RetrogeneDB ID:

retro_hsap_3930

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:8:7276366..7278062(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000255128
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPD1
Ensembl ID:ENSG00000144381
Aliases:HSPD1, CPN60, GROEL, HLD4, HSP-60, HSP60, HSP65, HuCHA60, SPG13
Description:heat shock 60kDa protein 1 (chaperonin) [Source:HGNC Symbol;Acc:5261]


Retrocopy-Parental alignment summary:






>retro_hsap_3930
ATGCTTCCATTACCCACAGTCTTTCACCAGATGAGACCAGTGTCCAGGCTACTGGCTCCTCACCTCACTTGAAGTGATGG
TAAAGATGTAAAATTTGGTGATGATGTCCGAGCCTTAATGCTTCAAAGTGTAGACTTTTTGTCGAGGCTGTAGCCATTAC
AATGGGGCCAAAGGGAAGAACAGTAATTATTGAACATAGCTGGGGAAGTCCCAAAGTAACAAAAGATGGTGTGACTGATG
CAAAGTCAATTGACTTAAAGGATAAATATAAAAGCATTGGAGCTAAACTTGTCCAAGATGTTGCCAATAACACAGATGAA
GAGACTGGGGGATGGCACTATCACTGCTGCTGTACTGGTATGCTCTATTTCCAAATAAGGCTTCCAGAAGGTTAGCAAAG
GTGCTAATCCAGTGGAAATCAAGAGAGGTGTGATGTTAGCTGTTGATGCTGTAATTGCTGAACTTAAAAAGCAGTCTAAA
CCTGTGACCAAACCTGAAGAAATTGCACAGGTTGCTACAATTTCTGCAAATGGAGACAAAGAAATTGGTAACATCATCTC
TGATGCAATGAAAAAGTTTGGAAGAAAGGGCATCATCACAGTAAAGGATGGAAAAACACTGACTGATGAATTAGAAATTA
TTGAAGGCATGAAAATTTGATCGAGGATATATTTCTCCATACTTTATTAATACATCAAAAGGTGAGAAATGTGAATTCCA
GGATGCCTATGTTCTGTTGCATGAAAAGAAAATTTCTAGTGTCCAGTCCATTGTAACTGCTCTTGAAATTGCCAATGCTT
ACTGTAAGCCTTTGGTCATAATTGCTGGAGACATTGATGGAGAAGCTCTAACTACACTCATCCTGAATAGGCTAAAGGTT
GGTCTTCAGGTTGTGGCAGTCAAAGCTCCAGGGTTTGGTGACAATAGAAAGAACCAGCTTAAAGATACGGTTATTGCTAC
TGGTGGTACAGTGTTTGGAGAAGAGGGCTGACACTAAATCTTGAAGACGTTCAGCCTCGTGACGTAGGAGAAGTTGGAGA
GGTCACTGTGATCAAAGATTATGCCATGCTCTTAAAAGGAAAAGGTAACAAGTCTCAAATTGAAAAATGTGTTCAAGAAA
TCATTGACCAGTCAGATGTCACAACTAGTGAATACGAAAAGGAAAAAGTGAGTGGAGAAACTTTCAGATGGAGTAGCTGT
GCTGAAGGTTGGTGGGACAAGTGATGTTGAAGTGAATGAAGAGAAAGACAGAGTTATAGGTGCACTTAATGCTACAAGAG
CTGCTGTTGAAGAAGGCATTGTTTAGGGAGGGGGTTGTGCCCTGCTTCGATGCATTCCAGCCTTGGACTCATTCACTCCA
GCTAATGAAGATAAAATAATTGGTATAGAAATTATTAAAAGAACACTCAAAATTCCAGCAATGACAATTGCTAAGAATGC
AGGTGTTGATGGATTTTTGATAGTTGAGAAAATTATGTAAAGTTCCTCAGAAGTTGGTTATGATACTATGTTAGGAGATG
TCGTGAATATGGTGGAAAAAGACATTATTGACCCAACAAAGGTTGTGAGAACTGCTTCATTGGATGCTGCTGGCATGGCC
TCTCTATTAACTACAGCAGCTGTTGTAGTCACAGAAATTCCTAAAGAAGGGAACAGCCCTGGAATGGGTGCAATGTGTGG
AATGGGAGGTGGCCTG

