RetrogeneDB ID:

retro_hsap_1006

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:12:56904785..56906502(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000257576
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_1006
ATGCTTCGGTTACCCACAGTCTTTCGCCAGATGAGACTGGTGTCCAGGGTGCTGGCTCCTCATCTCACTGGGGCTTATGC
CAAAGATGTAAAATTCGGTGCAGATGCCCGAGCCTTAATGCTTCAAGGTATAGACCTTTTAGCCGATGCTGTAGCCCTTA
CAATGGGGCCAAAGGGAAGAAGAACAGTGATTATCGAGCAGAGCTGGGGAAGTCCCAAAGTAACAAAAGATGGTGTGACT
GTTGCAAAGTCAATTGACTTAAAGGATAAATATAAAAACATTGGAGCTAAACTTGTTCAAGATGTTGCCAATAACACAAA
TGAAGAGACTGGGGATGGCCCTACCACTGCTACTGTACTGGCACGCTCTATAGCCAAGGAAGGCATCGAGAAGATTAGCA
AAGGTGCTAATCCAGTGGAAATCAGGAGAGGTGTGATGTTAGTTGTTGATGCTGTAATTGCTGAACTTAAAAAGCAGTCT
AAACCTGTGACCACCCCTGAAGAAATTGCACAGGTTGCTACAATTTCTGCAAACGGAGACAAAGAAATTGGCAATATCTC
TGATGCAATGAAAAAGGTTGGAAGAAAGGGTGTCATCACAGTAAAGGATGGAAAAACACTGAATGATGAATTAGAAATTA
TTGAAGGCATAAAGTTTGATCGAGGCTATATTTCTCCATACTTTATTAATACATCAAAAGGTCAGAAATGTGAATTCCAG
GATGCCTATGTTCTGTTGAGCGAAAAGAAAATTTCTAGTGTCCAGTCCGTTGTACCTGCTCTTGAAATTGCCAATGCTCA
CCGTAAGCCTTTGGTCATAATCGCTGAAGACGTTGATGGAGAAGCTCTAAGTACACTCGTCTTGAATAGGCTAAAGGTTG
GTCTTCAGGATGTGGCAATCAAGGCTCCAGGGTTTGGTGACAATAGAAAGAACCAGCTTAAAGATATGGCAATTGCTACT
GGTGGTGCAGTGTTTGGAGAAGAGGGGCTGACCCTAAATCTTGAAGATGTTCAGCCTCATGACTTAGGAAACGTTGGAGA
GGTCATTGTGACCAAAGATGATGCCACGCTCTTAAAAGAAAAAGGTGACAAGGCTCAAATTGAAAAACGTATTCAAGAAA
TCATTGAGCAGTTAGATGTCACAACTAGTGAATATGAAAAGGAAAAACTGAATGAACGGCTGGCAAAACTTTCAGATGTA
GTAGCTGTGCTGAAGGTTGGTGGGACAAGTGATGTTGAAGTGAATGAAAAGAAAGACAGAGTTCGGATGCCCTTAATGCT
ACAAGAGCTGCTGTTGAAGAAGGCTTTGTATTGGGAGGGGGTTGTGCCCTGCTTCGATGCATTCTAGCCTTGGACTCATT
GACTCCAGCTAATGAAGATCAAAAAATTGGTACAGAAATTATTAAAGAACACTCAAAATTCCAGCAATGACCATTGCTAA
GAATGCAGGTGTTGAAGGATCTTCGATAGTTGAGAAAATTACGCAAATTTCCTCAGAAGCTGGTTATGATGCTATGGTTG
GAGATTTTGTGAATATGGTGGAAAAATGAATTATTGACCCAACAAAGGTTGTGAGAACTGCTTTATTGGATGCCGCTGGT
GTGACCTCTCTGTTAACTACAGCAGAAGTTGTAGTCACAGAAATTCCTAAAGAAGAGAAGGACCCTGGAATGGGTGCAAT
GGGTAGAATGGGAGGTGGTATGGGAAGTGGCATGTTC

