RetrogeneDB ID:

retro_hsap_147

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:48901638..48902892(+)
Located in intron of:ENSG00000132122
Retrocopy
information
Ensembl ID:ENSG00000235105
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:STRADB
Ensembl ID:ENSG00000082146
Aliases:STRADB, ALS2CR2, CALS-21, ILPIP, ILPIPA, PAPK
Description:STE20-related kinase adaptor beta [Source:HGNC Symbol;Acc:13205]


Retrocopy-Parental alignment summary:






>retro_hsap_147
ATGTCTCTTTTGGATTGCTTCTGCACTTCAAGAACACAAGATGAATCACTCAGACCTGAAAAACAGTCTGAAACCAGTAT
CCATCAATACTTGGTTGATGAGCCAACCCTTTCCTGGTCACCTCCATCCACTAGAGCCAGTGAAGTACTATGTTCCACCA
ACGTTTCTCACTACGAGCTCCAAGTAGAAACAGGAAGAGGATTTGACAACTTGACTTCTGTCCATCTTGCATGGCATACT
CCCACGGGAACACTGGTAACTATAAAAATTACAAATCTGGAAAACTGCAATGAAGAACGCCTGAAAGCTTTACAGAAAGC
CGTGATTCTATCCCACTTTTTCCGGCATCCCAATATTACAACTTACTGGACAGTTTTCACTGTTGGCAGCTGGCTTTGGG
TTATTTCTCCATTTATGGCCTATGGTTCAGCAAGTCAACTCTTGAGGACCTGTTTTCCTGAAGGAATGAGTGAAACTTTA
ATAAGAAACATTATCTTTGGAGCTGTGAGAGGGTTGAACTATCTGTACCAAAATGGCTGTATTCACAGGAGTATTAAAGC
CAGCCATATCCTCATTTCTGGTGATGGCCTAGTGACCCTCTCTGGCCTGTCCCATCTGCATAGTTTGGTTAAGCATGGAC
AGAGGCATAGGGCTGTGTATGATTTCCCACAGTTCAGCACATCAGTGCAGCCGTGGCTGAGTCCAGAACTACTGAGACAG
GATTTACATGGGTATAATGTGAAGTCAGATATTTACAGTGTTGGGATTACAGCATGTGAATTAGCCAGTGGGCAGGTGCC
TTTCCAGGACATGCATAGAACTCAGATGCTGTTACAGAAACTGAAAGGTCCTCCTTATAGCCCATTGGATATCAGTATTT
TCCCTCAATCAGAATCCAGAATGAAAAATTCCCGGTCAGGTGTAGACTCTGGAATTGGAGAAAGTGTGCTTGTCTCCAGT
GGAACTCACACAGTAAATAGTGACCGATTACACACACCATCCTCAAAAACTTTCTCTCCTGCCTTCTTTAGCTTGGTACA
GCTCTGTTTGCAACAAGATCCTGAGAAAAGGCCATCAGCAAGCAGTTTATTGTCCCATGTTTTCTTCAAACAGATGAAAG
AAGAAAGCCAGGATTCAATACTTTCACGGTTGCCTCCTGCTTATAACAAGCCATCAATACCATTGCCTCCAGTGTTACCT
TGGACTGAGCCAGAATGTGATTTTCCTGATGAAAAAGACTCATACTTGGAATTC

