RetrogeneDB ID:

retro_hsap_1731

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:20492605..20493679(+)
Located in intron of:ENSG00000231258
Retrocopy
information
Ensembl ID:ENSG00000188013
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MEIS3
Ensembl ID:ENSG00000105419
Aliases:MEIS3, MRG2
Description:Meis homeobox 3 [Source:HGNC Symbol;Acc:29537]


Retrocopy-Parental alignment summary:






>retro_hsap_1731
ATGGCCCGGAGGTACGATGAGCTGCCGCACTACCCAAGCATCGCGGATGGCCCCGCAGCCCTGGCTGGCTTCCCAGAGGC
AGTGCCCGCGGCACCAGGGCCCTATGGCCCTCACCGGCCTCCCCAGCCCCTACCCCCAGGCTTGGACAGCGACGGCCTGA
AGAGGGACAAGGATGAGATCTATGGACACCCGCTCTTCCCCCTCTTGGCCCTGGTCTTTGAGAAATGTGAACTGGCTACA
TGCTCTCCCCGTGATGGGGCCGGAGCTGGGCTGGGGACACCCCGCGGCGGCGACGTCTGCTCCTCTGATTCCTTCAACGA
GGACAACACTGCCTTCGCCAAGCAGGTTCGCTCTGAGAGGCCCTTCTTCTCCTCCAACCCAGAACTGGACAATCTGATGA
TCCAGGCCATCCAAGTGCTGCGGTTCCACCTGCTGGAGCTGGAGAAGGGAAAGATGCCCATCGACCTGGTCATCGAGGAT
CGGGATGGCGGCTGCAGGGAGGACTTCGAGGACTACCCAGCCTCCTGCCTCAGCCTCCCAGACCAGAATAATATATGGAT
TCGAGACCATGAGGATAGCGGGTCTGTACATTTGGGGACCCCAGGTCCATCCAGCGGGGGCCTGGCCTCCCAGAGTGGGG
ACAACTCCAGTGACCAAGGAGTCGGGCTGGACACCAGCGTGGCCTCTCCCAGTTCTGGTGGAGAAGATGAGGACTTGGAC
CAGGAGCCACGGCGAAACAAGAAGAGGGGGATCTTCCCCAAGGTGGCCACCAACATCATGCGAGCCTGGTTGTTCCAGCA
CCTCTGGCACCCGTACCCCTCGGAGGAGCAGAAGAAACAGCTGGTGCAGGACACGGGGCTCACCATCCTGCAAGTCAACA
ACTGGTTCATTAATGCCCGGAGACGCATGGTGCAACCTATGATCGATCAATCCAACCGCATAGGGCAGGGTGCAGCCTTC
AGCCCAGAGGGCCAGCCCATCGGGGGCTATACCGAGACAGAGCCACACGTGGCCTTCCGGCCTCCAGCATCAGTGGGGAT
GAGTTTGAACTTGGAAGGAGAATGGCATTATCTA

ORF - retro_hsap_1731 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.13 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMARRYDELPHYPGIVDGPAALASFPETVPAVPGPYGPHRPPQPLPPGLDSDGLKREKDEIYGHPLFPLLA
MARRYDELPHYP.I.DGPAALA.FPE.VPA.PGPYGPHRPPQPLPPGLDSDGLKR.KDEIYGHPLFPLLA
RetrocopyMARRYDELPHYPSIADGPAALAGFPEAVPAAPGPYGPHRPPQPLPPGLDSDGLKRDKDEIYGHPLFPLLA
ParentalLVFEKCELATCSPRDGAGAGLGTPPGGDVCSSDSFNEDIAAFAKQVRSERPLFSSNPELDNLMIQAIQVL
LVFEKCELATCSPRDGAGAGLGTP.GGDVCSSDSFNED..AFAKQVRSERP.FSSNPELDNLMIQAIQVL
RetrocopyLVFEKCELATCSPRDGAGAGLGTPRGGDVCSSDSFNEDNTAFAKQVRSERPFFSSNPELDNLMIQAIQVL
ParentalRFHLLELEKGKMPIDLVIEDRDGGCREDFEDYPASCPSLPDQNNMWIRDHEDSGSVHLGTPGPSSGGLAS
RFHLLELEKGKMPIDLVIEDRDGGCREDFEDYPASC.SLPDQNN.WIRDHEDSGSVHLGTPGPSSGGLAS
RetrocopyRFHLLELEKGKMPIDLVIEDRDGGCREDFEDYPASCLSLPDQNNIWIRDHEDSGSVHLGTPGPSSGGLAS
ParentalQSGDNSSDQGDGLDTSVASPSSGGEDEDLDQERRRNKKRGIFPKVATNIMRAWLFQHLSHPYPSEEQKKQ
QSGDNSSDQG.GLDTSVASPSSGGEDEDLDQE.RRNKKRGIFPKVATNIMRAWLFQHL.HPYPSEEQKKQ
RetrocopyQSGDNSSDQGVGLDTSVASPSSGGEDEDLDQEPRRNKKRGIFPKVATNIMRAWLFQHLWHPYPSEEQKKQ
ParentalLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRTGQGAAFSPEGQPIGGYTETQPHVAVRPPGSVGMSLN
L.QDTGLTILQVNNWFINARRR.VQPMIDQSNR.GQGAAFSPEGQPIGGYTET.PHVA.RPP.SVGMSLN
RetrocopyLVQDTGLTILQVNNWFINARRRMVQPMIDQSNRIGQGAAFSPEGQPIGGYTETEPHVAFRPPASVGMSLN
ParentalLEGEWHYL
LEGEWHYL
RetrocopyLEGEWHYL

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 .68 RPM 9 .50 RPM
bodymap2_adrenal 0 .27 RPM 8 .66 RPM
bodymap2_brain 0 .54 RPM 16 .22 RPM
bodymap2_breast 0 .02 RPM 4 .03 RPM
bodymap2_colon 0 .10 RPM 7 .37 RPM
bodymap2_heart 0 .26 RPM 1 .57 RPM
bodymap2_kidney 0 .08 RPM 3 .41 RPM
bodymap2_liver 0 .02 RPM 0 .40 RPM
bodymap2_lung 0 .16 RPM 2 .73 RPM
bodymap2_lymph_node 0 .00 RPM 6 .40 RPM
bodymap2_ovary 0 .35 RPM 19 .64 RPM
bodymap2_prostate 0 .29 RPM 9 .18 RPM
bodymap2_skeletal_muscle 0 .13 RPM 0 .33 RPM
bodymap2_testis 0 .51 RPM 8 .09 RPM
bodymap2_thyroid 0 .83 RPM 2 .43 RPM
bodymap2_white_blood_cells 0 .08 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1731 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 17:20491964..20492394
ENCFF002CFX POLR2A 17:20492051..20492308

EST - click to see more details

No EST(s) were mapped for retro_hsap_1731 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_56249671 libraries401 libraries657 libraries95 libraries5 libraries

The graphical summary, for retro_hsap_1731 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_1731 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1731 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000105419 2 retrocopies
retro_hsap_1718, retro_hsap_1731 ,
Gorilla gorilla ENSGGOG000000010931 retrocopy
retro_ggor_2263,
Mustela putorius furoENSMPUG000000047601 retrocopy
retro_mputfur_69,
Pan troglodytes ENSPTRG000000112081 retrocopy
retro_ptro_3061,

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 ) Legend:


Library Retrogene expression
CEU_NA11831 0 .00 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 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 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 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 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 .00 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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