RetrogeneDB ID:

retro_hsap_3230

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:114847773..114849391(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000250444
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CCT5
Ensembl ID:ENSG00000150753
Aliases:CCT5, CCT-epsilon, CCTE, HEL-S-69, TCP-1-epsilon
Description:chaperonin containing TCP1, subunit 5 (epsilon) [Source:HGNC Symbol;Acc:1618]


Retrocopy-Parental alignment summary:






>retro_hsap_3230
ATGGCATCCATGGGAACCCTCGCCTTTGATGAATATGGGCACCCTTTCCTCATCATCAAGGATCAGGACCTCAAGTCCTG
TCTTATGGGACTGAGGCCCTTAAGTCTCATATAGTGGCAGAAAAGGCTGTAGCAAATATGATGAGAACATCACTTGGGCC
AAATGGGCTTGATAAGATGATGGTGGATAAGGATGGTGATATGACTGTAACTAACGATGGGTCCCCATCTTAAGCATGAT
GGATGTCGATCATCAGATTGCTAAGCTGATGGCGGAACTGTCCAAGTCTCAGGATGATGAAATTGGACTTGGAACCACAG
GAGTGGTAGTCCTGGCTGCTGCCTTGTTAGAAGAAGCCAAGCAGTTGCTAGACTGAGGCATTCACCCAATCAGAATAGCT
GATGGTTATGAGCAGGCTGCCAGCGTTGCTGTTGAACACCTGGACAAGATCAGTCATAGTGTCCTTGTTGACATAAAGGA
CACTGAACCCCTGATTCCGACTGCAAAAACCATGCTGGGCTGCTCCAAAGTGGTCAAAGTTGGCACCAACAAATGGCTGA
GATTGCTGTGAATGCTGTCCTCACTGTAGCAGATATGGAGCGGAGAGATACTGACTTTGAGCTCGTCAACGTAGAAGGCA
AAGTGGGCGGGAGGCTGGAGGACACAAAACTGATCAAGGGCGTGATTGTGGACAAGGATTTCCAGTCACCTATAGGTGCC
GAAAAAAGTGGAAGATGCTAAGATTGCAATTCTCACATGTCCATTTGAACCACCCAAGCCAAAAACAAAGCATAAGCTGG
ATGTGACCTCCATAGATCATAAAGCTCTTCACAAATATGAAAAGGAGAAATTTGAAGAGATGATTCAACAAATTAAAGAG
ACTGGTGCTAACCTAGCAATTTGTCAGTGGGGCTTTGATGATTAAGCAAATCACTTATTTCTTCAGAACAACTTGCCTGT
GGTTCGCTGGGTAGGGGGACTTGAAATTGAACTGATTGCCATCTCAACAAGAGGGCGGATTGTCCCAGGTTCTCAGAGCT
CACGGCCAAGATGCTGGGCTTTACCGGTCTTGTACAGGAGATCTCATTTGGGACAACTAAGGATAAAATGCTGGTCATCG
AGCAGTGTAAGAACTCCAGAGCTGTAACCATTTTTATCAGAGGAGGAAATAAGATGATCATTGAGGAGGTGAAACGATCC
CTTCACGATGCTTTGTGTGTCATCAGCAACCTCATCCGCGATAATCGTGTGGCATACAGAGGAGGGTTTGCTGAGATATC
CTGTGCTCTGGCAGTTAGCCAAGAGGTGGATAAGTGCCCCACCTTAGACCAGTACACCATAAGAGCGTTTGCCGACGCTC
TGGAGTCGCCCCATGGCCCTTTCTGAAAACAGTGGCATGAATCCCATCCAGACTACGACAAAAGTCCGAGCCAGACAAGT
GAAGGAGATGAACCCTGCTCTCGGTACTGACTGTTTGCACAAGGGGACAAATGATATGAAGCGACAACATGTCATAGAAA
TCTTGATTGGCAAAAAGCAACAGACATCTTTCGCAACACAAATGGTTAGAATGATTTTGAAGATTGACGACATTCATAAG
CCTGGAGAATCTGAAGAA