ORF - retro_hsap_1006 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.1 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMLRLPTVFRQMRPVSRVLAPHLTRAYAKDVKFGADARALMLQGVDLLADAVAVTMGPKGR-TVIIEQSWG
MLRLPTVFRQMR.VSRVLAPHLT.AYAKDVKFGADARALMLQG.DLLADAVA.TMGPKGR.TVIIEQSWG
RetrocopyMLRLPTVFRQMRLVSRVLAPHLTGAYAKDVKFGADARALMLQGIDLLADAVALTMGPKGRRTVIIEQSWG
ParentalSPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEEAGDGTTTATVLARSIAKEGFEKISKGANPVE
SPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEE.GDG.TTATVLARSIAKEG.EKISKGANPVE
RetrocopySPKVTKDGVTVAKSIDLKDKYKNIGAKLVQDVANNTNEETGDGPTTATVLARSIAKEGIEKISKGANPVE
ParentalIRRGVMLAVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNIISDAMKKVGRKGVITVKDGKTLND
IRRGVML.VDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNI.SDAMKKVGRKGVITVKDGKTLND
RetrocopyIRRGVMLVVDAVIAELKKQSKPVTTPEEIAQVATISANGDKEIGNI-SDAMKKVGRKGVITVKDGKTLND
ParentalELEIIEGMKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSIQSIVPALEIANAHRKPLVIIAEDVD
ELEIIEG.KFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISS.QS.VPALEIANAHRKPLVIIAEDVD
RetrocopyELEIIEGIKFDRGYISPYFINTSKGQKCEFQDAYVLLSEKKISSVQSVVPALEIANAHRKPLVIIAEDVD
ParentalGEALSTLVLNRLKVGLQVVAVKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGKVGEVI
GEALSTLVLNRLKVGLQ.VA.KAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLG.VGEVI
RetrocopyGEALSTLVLNRLKVGLQDVAIKAPGFGDNRKNQLKDMAIATGGAVFGEEGLTLNLEDVQPHDLGNVGEVI
ParentalVTKDDAMLLKGKGDKAQIEKRIQEIIEQLDVTTSEYEKEKLNERLAKLSDGVAVLKVGGTSDVEVNEKKD
VTKDDA.LLK.KGDKAQIEKRIQEIIEQLDVTTSEYEKEKLNERLAKLSD.VAVLKVGGTSDVEVNEKKD
RetrocopyVTKDDATLLKEKGDKAQIEKRIQEIIEQLDVTTSEYEKEKLNERLAKLSDVVAVLKVGGTSDVEVNEKKD
ParentalRV-TDALNATRAAVEEGIVLGGGCALLRCIPALDSLTPANEDQKIGIEIIK-RTLKIPAMTIAKNAGVEG
RV..DALNATRAAVEEG.VLGGGCALLRCI.ALDSLTPANEDQKIG.EIIK.RTLKIPAMTIAKNAGVEG
RetrocopyRV<SDALNATRAAVEEGFVLGGGCALLRCILALDSLTPANEDQKIGTEIIK<RTLKIPAMTIAKNAGVEG
ParentalSLIVEKIMQSSSEVGYDAMAGDFVNMVEKGIIDPTKVVRTALLDAAGVASLLTTAEVVVTEIPKEEKDPG
S.IVEKI.Q.SSE.GYDAM.GDFVNMVEK.IIDPTKVVRTALLDAAGV.SLLTTAEVVVTEIPKEEKDPG
RetrocopySSIVEKITQISSEAGYDAMVGDFVNMVEK*IIDPTKVVRTALLDAAGVTSLLTTAEVVVTEIPKEEKDPG
ParentalMGAMGGMGGGMGGGMF
MGAMG.MGGGMG.GMF
RetrocopyMGAMGRMGGGMGSGMF

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 .12 RPM 169 .50 RPM
bodymap2_adrenal 0 .76 RPM 142 .79 RPM
bodymap2_brain 0 .40 RPM 143 .10 RPM
bodymap2_breast 0 .37 RPM 184 .30 RPM
bodymap2_colon 0 .17 RPM 473 .77 RPM
bodymap2_heart 0 .13 RPM 84 .42 RPM
bodymap2_kidney 0 .02 RPM 383 .99 RPM
bodymap2_liver 0 .04 RPM 451 .41 RPM
bodymap2_lung 0 .11 RPM 244 .20 RPM
bodymap2_lymph_node 0 .04 RPM 301 .77 RPM
bodymap2_ovary 0 .35 RPM 367 .40 RPM
bodymap2_prostate 0 .23 RPM 232 .90 RPM
bodymap2_skeletal_muscle 0 .04 RPM 104 .58 RPM
bodymap2_testis 0 .45 RPM 196 .47 RPM
bodymap2_thyroid 0 .30 RPM 841 .36 RPM
bodymap2_white_blood_cells 0 .02 RPM 121 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1006 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1006 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_27168155 libraries220 libraries724 libraries325 libraries405 libraries
TSS #2 TSS_271691154 libraries605 libraries70 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_1006 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_1006 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1006 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_800
Pongo abelii retro_pabe_848
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 = 0.69 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .26 RPM
CEU_NA11843 0 .40 RPM
CEU_NA11930 0 .52 RPM
CEU_NA12004 0 .27 RPM
CEU_NA12400 0 .35 RPM
CEU_NA12751 0 .27 RPM
CEU_NA12760 0 .31 RPM
CEU_NA12827 0 .47 RPM
CEU_NA12872 0 .27 RPM
CEU_NA12873 0 .41 RPM
FIN_HG00183 0 .27 RPM
FIN_HG00277 0 .55 RPM
FIN_HG00315 0 .47 RPM
FIN_HG00321 0 .24 RPM
FIN_HG00328 0 .43 RPM
FIN_HG00338 0 .26 RPM
FIN_HG00349 0 .54 RPM
FIN_HG00375 0 .29 RPM
FIN_HG00377 0 .40 RPM
FIN_HG00378 0 .47 RPM
GBR_HG00099 0 .52 RPM
GBR_HG00111 0 .60 RPM
GBR_HG00114 0 .42 RPM
GBR_HG00119 0 .26 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .24 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .19 RPM
GBR_HG00142 0 .39 RPM
GBR_HG00143 0 .35 RPM
TSI_NA20512 0 .20 RPM
TSI_NA20513 0 .46 RPM
TSI_NA20518 0 .69 RPM
TSI_NA20532 0 .48 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .41 RPM
TSI_NA20765 0 .37 RPM
TSI_NA20771 0 .23 RPM
TSI_NA20786 0 .31 RPM
TSI_NA20798 0 .22 RPM
YRI_NA18870 0 .58 RPM
YRI_NA18907 0 .17 RPM
YRI_NA18916 0 .23 RPM
YRI_NA19093 0 .16 RPM
YRI_NA19099 0 .40 RPM
YRI_NA19114 0 .21 RPM
YRI_NA19118 0 .27 RPM
YRI_NA19213 0 .29 RPM
YRI_NA19214 0 .20 RPM
YRI_NA19223 0 .16 RPM

Indel association:

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





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