RetrogeneDB ID:

retro_hsap_2545

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:20804520..20806108(+)
Located in intron of:ENSG00000099910
Retrocopy
information
Ensembl ID:ENSG00000215493
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KLHL12
Ensembl ID:ENSG00000117153
Aliases:KLHL12, C3IP1, DKIR, hDKIR
Description:kelch-like family member 12 [Source:HGNC Symbol;Acc:19360]


Retrocopy-Parental alignment summary:






>retro_hsap_2545
GTAGAGCAGAAAGACTTTCCTGCCCATGAGATTGTGCTGGCTGCCTGTAGTGATTACTTCTGTGCCATGTTCACTAGTGA
CCTTTATAGAAGGGGAAACCCTATGTTGACATCCAAGGTTTGACTGCCTCTACCATGGAAATTTTATTGGACTTTGTGTA
CACGGAAACAGTACATGTGACATGGAGAATGTACAGGAACTGCTTCCTGCAGCCTGTCTGCTTCAGTTGAAAGGTGTGAA
ACAAGCCTGCTGTGAGTTCTTAGAAAGTCAGTTGGACCCTTCTAATTGCCTGGGTATTAGGGATTTTGCTGAAACCCACA
ATTGTGTTGACCTGACACAAGCAGCTGAGGTTTTTAGCCAGAAGAATTTTCCTGAAGTGGTACAGCATGAAGAGTTCATT
CTTCTGAGGCAAGGAGAGGTGGAAAAGCTAATCAAGTGCGATGAAATTCAGGTGGATCCTGAAGAACCAGTCTTTGAGGC
TGTCATCAGTTGGGTGAAGCATGCCAAGAAAGAGCAGAAAGACTCCTTGCCCAGCCTGCTACAGTATATGCAGATGCCCC
TGCTAACCCTCAGGTATATCACAGATGTAATAGATGCTGAGCCTTTCATCCACTATGGTTTACAATGCAGGGATCTGGTT
GATGAAGCAAAGAAGTTTCATCTGAGGCCTGAACTTCAGAGTCAGATGCAGGGACCCAGGACAAGGGCTCGCCTAGGAGC
CAATGAAGTGCTTTTGGTGGCTGGGGGCTTCGGAAGCCAGCAGTCTCCCATCGATGCAGTAGAGAAATATGACCCCAAGA
CTCAGGAGTGGAGCTTTTTGCCAAGCATCACTTGTAAGAGATGTTATGTGGCCTCAGTGTCCCTACATGACCAGATCTAC
GTCATTGGTGGCTGTGATGGTCGTTCCAGCCTTAGTTCAGTGGAATGTCTAGACTACACAGCAGATGAGGATGGGGTCTG
GTATTCTGTGGCCCCTATGAATGTCTGATGAGGTCTTGCTGGAGCCACCACCCTGGGAGATTTGATCTATGTCTCTGGAG
GCTTTGATGGAAGCAGGCGTCACACCAGTATGGAGCGGTATGATCCAAACATTGACCAGAGGAGCATGCTGGGAGATATG
CAGACAGCCCGGGAAGGTGCCGGACTCGTAGTGGCCAGTGGAGTGATCCACTGTCTAGGAGGATATGACGGCTTGAATAT
CTTAAATTCAGTTGAGAAATATGACCCTCATACAGGACACTGGACTAATGTTACACCAATGGCCACCAAGCGTTCTGGTG
CAGGAGTAGCCCTGCTGAATGACCGTATTTATGTGGTGGGGAGATTTGATGGTACAGCCCACCTTTCTTCCGTTGAAGCA
TACAACATTCGCACTGATTCCCGGACAACTGCCACCAGTATGACCACTCCACGATGCTATGTAGGGGCCACAGTGCTTCG
GGGGAGACTCTATGCAATTGCAGGATATGAAGGTAAGTCCCTGCTAAGTAGCATTGAATGTTACAACCCTATCATCAACA
GCTGGGAAGTCGTGACATCCATGGGAACCCAGCGCTGTGATGCTGGTGTGTGTGTTCTCCACAAGAAG

