RetrogeneDB ID:

retro_hsap_3005

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:165109535..165111485(+)
Located in intron of:ENSG00000145416
Retrocopy
information
Ensembl ID:ENSG00000250746
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA5
Ensembl ID:ENSG00000044574
Aliases:HSPA5, BIP, GRP78, HEL-S-89n, MIF2
Description:heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) [Source:HGNC Symbol;Acc:5238]


Retrocopy-Parental alignment summary:






>retro_hsap_3005
ATGAAGCTCTCCCTGGTGGCGGCGATGCTGCTGCTACTCGGTGAGGCGTGGTTCGAGGACAAGGAGGAGGACGTGGGCAC
GGTGGTCTGCGTCGACCTGGGGACCACCTACTGCTGCGTCTGTGTGTTCAAGACCGGCTGCGTGGAGATCACCGCCAACA
ATCAGAGCAAACGCATCACGCGGTCCTATGTGCCCTTCACTCTTGAAGGGGAATATCTGATCGGCGATGCCGCCACGAAC
CAGCTCACCTCCAATCCCAAGAACACGGTCTTTGACGCCAAGTGGCTCATCGGCCGCACGTGGAACGACCTGTCTATGCA
GCAGGACATCAAGTTCTTGCGGTTCAAGGTAGTTGAAAAGAAAACTAAACCATACGTTCAAGTTGATATTGGAGGTGGGC
AAACAAAGACATTTGCTCCTGAAGAAATTTCTGCCATGGTTCTCACTAAAATGCAATAAACCGCTGAGGCTTATTTGAGA
AAGAAGTTTACCCATGCAGTTTTTACCTTACCAGCCTATTTCAATGATGCCCAATGCGAAGCAACCAAAGATATTGGAAC
TATTGCTGAGCTAAATGTTATGAGGATCATTAACGAGCCTATGGCAGCTGCTATTGGTTATGGCCTGGATAAGAGGGAGG
GGGAGAAGACATCCTGTTGTTCCACCTGGGTGGCAGAACCTTCAATGCGTCTCCTCTCACCATTGACAATGGTGTCTTCG
GAGTCGTGGCCACTAATGGAGATACTCATCTGCGTGCAGAAGACTATGACTAGCGTGTCATGGAACATTTCATCAAGTTG
TACAAAAAGAAGACTGACAAAGATGTCAGGAAAGACGATAGGGCTGTGCAGAAACTCCAGCTAGAGGTAGAAAAGGCCAG
ATGGGCCCTGTCTCCTCAACATCAAGCAAGAATTGAAATTGAGTCCTTCTATGAAGGAGAAGACTTTTCTGAGACCCTGA
CTCAGGCCAAATTTTAAGAGCTAAACATGGATCTGTTCTGGTCTACTATGAGGCCTGTCCAGAAAGTGTTGGAAAATTCT
GATTTGAAGAATTCTGATATTGATGATGTTGTTCTTGGTGGCTCTACTCGAATTCCAAAGATTCAGCAACTGGTTAAAAA
GTCCTTCAATGGCAAGGAGTCCTCCCATGGCATAAACCCAGATGAAGCTGTAGTGCATGGTGCTGCTGTCCAGGCTGGAG
TGCTCTCTGGTGATCAAGATACAGGTGACCTGGTAGTGCTTGATGTATGTCCCCTTACATTTGGTATTGAAACTGTGGGA
GGTGTCATGATCAAACTGATTCCAAGGAACACAGTGGTACCTACCAAGAAGTCCATATCTTTTCTATAGCTTCTGATAAT
CAACCAACTGTCATAATCAAGGTCTATGAGGATGAATGACCCCTGACAAAAGACATTCATCTTCTGGGTACATTTGATCT
GACTGGAATTCCTCCTGCTCCTCGTGGGGTCCCACAGATTGAAGTCACCTTTGAGATAGATGTGAATGGTATTCTTCGAG
TGACAGCTGAAGACAAGGGTACAGGGAACAAAAATAAGATCACAATTACCAATGACCAGAATCACCTGACACCTGAAGAA
ATCAAAAGGATGGTTAATGATGCTGAGAAGTTTGCTGAGGAAGACACAAAGCTCAAGGAGTGCATTGATACTACAAATGA
GCTGGAAAGCTATGGCTATTCTCTAAAGAATCAGATTGGAGATAAAGAAAAGCTGGGAGGTAAACTTTCCTCTGAAGATA
AGGAGACCATGGAAAAAGCTGTAGAAGAAAAGATTGAATGGCTGGAAAGCCACCAAGCTGCTGACATTGAAGACTTCGAA
GCTAACAAGAAGGAACTGGAAGAAATTGTTCAGCCACTTATCAGCAAACTCTATGGAAGTGCAAGCCCTCTCCCAGCCAC
GAAGAGGATACGGCAGAAAAAGATGAGTTG

