RetrogeneDB ID:

retro_hsap_340

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:247393241..247394561(+)
Located in intron of:ENSG00000232347
Retrocopy
information
Ensembl ID:ENSG00000214144
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSG00000109971
Aliases:HSPA8, HEL-33, HEL-S-72p, HSC54, HSC70, HSC71, HSP71, HSP73, HSPA10, LAP1, NIP71
Description:heat shock 70kDa protein 8 [Source:HGNC Symbol;Acc:5241]


Retrocopy-Parental alignment summary:






>retro_hsap_340
ATGTTGAAGGGAACTGCAGTTGATATTGATATTGGCACCACCTACTCTTGTGTGGGTGTTTTCCAGCACGGGAAAGTAGA
GATAATTGCCAATGATCAGGGAAACCGAACCACTCCAAGCTATGTTGCCTTTACAGACACTGAACGATTGATAGGTGATG
CCACAAAGAATCAAGTTGCAATGAACCCCACCAACATGGTTTTTTGATGCCAAACATCTAATTGGATGCAGATTTGATGA
TGCTGTTGTCCAGCCTGATATGAAGTATTGGCCCTTCATGGTGGTGAATGATGCTGGCAGGCCCAAGGTCCAAGTGGAAT
ACAAGGGAGAGACCAAAAGCTTCTACCCAGAGGAGGTACCCTCTATGGTTCTGACAAAGATGAAGGAAATTGCAGAAGCA
TACCTTGGGAATATGGTTACCAATGCTGTGGTCACAGTGCCAGCTTACTTTAATGACCCTCAGCATCAGGCTACCAAATA
TGCTAGAACTATTGCTGGTCTCAATGTACTTAGAAGTATCAGTGAGCCAACTGTAGCTGCTACTGCTTACAGCTTAGACA
AAAAGGTTGGAGCTGAAAGAAATGTGCTGACCTTTGACCTGAGAGGTGGGACTTTTGATGTGTCAATCCTCACTATTGAG
GATGGAATCTTTGAGGTCAGATCTACAGCTGGAGACACCCACTTGGGTGGAGAAGACTTTGACAACCGAATGTCAACCAT
TTTATTGCTGAGTTCAAGAGCAAGCATAAGAAGGACATCAGTGAGAATAAGAGAGCTGTAAGATGCCTCCATACTGCTTA
TGAACATGCTAAGTGTACTCTCTCTTCCAGCATCCAGGCCAGTATTGGGATCGATTCTCTCTATGAAGGAATAAACTTCT
ATATGTCCATTGCCTGTGCCCGATTTGAAGAATTGAATGCTGACCTGTTCCATAGCACCCTAGACCCCATAGAGAAAGCC
CTTCAAGATGCCAAACTGGACAAGTCAAAGATTCATGATATTGTCCTGTTTGGTGGTTCTACTCATATCCCCAAGATTCA
GAAGCTTCTCCAAGACTTCATCAATGGAAAAGAACCGAATAAGAGCATCAATCCTGATGAAGCTCTTGCTTATGGTGCAG
CTGTTCAGGCAGCCATCCTATCTGGAGACAAGTCTGAAAATGTTCAAGAGTTGCTCCTCTTAGATGTCTCTCCTCTTTCC
CTTGGTATTGAAACTGCTGGTGGAGTCACCACTGTCTTCATCAAGCGTAATACTACCATTCCTACCAAGCAGACACAGAC
CTTCACTACCTATTCTGGCAACCAGCCTGGTGTGCTTATT