ORF - retro_hsap_2545 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.54 %
Parental protein coverage: 93.31 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVEQKDFPAHRIVLAACSDYFCAMFTSELSE-KGKPYVDIQGLTASTMEILLDFVYTETVHVT-VENVQEL
VEQKDFPAH.IVLAACSDYFCAMFTS.L...KGKPYVDIQGLTASTMEILLDFVYTETVHVT..ENVQEL
RetrocopyVEQKDFPAHEIVLAACSDYFCAMFTSDLYR<KGKPYVDIQGLTASTMEILLDFVYTETVHVT<MENVQEL
ParentalLPAACLLQLKGVKQACCEFLESQLDPSNCLGIRDFAETHNCVDLMQAAEVFSQKHFPEVVQHEEFILLSQ
LPAACLLQLKGVKQACCEFLESQLDPSNCLGIRDFAETHNCVDL.QAAEVFSQK.FPEVVQHEEFILL.Q
RetrocopyLPAACLLQLKGVKQACCEFLESQLDPSNCLGIRDFAETHNCVDLTQAAEVFSQKNFPEVVQHEEFILLRQ
ParentalGEVEKLIKCDEIQVDSEEPVFEAVINWVKHAKKEREESLPNLLQYVRMPLLTPRYITDVIDAEPFIRCSL
GEVEKLIKCDEIQVD.EEPVFEAVI.WVKHAKKE...SLP.LLQY..MPLLT.RYITDVIDAEPFI...L
RetrocopyGEVEKLIKCDEIQVDPEEPVFEAVISWVKHAKKEQKDSLPSLLQYMQMPLLTLRYITDVIDAEPFIHYGL
ParentalQCRDLVDEAKKFHLRPELRSQMQGPRTRARLGANEVLLVVGGFGSQQSPIDVVEKYDPKTQEWSFLPSIT
QCRDLVDEAKKFHLRPEL.SQMQGPRTRARLGANEVLLV.GGFGSQQSPID.VEKYDPKTQEWSFLPSIT
RetrocopyQCRDLVDEAKKFHLRPELQSQMQGPRTRARLGANEVLLVAGGFGSQQSPIDAVEKYDPKTQEWSFLPSIT
ParentalRKRRYVASVSLHDRIYVIGGYDGRSRLSSVECLDYTADEDGVWYSVAPMNVRRGLAGATTLGDMIYVSGG
.KR.YVASVSLHD.IYVIGG.DGRS.LSSVECLDYTADEDGVWYSVAPMNV..GLAGATTLGD.IYVSGG
RetrocopyCKRCYVASVSLHDQIYVIGGCDGRSSLSSVECLDYTADEDGVWYSVAPMNV**GLAGATTLGDLIYVSGG
ParentalFDGSRRHTSMERYDPNIDQWSMLGDMQTAREGAGLVVASGVIYCLGGYDGLNILNSVEKYDPHTGHWTNV
FDGSRRHTSMERYDPNIDQ.SMLGDMQTAREGAGLVVASGVI.CLGGYDGLNILNSVEKYDPHTGHWTNV
RetrocopyFDGSRRHTSMERYDPNIDQRSMLGDMQTAREGAGLVVASGVIHCLGGYDGLNILNSVEKYDPHTGHWTNV
ParentalTPMATKRSGAGVALLNDHIYVVGGFDGTAHLSSVEAYNIRTDSWTTVTSMTTPRCYVGATVLRGRLYAIA
TPMATKRSGAGVALLND.IYVVG.FDGTAHLSSVEAYNIRTDS.TT.TSMTTPRCYVGATVLRGRLYAIA
RetrocopyTPMATKRSGAGVALLNDRIYVVGRFDGTAHLSSVEAYNIRTDSRTTATSMTTPRCYVGATVLRGRLYAIA
ParentalGYDGNSLLSSIECYDPIIDSWEVVTSMGTQRCDAGVCVLREK
GY.G.SLLSSIECY.PII.SWEVVTSMGTQRCDAGVCVL..K
RetrocopyGYEGKSLLSSIECYNPIINSWEVVTSMGTQRCDAGVCVLHKK

