RetrogeneDB ID:

retro_hsap_4151

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:34318404..34319647(+)
Located in intron of:ENSG00000186638
Retrocopy
information
Ensembl ID:ENSG00000229207
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:SERPINH1
Ensembl ID:ENSG00000149257
Aliases:SERPINH1, AsTP3, CBP1, CBP2, HSP47, OI10, PPROM, RA-A47, SERPINH2, gp46
Description:serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1) [Source:HGNC Symbol;Acc:1546]


Retrocopy-Parental alignment summary:






>retro_hsap_4151
CGCTCCCTCCTGCTCCTCAGCGCCTTCTGCCTCCTGGCGGTGGCCTTGGCGACCGAGGTGAAGAAACCTGCAGCCACAGC
AGCTCCTGGCACCGCAGAGAAGCTGAGCCCCAAGGCAGCCACGCTGGCCGAACACAGCGCCGGCCTGGCCTTCAGCCTGT
ACCAGGCCATGGCCAAGGACCAGGCGGTGGAGAACATCCTGGTGTCGCCCGTGGTGGTGGCCTCGTCGTTGGGGCTCGTG
TCGCTGGGCGGCAAGGCGACCACGGCGTCGGAGGCCAAGGCAGTGCTGAGTGCCAAGCAGCTGAGCGACGAGGAGGTGCA
CGCCGGCGTGGGCGAGCCGCTGCGTTCACTCAGCAACTCCACCGCGCGCAACGTGACCTGGAAGCTGTGCAGTCGCCTGT
AGGGACCCAGCTCAGTGAGTTTCGCTGATGACTTCGTGCGCAGCAGCAAGCAGCACTACAACTGCGAGCACTCCAAGATC
AATTTCCATGACAAGCGCAGTGCGCTGCAGTCCATCCACGAGTGGGCCGTGCAGACCACCGACGGCAAGCTGCCCAAGGT
CACCAAGGACATGGAGTGCATGGATGGCGCCCTGCTTGTCAACACCATGTTCTTCAAGCCACACTGGAATGAGAAATTCC
ACCACAAGATGGTGGAAAACCGTGGCTTCATGGTGACTCGGTTCTATACCGTGGGTGTCATGGTGATGCACCAGACAGGC
CTCTACAACTACTATGACAATGAGAAGGAAAAGCTGCAAATCGTGGAGATGCCCCTGGCCCACAAGCTCTCCAGCCTCAT
CATCCTCATGCCCCACCACGTGGAGCCCCTCGAGGCCTTAAAAAGCTGGTAACCAAAGAGCAGCTGAAGATCTGGATGGG
GAAGAAGCAGAAGCCTGTCGCCATCTCCTTGCCCAAGCGGGTGGTGGAAGTTCCCATGACCTGCAGAAACTCCTGGCTAG
GCTTGGCCTGACTGAGGCCATTGACAAGAACAAGGCAAACTTGTCACGCATGCCACACAAGAAGGACCTGTACCTGACCA
GCGTGTTCCACGCCACCGCCTTTGAGTTGGACACAGACGGCAACTCCTTTGACCAGGACATCTATGGGAGCAAGGAGCTG
CGCAGCCCCAAGCTGTTCTACTCCGACCACCCCTTCATCTTCCTGGTGTGGGACACCCAGAGCGGCTCCCTGCTGTTCAC
TGGGCACCTGGTCCGGCCTAAGGTTGACAAGATGCAAGACGAG