ORF - retro_hsap_340 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.78 %
Parental protein coverage: 68.11 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVF-D
M.KG.AV.ID.GTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDA.KNQVAMNPTN.VF.D
RetrocopyMLKGTAVDIDIGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDATKNQVAMNPTNMVF>D
ParentalAKRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTV
AK.LIG.RFDDAVVQ.DMK.WPFMVVNDAGRPKVQVEYKGETKSFYPEEV.SMVLTKMKEIAEAYLG..V
RetrocopyAKHLIGCRFDDAVVQPDMKYWPFMVVNDAGRPKVQVEYKGETKSFYPEEVPSMVLTKMKEIAEAYLGNMV
ParentalTNAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKKVGAERNVLIFDLGGGTFDVSI
TNAVVTVPAYFND.Q.QATK.A.TIAGLNVLR.I.EPT.AA.AY.LDKKVGAERNVL.FDL.GGTFDVSI
RetrocopyTNAVVTVPAYFNDPQHQATKYARTIAGLNVLRSISEPTVAATAYSLDKKVGAERNVLTFDLRGGTFDVSI
ParentalLTIEDGIFEVKSTAGDTHLGGEDFDNRM-VNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSST
LTIEDGIFEV.STAGDTHLGGEDFDNRM.VNHFIAEFK.KHKKDISENKRAVR.L.TA.E.AK.TLSSS.
RetrocopyLTIEDGIFEVRSTAGDTHLGGEDFDNRM<VNHFIAEFKSKHKKDISENKRAVRCLHTAYEHAKCTLSSSI
ParentalQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQK
QASI.IDSLYEGI.FY.SI..ARFEELNADLF..TLDP.EKAL.DAKLDKS.IHDIVL.GGST.IPKIQK
RetrocopyQASIGIDSLYEGINFYMSIACARFEELNADLFHSTLDPIEKALQDAKLDKSKIHDIVLFGGSTHIPKIQK
ParentalLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNT
LLQDF.NGKE.NKSINPDEA.AYGAAVQAAILSGDKSENVQ.LLLLDV.PLSLGIETAGGV.TV.IKRNT
RetrocopyLLQDFINGKEPNKSINPDEALAYGAAVQAAILSGDKSENVQELLLLDVSPLSLGIETAGGVTTVFIKRNT
ParentalTIPTKQTQTFTTYSDNQPGVLI
TIPTKQTQTFTTYS.NQPGVLI
RetrocopyTIPTKQTQTFTTYSGNQPGVLI

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 378 .65 RPM
bodymap2_adrenal 0 .00 RPM 331 .67 RPM
bodymap2_brain 0 .05 RPM 863 .93 RPM
bodymap2_breast 0 .00 RPM 569 .52 RPM
bodymap2_colon 0 .00 RPM 1201 .80 RPM
bodymap2_heart 0 .00 RPM 645 .86 RPM
bodymap2_kidney 0 .00 RPM 1396 .28 RPM
bodymap2_liver 0 .00 RPM 656 .44 RPM
bodymap2_lung 0 .00 RPM 884 .51 RPM
bodymap2_lymph_node 0 .00 RPM 1648 .41 RPM
bodymap2_ovary 0 .00 RPM 901 .10 RPM
bodymap2_prostate 0 .00 RPM 540 .08 RPM
bodymap2_skeletal_muscle 0 .00 RPM 473 .34 RPM
bodymap2_testis 0 .00 RPM 864 .58 RPM
bodymap2_thyroid 0 .00 RPM 1387 .20 RPM
bodymap2_white_blood_cells 0 .02 RPM 1500 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_340 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_340 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_340 retrocopy 5' end.

Lab - click to see more details

retro_hsap_340 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_340 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_272
Gorilla gorilla retro_ggor_360
Pongo abelii retro_pabe_355
Macaca mulatta retro_mmul_580
Parental genes homology:
Parental genes homology involve 29 parental genes, and 76 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
retro_amel_126,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Bos taurus ENSBTAG000000131621 retrocopy
retro_btau_354,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Dipodomys ordii ENSDORG000000154671 retrocopy
retro_dord_16,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Felis catus ENSFCAG000000011326 retrocopies
retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Homo sapiens ENSG000000445741 retrocopy
retro_hsap_3005,
Homo sapiens ENSG00000109971 8 retrocopies
retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340 , retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Homo sapiens ENSG000001130131 retrocopy
retro_hsap_2214,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Loxodonta africana ENSLAFG000000303124 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Macaca mulatta ENSMMUG000000046967 retrocopies
retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 retrocopies
retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Pan troglodytes ENSPTRG000000044045 retrocopies
retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259, retro_ptro_3264,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Tursiops truncatus ENSTTRG000000111396 retrocopies
retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,

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 .02 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 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .03 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .03 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 .02 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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