RetrogeneDB ID:

retro_hsap_3087

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:120314453..120316112(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000249244
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GK
Ensembl ID:ENSG00000198814
Aliases:GK, GK1, GKD
Description:glycerol kinase [Source:HGNC Symbol;Acc:4289]


Retrocopy-Parental alignment summary:






>retro_hsap_3087
ATGGCAGCCTCAAAAAAGGCAGTTTTGGGGCCATTGGTGGGGGCAGTGGACCAGGGCACCAGTTCCACGCGCTTTTTGGT
TTTCAATTCAAGAACAGCTGAACTACTTAGTCATCATCAAGTGGAAATAAAACAAGAGTTCCCAAGAGAAGGATGGGTGG
AACAGGACCCTAAGGAAATTCTACATTCTGTCTATGAGTGTATAGCGAAAACATGTGAGAAACTTGGACAGCTCAATATT
GGTATTTCCAACATAAAAGCTATTGGTGTCAGCAACCAGAGGGAAACCACTGTAGTCTGGGACAAGATAACTGGAGAGCC
TCTCTACAATGCTGTGGTGTGGCTTGAACTAAGAACACAGTCTACCGTTGAGAGTCTTAGTAAGAGAATTCCAGGAAATA
ATAACTTTGTCAAGTCCAAGACAGGCCTTCCACTTAACACTTACTTCAGTGCAGTGAAACTTCGCTGGCTCCTTGACAAT
GTGAGAAAAGTTCAAAAGGCCGTTGAAGAAAAACGAGCTCTTTTTGGGACTATTGATTCATGGCTTATTTGGAGTTTGAC
AGGAGGCGTCAATGGAGGTGTCCACTGTACAGATGTAACAAATGCAAGTAGGACTATGCTTTTCAACATTCATTCTTTGG
AATGGGATAAACAACTCTGTGAATTTTTTGGAATTCCAACGGAAATTCTTCCACATGTTCGGAGTTCTTCTGAGATCTAT
GGCCTAATGAAAGCTGGGGCCTTGGAAGGTGTGCCAATATCTGGGTGTTCAGGGGACCAGTCTGCTGCACTGGTGGGACA
AATGTGTTTCCAGATTGGACAAGCCAAAAATACGTATGGAACAGGATATTTCTTACTATGTAATACATGCCATAAGTGTG
TATTTTCTGATCATGGCCTTCTCACCACAATGGCTTACAAACTTGGCAGAGACAAACCGGTATATTATGCTTTGGAAGGT
TCTGTAGCTATAGCTGGTGCTGTTATTCGCTGGCTAAGAGACAATCTTGGAATTATAAAGACCTCAGAAGAAATTGAAAA
ACTTGCTAAAGAAGTAGGTACTTCTTATGGCAGCTACTTCGTCCCAGCATTTTCGGGGTTATATGCACCTTATTGGGAGC
CCAGCGCAAGAGGGATAATCTGTGGACTCACTCAGTTTACCAATAAATGCCATATTGCTTTTGCTGCATTAGAAGCTGTT
TGTTTCCATATTCGAGAGATTTTGGATGCCATGAATTGAGACTGTGGAATTCCACTCAGTCATTTGCAGGTTGATGGAGG
AAGGACCAGCAACAAAATTCTTATGCAGCTACAAGCAGACATTCTGTATATTCCAGTAGTGAAGCCCTTGATGCCCGAAA
CCACTGCATTGGGTGCTGCCATGGCGGCAGGGGCTGCAGAAGGAGTCGTCGTATGGAGTCTTGAACCTGAGGATTTCTCC
GCCGTCACAATGGAGCGGTTTGAACCTCAGATTAATGCTGAGGAAAGTGAAATTCGTTATTCTACATGGAAGAAAGCTGT
GATGAAGTCAATGGGTTGGGTTACAACTCAATCTCCAGAAAGTGGTGACCCTAGTGTCTTCTGTAGTCTGCCCTTGGGCT
TTTTTATAGTGAGTAGCATGGCAATGTTAATCAGAGCAAGGTACATCTCAGGTATTCCA