ORF - retro_hsap_147 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.37 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSLLDCFCTSRTQVESLRPEKQSETSIHQYLVDEPTLSWSRPSTRASEVLCSTNVSHYELQVEIGRGFDN
MSLLDCFCTSRTQ.ESLRPEKQSETSIHQYLVDEPTLSWS.PSTRASEVLCSTNVSHYELQVE.GRGFDN
RetrocopyMSLLDCFCTSRTQDESLRPEKQSETSIHQYLVDEPTLSWSPPSTRASEVLCSTNVSHYELQVETGRGFDN
ParentalLTSVHLARHTPTGTLVTIKITNLENCNEERLKALQKAVILSHFFRHPNITTYWTVFTVGSWLWVISPFMA
LTSVHLA.HTPTGTLVTIKITNLENCNEERLKALQKAVILSHFFRHPNITTYWTVFTVGSWLWVISPFMA
RetrocopyLTSVHLAWHTPTGTLVTIKITNLENCNEERLKALQKAVILSHFFRHPNITTYWTVFTVGSWLWVISPFMA
ParentalYGSASQLLRTYFPEGMSETLIRNILFGAVRGLNYLHQNGCIHRSIKASHILISGDGLVTLSGLSHLHSLV
YGSASQLLRT.FPEGMSETLIRNI.FGAVRGLNYL.QNGCIHRSIKASHILISGDGLVTLSGLSHLHSLV
RetrocopyYGSASQLLRTCFPEGMSETLIRNIIFGAVRGLNYLYQNGCIHRSIKASHILISGDGLVTLSGLSHLHSLV
ParentalKHGQRHRAVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGITACELASGQVPFQDMHRTQMLLQK
KHGQRHRAVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGITACELASGQVPFQDMHRTQMLLQK
RetrocopyKHGQRHRAVYDFPQFSTSVQPWLSPELLRQDLHGYNVKSDIYSVGITACELASGQVPFQDMHRTQMLLQK
ParentalLKGPPYSPLDISIFPQSESRMKNSQSGVDSGIGESVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLVQLCL
LKGPPYSPLDISIFPQSESRMKNS.SGVDSGIGESVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLVQLCL
RetrocopyLKGPPYSPLDISIFPQSESRMKNSRSGVDSGIGESVLVSSGTHTVNSDRLHTPSSKTFSPAFFSLVQLCL
ParentalQQDPEKRPSASSLLSHVFFKQMKEESQDSILSLLPPAYNKPSISLPPVLPWTEPECDFPDEKDSYWEF
QQDPEKRPSASSLLSHVFFKQMKEESQDSILS.LPPAYNKPSI.LPPVLPWTEPECDFPDEKDSY.EF
RetrocopyQQDPEKRPSASSLLSHVFFKQMKEESQDSILSRLPPAYNKPSIPLPPVLPWTEPECDFPDEKDSYLEF

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 .32 RPM 24 .77 RPM
bodymap2_adrenal 0 .12 RPM 11 .16 RPM
bodymap2_brain 0 .28 RPM 24 .99 RPM
bodymap2_breast 0 .12 RPM 41 .81 RPM
bodymap2_colon 0 .00 RPM 11 .68 RPM
bodymap2_heart 0 .22 RPM 58 .47 RPM
bodymap2_kidney 0 .04 RPM 37 .76 RPM
bodymap2_liver 0 .23 RPM 46 .94 RPM
bodymap2_lung 0 .00 RPM 26 .81 RPM
bodymap2_lymph_node 0 .26 RPM 18 .09 RPM
bodymap2_ovary 0 .27 RPM 13 .96 RPM
bodymap2_prostate 0 .02 RPM 13 .87 RPM
bodymap2_skeletal_muscle 0 .78 RPM 48 .87 RPM
bodymap2_testis 0 .32 RPM 22 .34 RPM
bodymap2_thyroid 0 .13 RPM 18 .19 RPM
bodymap2_white_blood_cells 0 .28 RPM 15 .49 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_147 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_147 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_951291550 libraries256 libraries16 libraries1 library6 libraries

The graphical summary, for retro_hsap_147 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_147 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_147 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000082146 2 retrocopies
retro_hsap_147 , retro_hsap_3920,
Gorilla gorilla ENSGGOG000000121831 retrocopy
retro_ggor_2638,
Macaca mulatta ENSMMUG000000181411 retrocopy
retro_mmul_1741,
Nomascus leucogenys ENSNLEG000000069671 retrocopy
retro_nleu_2158,
Otolemur garnettii ENSOGAG000000107441 retrocopy
retro_ogar_1019,
Pongo abelii ENSPPYG000000130741 retrocopy
retro_pabe_3192,

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 = 0.11 RPM Legend:


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