ORF - retro_hsap_3930 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.12 %
Parental protein coverage: 99.13 %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMLRLPTVFRQMRPVSRVLAPHLTRAYAKDVKFGADARALMLQGVDLLA-DAVAVTMGPKGRTVIIEQSWG
ML.LPTVF.QMRPVSR.LAPHLT....KDVKFG.D.RALMLQ.VD.L...AVA.TMGPKGRTVIIE.SWG
RetrocopyMLPLPTVFHQMRPVSRLLAPHLT*SDGKDVKFGDDVRALMLQSVDFLS<EAVAITMGPKGRTVIIEHSWG
ParentalSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAG-DGTTTATVLARSIAKEGFEKISKGANPV
SPKVTKDGVT.AKSIDLKDKYK.IGAKLVQDVANNT.EE.G.DGT.TA.VL..SI.K.GF.K.SKGANPV
RetrocopySPKVTKDGVTDAKSIDLKDKYKSIGAKLVQDVANNTDEETG>DGTITAAVLVCSISK*GFQKVSKGANPV
ParentalEIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLN
EI.RGVMLAVDAVIAELKKQSKPVT.PEEIAQVATISANGDKEIGNIISDAMKK.GRKG.ITVKDGKTL.
RetrocopyEIKRGVMLAVDAVIAELKKQSKPVTKPEEIAQVATISANGDKEIGNIISDAMKKFGRKGIITVKDGKTLT
ParentalDELEIIEGMK-FDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSIQSIVPALEIANAHRKPLVIIAED
DELEIIEGMK.FDRGYISPYFINTSKG.KCEFQDAYVLL.EKKISS.QSIV.ALEIANA..KPLVIIA.D
RetrocopyDELEIIEGMK>FDRGYISPYFINTSKGEKCEFQDAYVLLHEKKISSVQSIVTALEIANAYCKPLVIIAGD
ParentalVDGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEE-GLTLNLEDVQPHDLGKVG
.DGEAL.TL.LNRLKVGLQVVAVKAPGFGDNRKNQLKD..IATGG.VFGEE.GLTLNLEDVQP.D.G.VG
RetrocopyIDGEALTTLILNRLKVGLQVVAVKAPGFGDNRKNQLKDTVIATGGTVFGEE<GLTLNLEDVQPRDVGEVG
ParentalEVIVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYEKEKLN-ERLAKLSDGVAVLKVGGTSDVEVN
EV.V.KD.AMLLKGKG.K.QIEK..QEII.Q.DVTTSEYEKEK...E.L....DGVAVLKVGGTSDVEVN
RetrocopyEVTVIKDYAMLLKGKGNKSQIEKCVQEIIDQSDVTTSEYEKEKVS>EKLS---DGVAVLKVGGTSDVEVN
ParentalEKKDRVTDALNATRAAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIGIEIIKRTLKIPAMTIAKNAGV
E.KDRV..ALNATRAAVEEGIV.GGGCALLRCIPALDS.TPANED..IGIEIIKRTLKIPAMTIAKNAGV
RetrocopyEEKDRVIGALNATRAAVEEGIV*GGGCALLRCIPALDSFTPANEDKIIGIEIIKRTLKIPAMTIAKNAGV
ParentalEGSLIVEKIMQSSSEVGYDAMAGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKD
.G.LIVEKIM.SSSEVGYD.M.GD.VNMVEK.IIDPTKVVRTA.LDAAG.ASLLTTA.VVVTEIPKE...
RetrocopyDGFLIVEKIM*SSSEVGYDTMLGDVVNMVEKDIIDPTKVVRTASLDAAGMASLLTTAAVVVTEIPKEGNS
ParentalPGMGAMGGMGGGM
PGMGAM.GMGGG.
RetrocopyPGMGAMCGMGGGL