ORF - retro_hsap_4151 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.8 %
Parental protein coverage: 99.52 %
Number of stop codons detected: 1
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalRSLLLLSAFCLLEAALAAEVKKPAAAAAPGTAEKLSPKAATLAERSAGLAFSLYQAMAKDQAVENILVSP
RSLLLLSAFCLL..ALA.EVKKPAA.AAPGTAEKLSPKAATLAE.SAGLAFSLYQAMAKDQAVENILVSP
RetrocopyRSLLLLSAFCLLAVALATEVKKPAATAAPGTAEKLSPKAATLAEHSAGLAFSLYQAMAKDQAVENILVSP
ParentalVVVASSLGLVSLGGKATTASQAKAVLSAEQLRDEEVHAGLGELLRSLSNSTARNVTWKLGSRLYGPSSVS
VVVASSLGLVSLGGKATTAS.AKAVLSA.QL.DEEVHAG.GE.LRSLSNSTARNVTWKL.SRL.GPSSVS
RetrocopyVVVASSLGLVSLGGKATTASEAKAVLSAKQLSDEEVHAGVGEPLRSLSNSTARNVTWKLCSRL*GPSSVS
ParentalFADDFVRSSKQHYNCEHSKINFRDKRSALQSINEWAAQTTDGKLPEVTKDVERTDGALLVNAMFFKPHWD
FADDFVRSSKQHYNCEHSKINF.DKRSALQSI.EWA.QTTDGKLP.VTKD.E..DGALLVN.MFFKPHW.
RetrocopyFADDFVRSSKQHYNCEHSKINFHDKRSALQSIHEWAVQTTDGKLPKVTKDMECMDGALLVNTMFFKPHWN
ParentalEKFHHKMVDNRGFMVTRSYTVGVMMMHRTGLYNYYDDEKEKLQIVEMPLAHKLSSLIILMPHHVEPLER-
EKFHHKMV.NRGFMVTR.YTVGVM.MH.TGLYNYYD.EKEKLQIVEMPLAHKLSSLIILMPHHVEPLE..
RetrocopyEKFHHKMVENRGFMVTRFYTVGVMVMHQTGLYNYYDNEKEKLQIVEMPLAHKLSSLIILMPHHVEPLEA<
ParentalLEKLLTKEQLKIWMGKMQKKAVAISLPKGVVEV-THDLQKHLAGLGLTEAIDKNKADLSRMSGKKDLYLA
L.KL.TKEQLKIWMGK.Q.K.VAISLPK.VVEV..HDLQK.LA.LGLTEAIDKNKA.LSRM..KKDLYL.
RetrocopyLKKLVTKEQLKIWMGKKQ-KPVAISLPKRVVEV<SHDLQKLLARLGLTEAIDKNKANLSRMPHKKDLYLT
ParentalSVFHATAFELDTDGNPFDQDIYGREELRSPKLFYADHPFIFLVRDTQSGSLLFIGRLVRPKGDKMRDE
SVFHATAFELDTDGN.FDQDIYG..ELRSPKLFY.DHPFIFLV.DTQSGSLLF.G.LVRPK.DKM.DE
RetrocopySVFHATAFELDTDGNSFDQDIYGSKELRSPKLFYSDHPFIFLVWDTQSGSLLFTGHLVRPKVDKMQDE

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 109 .47 RPM
bodymap2_adrenal 0 .00 RPM 113 .38 RPM
bodymap2_brain 0 .02 RPM 7 .97 RPM
bodymap2_breast 0 .00 RPM 120 .47 RPM
bodymap2_colon 0 .02 RPM 217 .03 RPM
bodymap2_heart 0 .00 RPM 26 .18 RPM
bodymap2_kidney 0 .00 RPM 99 .78 RPM
bodymap2_liver 0 .00 RPM 15 .27 RPM
bodymap2_lung 0 .02 RPM 344 .73 RPM
bodymap2_lymph_node 0 .00 RPM 210 .73 RPM
bodymap2_ovary 0 .02 RPM 260 .55 RPM
bodymap2_prostate 0 .00 RPM 96 .72 RPM
bodymap2_skeletal_muscle 0 .00 RPM 15 .00 RPM
bodymap2_testis 0 .08 RPM 109 .03 RPM
bodymap2_thyroid 0 .02 RPM 38 .59 RPM
bodymap2_white_blood_cells 0 .00 RPM 5 .75 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_4151 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4151 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_192758609 libraries 364 libraries 524 libraries 207 libraries 125 libraries

The graphical summary, for retro_hsap_4151 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_4151 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4151 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2822
Parental genes homology:
Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000149257 1 retrocopy
retro_hsap_4151 ,
Macaca mulatta ENSMMUG000000076751 retrocopy
retro_mmul_1180,
Nomascus leucogenys ENSNLEG000000168821 retrocopy
retro_nleu_1389,
Pongo abelii ENSPPYG000000036912 retrocopies
retro_pabe_3459, retro_pabe_3514,
Pan troglodytes ENSPTRG000000040831 retrocopy
retro_ptro_2822,

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 = 0.34 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .29 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .12 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .08 RPM
CEU_NA12873 0 .16 RPM
FIN_HG00183 0 .14 RPM
FIN_HG00277 0 .15 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .12 RPM
FIN_HG00328 0 .19 RPM
FIN_HG00338 0 .13 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .06 RPM
GBR_HG00099 0 .12 RPM
GBR_HG00111 0 .06 RPM
GBR_HG00114 0 .11 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .09 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .13 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .19 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .14 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .12 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .10 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .14 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .11 RPM
YRI_NA19093 0 .34 RPM
YRI_NA19099 0 .21 RPM
YRI_NA19114 0 .10 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .26 RPM
YRI_NA19214 0 .12 RPM
YRI_NA19223 0 .14 RPM

Indel association:

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



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