPM
YRI_NA19214 1 .25 RPM
YRI_NA19223 1 .03 RPM

Indel association:

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



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