RetrogeneDB ID:

retro_hsap_1535

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:22015704..22016797(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000258712
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CXADR
Ensembl ID:ENSG00000154639
Aliases:CXADR, CAR, CAR4/6, HCAR
Description:coxsackie virus and adenovirus receptor [Source:HGNC Symbol;Acc:2559]


Retrocopy-Parental alignment summary:






>retro_hsap_1535
GTGGCGCTCCTGCTGCGCTTCGTGCTCCTGTGCAGAGTCGCGGATTTCATCAGAGGTTGGAGTATCACTACTCCTGAGCA
GATGATTGAAAAAGCCAAAGGGGAAACTGCCTATCTGCCATGCAAATTTACGCTTAGTCCTGAAGACCAGGGACCACTGG
ACATCGAGTGGCTGATATCACCAGCTGATAATCAGAAGGTGGATCAAGTGATTATTTTATATTCTGGAGACAAAAATTAT
GATGACTACTATCCAGATCTGAAAGGCCGAGTACATTTTAAGAGTAATGATCTCAAATCTGGTGATGCATCAATAAATGT
AACGAATTTTCAGCTGTCAGATATTGGCACAGATCAGTGCAAAGTGAAAAGAGCTCCTGGTGTTGCAAATAGGAAGATTC
AGCTGGTAGTTCTTGGTAAGCCTTCAGGTACAAGATGTTACGTTGATGGATCAGAAGAAATTGGAAGTGACTTTAAATTA
AAATGTGAACCAAAAGAAGGTTCACTTCCATTACAGTATGAGTGGCAAAAATTGTCTGACTCACAGAAAATGCCCACTTC
ATGGTTAGCAGAAATGACTTCATCTGTTATATCTGTAAAAATGCTTCTTCTGAGTACTCTGGGACATACAGCTGTACATC
AGAAACAGAGTGGGCTCTGATCAGTGCCTGTTGCGTGTAAACGTTGTCCCTCCTTCAAATAAAGCTGGACTAATTGCAGG
AGCCATTATAGGAACTTTGCTTGCTCTAGTGCTCATTGGTCTTATCATCTTTTGCTGTCGTAAAAAGCGCAGAGAAGAAA
AATATGAAAAGGAAGTTCATCACGATATCAAGGAAGATGTGCCGCCTCCAAAGAGCCACACGTCCACTGCCAGAAGCTAC
ATAGGCAGTAATCATTCATCCCTGGGATCCATATCTCCTTCCAACATGGAAGGATATTCCAAGACTCAGTATAAACAAGT
ACCAAGTGAAGACTTTGAACGCACTCCTCAGAGTCCGACTCTCCCACCTGCTAAGGTAGCTGCCCCTAATCTAAGTCGAA
TGGGCGCGATTCCTGTGATGATTCCCGCACAGAGCAAGGATGGGTCTATAGTA

ORF - retro_hsap_1535 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.64 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMALLLCFVLLCGVVDFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
.ALLL.FVLLC.V.DF.R..SITTPE.MIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
RetrocopyVALLLRFVLLCRVADFIRGWSITTPEQMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
ParentalIILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVK
IILYSGDK.YDDYYPDLKGRVHF.SNDLKSGDASINVTN.QLSDIGT.QCKVK.APGVAN.KI.LVVL.K
RetrocopyIILYSGDKNYDDYYPDLKGRVHFKSNDLKSGDASINVTNFQLSDIGTDQCKVKRAPGVANRKIQLVVLGK
ParentalPSGARCYVDGSEEIGSDFKIKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISV-KNASSEYSGT
PSG.RCYVDGSEEIGSDFK.KCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISV.KNASSEYSGT
RetrocopyPSGTRCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVISV<KNASSEYSGT
ParentalYSCT-VRNRVGSDQCLLRLNVVPPSNKAGLIAGAIIGTLLALALIGLIIFCCRKKRREEKYEKEVHHDIR
YSCT..RNRVGSDQCLLR.NVVPPSNKAGLIAGAIIGTLLAL.LIGLIIFCCRKKRREEKYEKEVHHDI.
RetrocopyYSCT<IRNRVGSDQCLLRVNVVPPSNKAGLIAGAIIGTLLALVLIGLIIFCCRKKRREEKYEKEVHHDIK
ParentalEDVPPPKSRTSTARSYIGSNHSSLGSMSPSNMEGYSKTQYNQVPSEDFERTPQSPTLPPAKVAAPNLSRM
EDVPPPKS.TSTARSYIGSNHSSLGS.SPSNMEGYSKTQY.QVPSEDFERTPQSPTLPPAKVAAPNLSRM
RetrocopyEDVPPPKSHTSTARSYIGSNHSSLGSISPSNMEGYSKTQYKQVPSEDFERTPQSPTLPPAKVAAPNLSRM
ParentalGAIPVMIPAQSKDGSIV
GAIPVMIPAQSKDGSIV
RetrocopyGAIPVMIPAQSKDGSIV

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 0 .74 RPM
bodymap2_adrenal 0 .00 RPM 23 .70 RPM
bodymap2_brain 0 .00 RPM 57 .03 RPM
bodymap2_breast 0 .00 RPM 14 .14 RPM
bodymap2_colon 0 .00 RPM 16 .67 RPM
bodymap2_heart 0 .00 RPM 32 .93 RPM
bodymap2_kidney 0 .00 RPM 43 .47 RPM
bodymap2_liver 0 .00 RPM 31 .35 RPM
bodymap2_lung 0 .00 RPM 21 .96 RPM
bodymap2_lymph_node 0 .00 RPM 5 .24 RPM
bodymap2_ovary 0 .00 RPM 14 .65 RPM
bodymap2_prostate 0 .05 RPM 62 .23 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .92 RPM 53 .18 RPM
bodymap2_thyroid 0 .00 RPM 45 .63 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .51 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1535 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1535 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1535 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1535 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1535 has 7 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1533
Pan troglodytes retro_ptro_995
Pan troglodytes retro_ptro_801
Homo sapiens retro_hsap_1918
Pan troglodytes retro_ptro_1244
Pan troglodytes retro_ptro_1444
Pongo abelii retro_pabe_1273
Parental genes homology:
Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000129751 retrocopy
retro_dnov_990,
Homo sapiens ENSG00000154639 6 retrocopies
retro_hsap_1533, retro_hsap_1535 , retro_hsap_1918, retro_hsap_2492, retro_hsap_4322, retro_hsap_4323,
Nomascus leucogenys ENSNLEG000000020632 retrocopies
retro_nleu_138, retro_nleu_58,
Pongo abelii ENSPPYG000000112952 retrocopies
retro_pabe_1273, retro_pabe_2776,
Pan troglodytes ENSPTRG000000137954 retrocopies
retro_ptro_1244, retro_ptro_1444, retro_ptro_801, retro_ptro_995,
Sarcophilus harrisii ENSSHAG000000053091 retrocopy
retro_shar_252,

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 = 0.07 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 .04 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 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 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 .07 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 .03 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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