ORF - retro_hsap_3230 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.8 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalMASMGTLAFDEYGRPFLIIKDQDRKSRLMGL-EALKSHIMAAKAVANTMRTSLGPNGLDKMMVDKDGDVT
MASMGTLAFDEYG.PFLIIKDQD.KS.LMGL.EALKSHI.A.KAVAN.MRTSLGPNGLDKMMVDKDGD.T
RetrocopyMASMGTLAFDEYGHPFLIIKDQDLKSCLMGL<EALKSHIVAEKAVANMMRTSLGPNGLDKMMVDKDGDMT
ParentalVTNDGAT-ILSMMDVDHQIAKLMVELSKSQDDEIGDGTTGVVVLAGALLEEAEQLLDRGIHPIRIADGYE
VTNDG...ILSMMDVDHQIAKLM.ELSKSQDDEIG.GTTGVVVLA.ALLEEA.QLLD.GIHPIRIADGYE
RetrocopyVTNDGSP<ILSMMDVDHQIAKLMAELSKSQDDEIGLGTTGVVVLAAALLEEAKQLLD*GIHPIRIADGYE
ParentalQAARVAIEHLDKISDSVLVDIKDTEPLIQTAKTTLG-SKVVN-SCHRQMAEIAVNAVLTVADMERRDVDF
QAA.VA.EHLDKIS.SVLVDIKDTEPLI.TAKT.LG.SKVV..S.H.QMAEIAVNAVLTVADMERRD.DF
RetrocopyQAASVAVEHLDKISHSVLVDIKDTEPLIPTAKTMLGCSKVVK<SWHQQMAEIAVNAVLTVADMERRDTDF
ParentalELIKVEGKVGGRLEDTKLIKGVIVDKDF-SHPQMPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSVEDYK
EL..VEGKVGGRLEDTKLIKGVIVDKDF.SH...PKKVEDAKIAILTCPFEPPKPKTKHKLDVTS..D.K
RetrocopyELVNVEGKVGGRLEDTKLIKGVIVDKDF>SHL*VPKKVEDAKIAILTCPFEPPKPKTKHKLDVTSI-DHK
ParentalALQKYEKEKFEEMIQQIKETGANLAICQWGFDDEANHLLLQNNLPAVRWVGGPEIELIAIATGGRIVP-R
AL.KYEKEKFEEMIQQIKETGANLAICQWGFDD.ANHL.LQNNLP.VRWVGG.EIELIAI.T.GRIVP.R
RetrocopyALHKYEKEKFEEMIQQIKETGANLAICQWGFDD*ANHLFLQNNLPVVRWVGGLEIELIAISTRGRIVP<R
ParentalFSELTAEKLGFAGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEAKRSLHDALCVIRNLIR
FSELTA..LGF.GLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEE.KRSLHDALCVI.NLIR
RetrocopyFSELTAKMLGFTGLVQEISFGTTKDKMLVIEQCKNSRAVTIFIRGGNKMIIEEVKRSLHDALCVISNLIR
ParentalDNRVVYGGGAAEISCALAVSQEADKCPTLEQYAMRAFADALE-VIP-MALSENSGMNPIQTMTEVRARQV
DNRV.Y.GG.AEISCALAVSQE.DKCPTL.QY..RAFADALE.V.P.MALSENSGMNPIQT.T.VRARQV
RetrocopyDNRVAYRGGFAEISCALAVSQEVDKCPTLDQYTIRAFADALE<VAP<MALSENSGMNPIQTTTKVRARQV
ParentalKEMNPALGIDCLHKGTNDMKQQHVIETLIGKKQQISLATQMVRMILKIDDIRKPGESEE
KEMNPALG.DCLHKGTNDMK.QHVIE.LIGKKQQ.S.ATQMVRMILKIDDI.KPGESEE
RetrocopyKEMNPALGTDCLHKGTNDMKRQHVIEILIGKKQQTSFATQMVRMILKIDDIHKPGESEE

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 83 .47 RPM
bodymap2_adrenal 0 .02 RPM 111 .54 RPM
bodymap2_brain 0 .05 RPM 60 .29 RPM
bodymap2_breast 0 .02 RPM 82 .61 RPM
bodymap2_colon 0 .00 RPM 104 .59 RPM
bodymap2_heart 0 .06 RPM 49 .25 RPM
bodymap2_kidney 0 .02 RPM 122 .02 RPM
bodymap2_liver 0 .00 RPM 59 .12 RPM
bodymap2_lung 0 .00 RPM 78 .66 RPM
bodymap2_lymph_node 0 .00 RPM 95 .90 RPM
bodymap2_ovary 0 .06 RPM 106 .27 RPM
bodymap2_prostate 0 .02 RPM 77 .39 RPM
bodymap2_skeletal_muscle 0 .00 RPM 107 .82 RPM
bodymap2_testis 0 .00 RPM 196 .13 RPM
bodymap2_thyroid 0 .02 RPM 120 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 121 .61 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3230 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3230 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3230 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3230 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3230 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2182
Gorilla gorilla retro_ggor_2197
Pongo abelii retro_pabe_2678
Macaca mulatta retro_mmul_2033
Parental genes homology:
Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000089771 retrocopy
retro_cjac_516,
Homo sapiens ENSG00000150753 2 retrocopies
retro_hsap_1219, retro_hsap_3230 ,
Gorilla gorilla ENSGGOG000000240641 retrocopy
retro_ggor_2197,
Macaca mulatta ENSMMUG000000201122 retrocopies
retro_mmul_1294, retro_mmul_2033,
Monodelphis domestica ENSMODG000000023561 retrocopy
retro_mdom_861,
Pan troglodytes ENSPTRG000000167252 retrocopies
retro_ptro_2182, retro_ptro_834,
Tupaia belangeri ENSTBEG000000012012 retrocopies
retro_tbel_1618, retro_tbel_4389,

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 = 0.1 RPM Legend:


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