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 169 .50 RPM
bodymap2_adrenal 0 .00 RPM 142 .79 RPM
bodymap2_brain 0 .00 RPM 143 .10 RPM
bodymap2_breast 0 .00 RPM 184 .30 RPM
bodymap2_colon 0 .00 RPM 473 .77 RPM
bodymap2_heart 0 .00 RPM 84 .42 RPM
bodymap2_kidney 0 .00 RPM 383 .99 RPM
bodymap2_liver 0 .00 RPM 451 .41 RPM
bodymap2_lung 0 .00 RPM 244 .20 RPM
bodymap2_lymph_node 0 .00 RPM 301 .77 RPM
bodymap2_ovary 0 .00 RPM 367 .40 RPM
bodymap2_prostate 0 .00 RPM 232 .90 RPM
bodymap2_skeletal_muscle 0 .00 RPM 104 .58 RPM
bodymap2_testis 0 .00 RPM 196 .47 RPM
bodymap2_thyroid 0 .00 RPM 841 .36 RPM
bodymap2_white_blood_cells 0 .00 RPM 121 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3930 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3930 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3930 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3930 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3930 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 18 parental genes, and 74 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000137701 retrocopy
retro_amel_771,
Canis familiaris ENSCAFG000000108654 retrocopies
retro_cfam_1185, retro_cfam_1620, retro_cfam_2165, retro_cfam_614,
Callithrix jacchus ENSCJAG000000039906 retrocopies
retro_cjac_1516, retro_cjac_1534, retro_cjac_1975, retro_cjac_3172, retro_cjac_3400, retro_cjac_4096,
Echinops telfairi ENSETEG000000091844 retrocopies
retro_etel_1440, retro_etel_426, retro_etel_885, retro_etel_925,
Homo sapiens ENSG00000144381 7 retrocopies
retro_hsap_1006, retro_hsap_2770, retro_hsap_2987, retro_hsap_3151, retro_hsap_3494, retro_hsap_3930 , retro_hsap_4018,
Gorilla gorilla ENSGGOG000000082676 retrocopies
retro_ggor_1927, retro_ggor_2069, retro_ggor_2361, retro_ggor_2698, retro_ggor_800, retro_ggor_985,
Loxodonta africana ENSLAFG000000000531 retrocopy
retro_lafr_476,
Macropus eugenii ENSMEUG000000119872 retrocopies
retro_meug_1688, retro_meug_224,
Myotis lucifugus ENSMLUG000000008714 retrocopies
retro_mluc_1458, retro_mluc_2280, retro_mluc_2348, retro_mluc_601,
Macaca mulatta ENSMMUG000000104891 retrocopy
retro_mmul_83,
Monodelphis domestica ENSMODG000000122893 retrocopies
retro_mdom_427, retro_mdom_493, retro_mdom_756,
Mustela putorius furoENSMPUG000000078183 retrocopies
retro_mputfur_1118, retro_mputfur_245, retro_mputfur_434,
Mus musculus ENSMUSG000000259805 retrocopies
retro_mmus_1225, retro_mmus_2494, retro_mmus_3206, retro_mmus_439, retro_mmus_706,
Nomascus leucogenys ENSNLEG000000068747 retrocopies
retro_nleu_1349, retro_nleu_2238, retro_nleu_229, retro_nleu_657, retro_nleu_675, retro_nleu_691, retro_nleu_787,
Otolemur garnettii ENSOGAG000000340535 retrocopies
retro_ogar_2335, retro_ogar_2420, retro_ogar_2740, retro_ogar_3221, retro_ogar_3497,
Pongo abelii ENSPPYG000000130465 retrocopies
retro_pabe_2040, retro_pabe_2244, retro_pabe_2476, retro_pabe_2887, retro_pabe_848,
Rattus norvegicus ENSRNOG000000145259 retrocopies
retro_rnor_1000, retro_rnor_1006, retro_rnor_1308, retro_rnor_1578, retro_rnor_1585, retro_rnor_2812, retro_rnor_2835, retro_rnor_596, retro_rnor_905,
Xenopus tropicalis ENSXETG000000075091 retrocopy
retro_xtro_63,

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 = 0.03 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 .00 RPM
CEU_NA12872 0 .00 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 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 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 .03 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 .00 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:

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





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