ORF - retro_hsap_3087 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.02 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAASKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILHSVYECIEK
MAASKKAVLGPLVGAVDQGTSSTRFLVFNS.TAELLSHHQVEIKQEFPREGWVEQDPKEILHSVYECI.K
RetrocopyMAASKKAVLGPLVGAVDQGTSSTRFLVFNSRTAELLSHHQVEIKQEFPREGWVEQDPKEILHSVYECIAK
ParentalTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKITGEPLYNAVVWLDLRTQSTVESLSKRIPGNNNFVKSK
TCEKLGQLNI.ISNIKAIGVSNQRETTVVWDKITGEPLYNAVVWL.LRTQSTVESLSKRIPGNNNFVKSK
RetrocopyTCEKLGQLNIGISNIKAIGVSNQRETTVVWDKITGEPLYNAVVWLELRTQSTVESLSKRIPGNNNFVKSK
ParentalTGLPLSTYFSAVKLRWLLDNVRKVQKAVEEKRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
TGLPL.TYFSAVKLRWLLDNVRKVQKAVEEKRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
RetrocopyTGLPLNTYFSAVKLRWLLDNVRKVQKAVEEKRALFGTIDSWLIWSLTGGVNGGVHCTDVTNASRTMLFNI
ParentalHSLEWDKQLCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQIGQAKNTYG
HSLEWDKQLCEFFGIP.EILP.VRSSSEIYGLMKAGALEGVPISGC.GDQSAALVGQMCFQIGQAKNTYG
RetrocopyHSLEWDKQLCEFFGIPTEILPHVRSSSEIYGLMKAGALEGVPISGCSGDQSAALVGQMCFQIGQAKNTYG
ParentalTGCFLLCNTGHKCVFSDHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKTSEEIEKLAK
TG.FLLCNT.HKCVFSDHGLLTT.AYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKTSEEIEKLAK
RetrocopyTGYFLLCNTCHKCVFSDHGLLTTMAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKTSEEIEKLAK
ParentalEVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
EVGTSYG.YFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCF..REILDAMN.DCGIPLS
RetrocopyEVGTSYGSYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFHIREILDAMN*DCGIPLS
ParentalHLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
HLQVDGG.TSNKILMQLQADILYIPVVKP.MPETTALGAAMAAGAAEGV.VWSLEPED.SAVTMERFEPQ
RetrocopyHLQVDGGRTSNKILMQLQADILYIPVVKPLMPETTALGAAMAAGAAEGVVVWSLEPEDFSAVTMERFEPQ
ParentalINAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSIFCSLPLGFFIVSSMVMLIGARYISGIP
INAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPS.FCSLPLGFFIVSSM.MLI.ARYISGIP
RetrocopyINAEESEIRYSTWKKAVMKSMGWVTTQSPESGDPSVFCSLPLGFFIVSSMAMLIRARYISGIP

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 4 .37 RPM
bodymap2_adrenal 0 .04 RPM 4 .46 RPM
bodymap2_brain 0 .23 RPM 9 .47 RPM
bodymap2_breast 0 .21 RPM 3 .07 RPM
bodymap2_colon 0 .21 RPM 2 .03 RPM
bodymap2_heart 0 .33 RPM 5 .48 RPM
bodymap2_kidney 0 .06 RPM 16 .75 RPM
bodymap2_liver 0 .09 RPM 45 .33 RPM
bodymap2_lung 0 .00 RPM 18 .74 RPM
bodymap2_lymph_node 0 .16 RPM 8 .90 RPM
bodymap2_ovary 0 .40 RPM 6 .25 RPM
bodymap2_prostate 0 .00 RPM 3 .41 RPM
bodymap2_skeletal_muscle 0 .29 RPM 0 .45 RPM
bodymap2_testis 2 .88 RPM 7 .47 RPM
bodymap2_thyroid 0 .26 RPM 6 .55 RPM
bodymap2_white_blood_cells 0 .20 RPM 25 .63 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3087 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3087 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_1393501666 libraries133 libraries27 libraries3 libraries0 libraries

The graphical summary, for retro_hsap_3087 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_3087 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3087 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000076333 retrocopies
retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus ENSCPOG000000032612 retrocopies
retro_cpor_11, retro_cpor_20,
Echinops telfairi ENSETEG000000082792 retrocopies
retro_etel_2000, retro_etel_247,
Felis catus ENSFCAG000000042641 retrocopy
retro_fcat_140,
Homo sapiens ENSG00000198814 4 retrocopies
retro_hsap_3087 , retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana ENSLAFG000000076321 retrocopy
retro_lafr_30,
Monodelphis domestica ENSMODG000000024171 retrocopy
retro_mdom_234,
Mus musculus ENSMUSG000000250592 retrocopies
retro_mmus_119, retro_mmus_97,
Nomascus leucogenys ENSNLEG000000101022 retrocopies
retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus ENSOCUG000000130232 retrocopies
retro_ocun_2, retro_ocun_81,
Rattus norvegicus ENSRNOG000000341162 retrocopies
retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii ENSSHAG000000064701 retrocopy
retro_shar_35,
Ictidomys tridecemlineatus ENSSTOG000000087321 retrocopy
retro_itri_1436,
Tarsius syrichta ENSTSYG000000082491 retrocopy
retro_tsyr_29,

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 = 0.45 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .11 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .18 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .32 RPM
FIN_HG00183 0 .19 RPM
FIN_HG00277 0 .33 RPM
FIN_HG00315 0 .17 RPM
FIN_HG00321 0 .18 RPM
FIN_HG00328 0 .45 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .21 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .13 RPM
GBR_HG00119 0 .31 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .11 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .19 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .08 RPM
TSI_NA20513 0 .07 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .20 RPM
TSI_NA20538 0 .37 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .21 RPM
YRI_NA19114 0 .13 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .17 RPM
YRI_NA19214 0 .07 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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