ORF - retro_hsap_3005 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.78 %
Parental protein coverage: 100. %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMKLSLVAAMLLLLSAARAEEEDKKEDVGTVVGIDLGTTYSCVGVFKNGRVEIIANDQGNRITPSYVAFTP
MKLSLVAAMLLLL..A..E..DK.EDVGTVV..DLGTTY.CV.VFK.G.VEI.AN.Q..RIT.SYV.FT.
RetrocopyMKLSLVAAMLLLLGEAWFE--DKEEDVGTVVCVDLGTTYCCVCVFKTGCVEITANNQSKRITRSYVPFTL
ParentalEGERLIGDAAKNQLTSNPENTVFDAKRLIGRTWNDPSVQQDIKFLPFKVVEKKTKPYIQVDIGGGQTKTF
EGE.LIGDAA.NQLTSNP.NTVFDAK.LIGRTWND.S.QQDIKFL.FKVVEKKTKPY.QVDIGGGQTKTF
RetrocopyEGEYLIGDAATNQLTSNPKNTVFDAKWLIGRTWNDLSMQQDIKFLRFKVVEKKTKPYVQVDIGGGQTKTF
ParentalAPEEISAMVLTKMKETAEAYLGKKVTHAVVTVPAYFNDAQRQATKDAGTIAGLNVMRIINEPTAAAIAYG
APEEISAMVLTKM..TAEAYL.KK.THAV.T.PAYFNDAQ..ATKD.GTIA.LNVMRIINEP.AAAI.YG
RetrocopyAPEEISAMVLTKMQ*TAEAYLRKKFTHAVFTLPAYFNDAQCEATKDIGTIAELNVMRIINEPMAAAIGYG
ParentalLDKREGEK-NILVFDLGGGTFDVSLLTIDNGVFEVVATNGDTHLGGEDFDQRVMEHFIKLYKKKTGKDVR
LDKREGEK..IL.F.LGG.TF..S.LTIDNGVF.VVATNGDTHL..ED.D.RVMEHFIKLYKKKT.KDVR
RetrocopyLDKREGEK<DILLFHLGGRTFNASPLTIDNGVFGVVATNGDTHLRAEDYD*RVMEHFIKLYKKKTDKDVR
ParentalKDNRAVQKLRREVEKAKRALSSQHQARIEIESFYEGEDFSETLTRAKFEELNMDLFRSTMKPVQKVLEDS
KD.RAVQKL..EVEKA..ALS.QHQARIEIESFYEGEDFSETLT.AKF.ELNMDLF.STM.PVQKVLE.S
RetrocopyKDDRAVQKLQLEVEKARWALSPQHQARIEIESFYEGEDFSETLTQAKF*ELNMDLFWSTMRPVQKVLENS
ParentalDLKKSDIDEIVLVGGSTRIPKIQQLVKEFFNGKEPSRGINPDEAVAYGAAVQAGVLSGDQDTGDLVLLDV
DLK.SDID..VL.GGSTRIPKIQQLVK..FNGKE.S.GINPDEAV..GAAVQAGVLSGDQDTGDLV.LDV
RetrocopyDLKNSDIDDVVL-GGSTRIPKIQQLVKKSFNGKESSHGINPDEAVVHGAAVQAGVLSGDQDTGDLVVLDV
ParentalCPLTLGIETVGGVMTKLIPRNTVVPTKKS-QIFSTASDNQPTVTIKVYEGERPLTKDNHLLGTFDLTGIP
CPLT.GIETVGGVM.KLIPRNTVVPTKKS..IFS.ASDNQPTV.IKVYE.E.PLTKD.HLLGTFDLTGIP
RetrocopyCPLTFGIETVGGVMIKLIPRNTVVPTKKS<HIFSIASDNQPTVIIKVYEDE*PLTKDIHLLGTFDLTGIP
ParentalPAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITITNDQNRLTPEEIERMVNDAEKFAEEDKKLKER
PAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITITNDQN.LTPEEI.RMVNDAEKFAEED.KLKE.
RetrocopyPAPRGVPQIEVTFEIDVNGILRVTAEDKGTGNKNKITITNDQNHLTPEEIKRMVNDAEKFAEEDTKLKEC
ParentalIDTRNELESYAYSLKNQIGDKEKLGGKLSSEDKETMEKAVEEKIEWLESHQDADIEDFKAKKKELEEIVQ
IDT.NELESY.YSLKNQIGDKEKLGGKLSSEDKETMEKAVEEKIEWLESHQ.ADIEDF.A.KKELEEIVQ
RetrocopyIDTTNELESYGYSLKNQIGDKEKLGGKLSSEDKETMEKAVEEKIEWLESHQAADIEDFEANKKELEEIVQ
ParentalPIISKLYGSAG-PPPTGEEDTAEKDEL
P.ISKLYGSA..P.P..EEDTAEKDEL
RetrocopyPLISKLYGSAS<PSPSHEEDTAEKDEL

