RetrogeneDB ID:

retro_hsap_1718

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:17:15689931..15691006(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000179277
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_1718
ATGGCCCAAAGGTACGATGAGCTGCCGCACTACCCAGGCATCGCGGATGGCCCCGCAGCCCTGGCTGGCTTCCCAGAGGC
AGTGCCCGCGGCACCAGGGCCCTATGGCCCTCACCGGCCTCCCCAGCCCCTACCCCCAGGCTTGGACAGCGACGGCCTGA
AGAGGGACAAGGATGAGATCTATGGACACCCGCTCTTCCCCGTCTTGGCCCTGGTCTTTGAGAAATGTGAACTGGCTACA
TGCTCTCCCCGTGATGGGGCCGGAGCTGGGCTGGGGACACCCCCGCGGCGGCGACGTCTGCTCCTCTGATTCCTTCAACG
AGGACAACACTGCCTTCGCCAAGCAGGTTCGCTCTGAGAGGCCCTTCTTCTCCTCCAACCCAGAACTGGACAATCTGATG
ATCCAGGCAATCCAAGTGCTGCGGTTCCACCTGCTAGAGCTGGAGAAGGGAAAGATGCCCATCGACCTGGTCATCGAGGA
TCGGGATGGCGGCTGCAGGGAGGACTTCGAGGACTACCCAGCCTCCTGCCCCAGCCTCCCAGACCAGAATAATATATGGA
TTCGAGACCATGAGGATAGCGGGTCTGTACATTTGGGGACCCCAGGTCCATCCAGCGGGGGGCTGGCCTCCCAGAGTGGG
GACAACTCCAGTGACCAAGGAGTCGGGCTGGACACCAGCGTGGCCTCTCCCAGTTCTGGTGGAGAAGATGAGGACTTGGA
CCAGGAGCCACGGCGAAACAAGAAGAGGGGGATCTTCCCCAAGGTGGCCACCAACATCATGCGAGCCTGGTTGTTCCAGC
ACCTCTCACACCCGTACCCCTCGGAGGAGCAGAAGAAACAGCTGGCGCAGGACACGGGGCTTACCATCCTGCAAGTCAAC
AACTGGTTCATTAATGCCCGGAGACGCATCGTGCAACCTATGATCGATCAATCCAACCGCACAGGGCAGGGTGCAGCCTT
CAGCCCAGAGGGCCAGCCCATCGGGGGCTATACCGAGACAGAGCCACACGTGGCCTTCCGGGCTCCAGCATCAGTGGGGA
TGAGTTTGAACTCGGAAGGAGAATGGCATTATCTA

ORF - retro_hsap_1718 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.71 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMARRYDELPHYPGIVDGPAALASFPETVPAVPGPYGPHRPPQPLPPGLDSDGLKREKDEIYGHPLFPLLA
MA.RYDELPHYPGI.DGPAALA.FPE.VPA.PGPYGPHRPPQPLPPGLDSDGLKR.KDEIYGHPLFP.LA
RetrocopyMAQRYDELPHYPGIADGPAALAGFPEAVPAAPGPYGPHRPPQPLPPGLDSDGLKRDKDEIYGHPLFPVLA
ParentalLVFEKCELATCSPRDGAGAGLGTPP-GGDVCSSDSFNEDIAAFAKQVRSERPLFSSNPELDNLMIQAIQV
LVFEKCELATCSPRDGAGAGLGTPP.GGDVCSSDSFNED..AFAKQVRSERP.FSSNPELDNLMIQAIQV
RetrocopyLVFEKCELATCSPRDGAGAGLGTPP>GGDVCSSDSFNEDNTAFAKQVRSERPFFSSNPELDNLMIQAIQV
ParentalLRFHLLELEKGKMPIDLVIEDRDGGCREDFEDYPASCPSLPDQNNMWIRDHEDSGSVHLGTPGPSSGGLA
LRFHLLELEKGKMPIDLVIEDRDGGCREDFEDYPASCPSLPDQNN.WIRDHEDSGSVHLGTPGPSSGGLA
RetrocopyLRFHLLELEKGKMPIDLVIEDRDGGCREDFEDYPASCPSLPDQNNIWIRDHEDSGSVHLGTPGPSSGGLA
ParentalSQSGDNSSDQGDGLDTSVASPSSGGEDEDLDQERRRNKKRGIFPKVATNIMRAWLFQHLSHPYPSEEQKK
SQSGDNSSDQG.GLDTSVASPSSGGEDEDLDQE.RRNKKRGIFPKVATNIMRAWLFQHLSHPYPSEEQKK
RetrocopySQSGDNSSDQGVGLDTSVASPSSGGEDEDLDQEPRRNKKRGIFPKVATNIMRAWLFQHLSHPYPSEEQKK
ParentalQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRTGQGAAFSPEGQPIGGYTETQPHVAVRPPGSVGMSL
QLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRTGQGAAFSPEGQPIGGYTET.PHVA.R.P.SVGMSL
RetrocopyQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNRTGQGAAFSPEGQPIGGYTETEPHVAFRAPASVGMSL
ParentalNLEGEWHYL
N.EGEWHYL
RetrocopyNSEGEWHYL

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 7 .59 RPM 9 .50 RPM
bodymap2_adrenal 3 .68 RPM 8 .66 RPM
bodymap2_brain 0 .70 RPM 16 .22 RPM
bodymap2_breast 3 .05 RPM 4 .03 RPM
bodymap2_colon 3 .64 RPM 7 .37 RPM
bodymap2_heart 1 .86 RPM 1 .57 RPM
bodymap2_kidney 2 .89 RPM 3 .41 RPM
bodymap2_liver 0 .32 RPM 0 .40 RPM
bodymap2_lung 4 .22 RPM 2 .73 RPM
bodymap2_lymph_node 1 .86 RPM 6 .40 RPM
bodymap2_ovary 3 .35 RPM 19 .64 RPM
bodymap2_prostate 4 .59 RPM 9 .18 RPM
bodymap2_skeletal_muscle 1 .40 RPM 0 .33 RPM
bodymap2_testis 2 .60 RPM 8 .09 RPM
bodymap2_thyroid 8 .53 RPM 2 .43 RPM
bodymap2_white_blood_cells 0 .12 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_1718 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 17:15689312..15689742

EST - click to see more details

1 EST(s) were mapped to retro_hsap_1718 retrocopy
EST ID Start End Identity Match Mis-match Score
HY092504 15689896 15690330 97.9 415 8 405

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_55731687 libraries386 libraries655 libraries90 libraries11 libraries

The graphical summary, for retro_hsap_1718 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_1718 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1718 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 ) > 0 RPM = 0.03 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 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 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 .03 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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