RetrogeneDB ID:

retro_hsap_210

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:115078615..115079584(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000236480
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PKM
Ensembl ID:ENSG00000067225
Aliases:PKM, CTHBP, HEL-S-30, OIP3, PK3, PKM2, TCB, THBP1
Description:pyruvate kinase, muscle [Source:HGNC Symbol;Acc:9021]


Retrocopy-Parental alignment summary:






>retro_hsap_210
ATGTTGAAGCCCCATAGTGAAGCCGGGACTGCCTTCATTCAGACCCAGCAGCTACATGCAGCCACGGCTGACACATTCCT
GGAGCACATGTGCCACCTGGACATTCACACACCACCCATCCCAGCCTGGAACACTGGCATCATCTGTACCATTAGCCCAG
CTTCCCAATCGGTGGAGATGTTGAAGGAGATGATTAAGTCTGGAACGAATGTGGCTTGTCTGAACTTCTCTCATGGAACT
CATGAGTACCACGTGGAGACCATCAAGAACATGTGCACAGCCACGGAAAGCTTTGCTGCTGACCCCATCCTCTACCGGCC
TGTTGCTTTGGCTCTGGATACTAAAGGACCTGAGATCCGAACTGGGCTCATCAAGGGCAGCAGCACCATGGAGGTGGGGC
TGAAGATGGGAGCCACTCTCAAAATCATGCTGGATAACACCTACATGAAAAAGTGTGACGAGAACATCCTGTGGCTGGAC
TACAAGAACATCTGCAAGGTGATGGAAGTGGGCAGCAAGATCTACGTGGATGATGGGCTTATTTCTCTCCAGGTAAAGCA
GAAAGGTGCTGACTTCCTGGTGACGGAGGTGGAAACTGGTGGTTCCTCGGGCAGCAAGAAGGGTGTGAACCTTCCTGGGG
CTGCTGTGGACTTGCCTGCTGTGTCAGAGGACATCCAGGACCTGAATTTTGGGGTCGAGCAGGATGTCGATATGGTGTTT
GCGTCGTTCATCCGCAAGGCATCTGATGTCCATGAAGTTAGGGAGGCCCTGGGAGAGAAGGGAAAGAACATCAAGACAAT
CAACACAATCGAGAATCATGTGGGGGTTCAGAGGTTTGATGAAATCCTAGAGGCCAGTGATGGGATCATGGTGGCTCGTG
GTAATCCAGGCATTGAGATTCCTGCAGAGAAGGTCTTCCTTGCTCAGAGGATGATGATTGGGCGTTGCAGCTGAGCTGGG
AAGCCTATC

ORF - retro_hsap_210 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.04 %
Parental protein coverage: 66.8 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSKPHSEAGTAFIQTQQLHAAMADTFLEHMCRLDIDSPPITARNTGIICTIGPASRSVETLKEMIKSGMN
M.KPHSEAGTAFIQTQQLHAA.ADTFLEHMC.LDI..PPI.A.NTGIICTI.PAS.SVE.LKEMIKSG.N
RetrocopyMLKPHSEAGTAFIQTQQLHAATADTFLEHMCHLDIHTPPIPAWNTGIICTISPASQSVEMLKEMIKSGTN
ParentalVARLNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIRTGLIKGSGTAEVELKKGATL
VA.LNFSHGTHEYH.ETIKN..TATESFA.DPILYRPVA.ALDTKGPEIRTGLIKGS.T.EV.LK.GATL
RetrocopyVACLNFSHGTHEYHVETIKNMCTATESFAADPILYRPVALALDTKGPEIRTGLIKGSSTMEVGLKMGATL
ParentalKITLDNAYMEKCDENILWLDYKNICKVVEVGSKIYVDDGLISLQVKQKGADFLVTEVENGGSLGSKKGVN
KI.LDN.YM.KCDENILWLDYKNICKV.EVGSKIYVDDGLISLQVKQKGADFLVTEVE.GGS.GSKKGVN
RetrocopyKIMLDNTYMKKCDENILWLDYKNICKVMEVGSKIYVDDGLISLQVKQKGADFLVTEVETGGSSGSKKGVN
ParentalLPGAAVDLPAVSEKDIQDLKFGVEQDVDMVFASFIRKASDVHEVRKVLGEKGKNIKIISKIENHEGVRRF
LPGAAVDLPAVSE.DIQDL.FGVEQDVDMVFASFIRKASDVHEVR..LGEKGKNIK.I..IENH.GV.RF
RetrocopyLPGAAVDLPAVSE-DIQDLNFGVEQDVDMVFASFIRKASDVHEVREALGEKGKNIKTINTIENHVGVQRF
ParentalDEILEASDGIMVARGDLGIEIPAEKVFLAQKMMIGRCNRAGKPV
DEILEASDGIMVARG..GIEIPAEKVFLAQ.MMIGRC..AGKP.
RetrocopyDEILEASDGIMVARGNPGIEIPAEKVFLAQRMMIGRCS*AGKPI

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 253 .23 RPM
bodymap2_adrenal 0 .00 RPM 405 .32 RPM
bodymap2_brain 0 .09 RPM 596 .88 RPM
bodymap2_breast 0 .00 RPM 314 .30 RPM
bodymap2_colon 0 .00 RPM 302 .49 RPM
bodymap2_heart 0 .00 RPM 527 .14 RPM
bodymap2_kidney 0 .02 RPM 802 .38 RPM
bodymap2_liver 0 .00 RPM 21 .21 RPM
bodymap2_lung 0 .02 RPM 317 .58 RPM
bodymap2_lymph_node 0 .00 RPM 426 .80 RPM
bodymap2_ovary 0 .04 RPM 321 .21 RPM
bodymap2_prostate 0 .17 RPM 477 .51 RPM
bodymap2_skeletal_muscle 0 .15 RPM 248 .10 RPM
bodymap2_testis 0 .06 RPM 418 .05 RPM
bodymap2_thyroid 0 .13 RPM 434 .59 RPM
bodymap2_white_blood_cells 0 .00 RPM 644 .17 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_210 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_210 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_210 retrocopy 5' end.

Lab - click to see more details

retro_hsap_210 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_210 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_335
Parental genes homology:
Parental genes homology involve 11 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000135041 retrocopy
retro_chof_1430,
Callithrix jacchus ENSCJAG000000184731 retrocopy
retro_cjac_236,
Felis catus ENSFCAG000000006531 retrocopy
retro_fcat_105,
Homo sapiens ENSG00000067225 2 retrocopies
retro_hsap_210 , retro_hsap_3418,
Gorilla gorilla ENSGGOG000000050621 retrocopy
retro_ggor_281,
Macropus eugenii ENSMEUG000000045063 retrocopies
retro_meug_1482, retro_meug_2043, retro_meug_912,
Macaca mulatta ENSMMUG000000234541 retrocopy
retro_mmul_183,
Nomascus leucogenys ENSNLEG000000138693 retrocopies
retro_nleu_1859, retro_nleu_2319, retro_nleu_2716,
Pan troglodytes ENSPTRG000000072462 retrocopies
retro_ptro_2322, retro_ptro_335,
Rattus norvegicus ENSRNOG000000113296 retrocopies
retro_rnor_1120, retro_rnor_2050, retro_rnor_2253, retro_rnor_2703, retro_rnor_515, retro_rnor_830,
Sarcophilus harrisii ENSSHAG000000103001 retrocopy
retro_shar_90,

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 = 0.15 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .10 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 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .15 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017