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 285 .92 RPM
bodymap2_adrenal 0 .00 RPM 487 .99 RPM
bodymap2_brain 0 .05 RPM 172 .10 RPM
bodymap2_breast 0 .00 RPM 293 .97 RPM
bodymap2_colon 0 .02 RPM 1067 .92 RPM
bodymap2_heart 0 .02 RPM 237 .28 RPM
bodymap2_kidney 0 .00 RPM 1434 .23 RPM
bodymap2_liver 0 .00 RPM 950 .08 RPM
bodymap2_lung 0 .02 RPM 1331 .80 RPM
bodymap2_lymph_node 0 .00 RPM 940 .07 RPM
bodymap2_ovary 0 .06 RPM 594 .23 RPM
bodymap2_prostate 0 .00 RPM 352 .91 RPM
bodymap2_skeletal_muscle 0 .04 RPM 161 .45 RPM
bodymap2_testis 0 .00 RPM 677 .67 RPM
bodymap2_thyroid 0 .00 RPM 308 .63 RPM
bodymap2_white_blood_cells 0 .02 RPM 364 .89 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3005 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3005 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_1414251190 libraries253 libraries347 libraries35 libraries4 libraries

The graphical summary, for retro_hsap_3005 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_3005 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3005 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2033
Gorilla gorilla retro_ggor_2082
Pongo abelii retro_pabe_2491
Callithrix jacchus retro_cjac_2221
Parental genes homology:
Parental genes homology involve 13 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000068801 retrocopy
retro_cjac_2221,
Homo sapiens ENSG00000044574 1 retrocopy
retro_hsap_3005 ,
Homo sapiens ENSG000001099718 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 ENSGALG000000010001 retrocopy
retro_ggal_21,
Gorilla gorilla ENSGGOG000000268791 retrocopy
retro_ggor_2082,
Macropus eugenii ENSMEUG000000167021 retrocopy
retro_meug_522,
Mus musculus ENSMUSG000000268641 retrocopy
retro_mmus_1299,
Nomascus leucogenys ENSNLEG000000173481 retrocopy
retro_nleu_751,
Otolemur garnettii ENSOGAG000000067861 retrocopy
retro_ogar_2901,
Pongo abelii ENSPPYG000000196091 retrocopy
retro_pabe_2491,
Pan troglodytes ENSPTRG000000005631 retrocopy
retro_ptro_2033,
Ictidomys tridecemlineatus ENSSTOG000000112434 retrocopies
retro_itri_1686, retro_itri_1687, retro_itri_1689, retro_itri_1879,

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 = 0.14 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .11 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .14 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .10 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .08 RPM
TSI_NA20532 0 .07 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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