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 .56 RPM 32 .94 RPM
bodymap2_adrenal 0 .63 RPM 31 .97 RPM
bodymap2_brain 0 .35 RPM 41 .91 RPM
bodymap2_breast 0 .16 RPM 37 .49 RPM
bodymap2_colon 0 .41 RPM 25 .50 RPM
bodymap2_heart 0 .06 RPM 22 .19 RPM
bodymap2_kidney 0 .58 RPM 50 .98 RPM
bodymap2_liver 0 .11 RPM 13 .71 RPM
bodymap2_lung 0 .19 RPM 13 .01 RPM
bodymap2_lymph_node 1 .11 RPM 27 .83 RPM
bodymap2_ovary 1 .04 RPM 52 .72 RPM
bodymap2_prostate 0 .97 RPM 42 .38 RPM
bodymap2_skeletal_muscle 0 .11 RPM 13 .46 RPM
bodymap2_testis 0 .64 RPM 97 .28 RPM
bodymap2_thyroid 0 .19 RPM 42 .41 RPM
bodymap2_white_blood_cells 0 .00 RPM 42 .72 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2545 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_2545 retrocopy
EST ID Start End Identity Match Mis-match Score
HY168100 20804733 20805017 99.7 283 1 282

TSS - click to see more details

No TSS is located nearby retro_hsap_2545 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2545 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2545 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1483
Parental genes homology:
Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000062311 retrocopy
retro_cjac_2151,
Dasypus novemcinctus ENSDNOG000000104361 retrocopy
retro_dnov_2190,
Echinops telfairi ENSETEG000000078002 retrocopies
retro_etel_2103, retro_etel_723,
Homo sapiens ENSG00000117153 1 retrocopy
retro_hsap_2545 ,
Macaca mulatta ENSMMUG000000178491 retrocopy
retro_mmul_612,
Nomascus leucogenys ENSNLEG000000181031 retrocopy
retro_nleu_2795,
Otolemur garnettii ENSOGAG000000147711 retrocopy
retro_ogar_1552,
Pongo abelii ENSPPYG000000003431 retrocopy
retro_pabe_1872,
Pan troglodytes ENSPTRG000000018611 retrocopy
retro_ptro_1483,

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 = 1.51 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .15 RPM
CEU_NA11843 0 .14 RPM
CEU_NA11930 0 .26 RPM
CEU_NA12004 0 .11 RPM
CEU_NA12400 0 .35 RPM
CEU_NA12751 1 .51 RPM
CEU_NA12760 0 .63 RPM
CEU_NA12827 0 .14 RPM
CEU_NA12872 0 .33 RPM
CEU_NA12873 0 .99 RPM
FIN_HG00183 0 .49 RPM
FIN_HG00277 0 .41 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .33 RPM
FIN_HG00328 0 .40 RPM
FIN_HG00338 0 .15 RPM
FIN_HG00349 0 .17 RPM
FIN_HG00375 0 .29 RPM
FIN_HG00377 0 .23 RPM
FIN_HG00378 0 .15 RPM
GBR_HG00099 0 .23 RPM
GBR_HG00111 0 .19 RPM
GBR_HG00114 0 .18 RPM
GBR_HG00119 0 .48 RPM
GBR_HG00131 0 .20 RPM
GBR_HG00133 0 .29 RPM
GBR_HG00134 0 .57 RPM
GBR_HG00137 0 .33 RPM
GBR_HG00142 0 .78 RPM
GBR_HG00143 0 .22 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .70 RPM
TSI_NA20518 0 .28 RPM
TSI_NA20532 0 .85 RPM
TSI_NA20538 0 .41 RPM
TSI_NA20756 0 .03 RPM
TSI_NA20765 0 .39 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .29 RPM
TSI_NA20798 0 .28 RPM
YRI_NA18870 0 .78 RPM
YRI_NA18907 0 .31 RPM
YRI_NA18916 0 .57 RPM
YRI_NA19093 0 .26 RPM
YRI_NA19099 0 .53 RPM
YRI_NA19114 0 .47 RPM
YRI_NA19118 0 .44 RPM
YRI_NA19213 0 .41 RPM
YRI_NA19214 0 .39 RPM
YRI_NA19223 0 .70 RPM

Indel association:

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



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