RetrogeneDB ID:

retro_hsap_4765

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:139173901..139174720(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230707
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:C16orf72
Ensembl ID:ENSG00000182831
Aliases:None
Description:chromosome 16 open reading frame 72 [Source:HGNC Symbol;Acc:30103]


Retrocopy-Parental alignment summary:






>retro_hsap_4765
ATGGAGGAGCAGCAGAAGGAGGGCGAGGCCGAGGTCGCGGAGCACTGGTTTTCCAAGTGGGAGCGCCAGTGCCTGGCTGA
GGCCGAGCAGGAGGAGCAGCTGCCCCCCGAGCTGCAGGAGGAGGCGGCTGCAGAGTTGGCAGGGCTCAAGAGCGAGAAGC
AGAAGCTGTGGCACCTCTTCCAGATCTCGGCCACCGCCGTTGCTCAGCTTTACAAGGATTCTGGGTGCCAACAGCAAGGA
CTTTCCATGTGGGACCCCTTCCAGAATGCGGCCATGGCCGTGACCAGCCTCTACAAAGAGAGCGGGGATGCCCACCAACG
AAGTTTTGACTTGGGTGTCCAGGTTGGCCACCAGCGTCGCATCAAAGATGTGCTGGAGTGGGTGAAAAAGGGCCGGAGCA
CCATTCGTCGCGAAGACTTGATTAGCTTCCTGTGTGGCAAAGTGCCCCCCGCTCCTCCTCCACCTCGCACTCCTAGGACA
CCCCCGAAGCCACCCACTGGGGTCACCAGCCAGGCTGTGGCAACTGAGTCCAGCTCATCGGTGGACGTCGACCTGCAGCC
CTTCCAGGAGGCGATCGCCCTGCATGGCCTCAGTGGTGCTATGGCCGGCATCAGCATGCGATCGGGCGACTCGCCTCAAG
ACAGCGGTGTCGCCAGCAGTGGGCGCCGAAAAACTAGCTTCTTGGAGGACGACTTGAATCCCTTCGACTCAGAGGAACTG
GCCCTCCACCTGGACAGTGGGGGGATCCGCAAGCGCACCTCGGCCCAATGCAGTGATGGCATCACAGACTCCCCAATCCA
AAAGCGCAACCGAATGGTC

ORF - retro_hsap_4765 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.5 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMEERKEEGEAEIQEHGPEHWFSKWERQCLAEAEQDEQLPPELQEEAAAA-AQPEHKQQKLWHLFQNSATA
MEE...EGEAE......EHWFSKWERQCLAEAEQ.EQLPPELQEEAAA..A......QKLWHLFQ.SATA
RetrocopyMEEQQKEGEAEVA----EHWFSKWERQCLAEAEQEEQLPPELQEEAAAELAGLKSEKQKLWHLFQISATA
ParentalVAQLYKDRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIR
VAQLYKD..CQQ.GLS.W.PFQNAA.AVT.LYKES.D.HQRSFD.G.Q.G.QRR.KDVL.WVKK.R.TIR
RetrocopyVAQLYKDSGCQQQGLSMWDPFQNAAMAVTSLYKESGDAHQRSFDLGVQVGHQRRIKDVLEWVKKGRSTIR
ParentalREDLISFLCGKVPP----PRNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHGLSGAMASISV
REDLISFLCGKVPP....PR..R.PP.........A..TE.SSSV..DLQPF.EAIALHGLSGAMA.IS.
RetrocopyREDLISFLCGKVPPAPPPPRTPRTPPKPPTGVTSQAVATESSSSVDVDLQPFQEAIALHGLSGAMAGISM
ParentalRSSTPGSPTHVSSGSNASRRRNGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRMI
RS...G.....S......RR.......DLN.F.SEE.ALHLD.GG.RKRTSAQC.D.ITDSP..KRNRM.
RetrocopyRS---GDSPQDSGVASSGRRKTSFLEDDLNPFDSEELALHLDSGGIRKRTSAQCSDGITDSPIQKRNRMV

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 .02 RPM 58 .44 RPM
bodymap2_adrenal 0 .08 RPM 42 .49 RPM
bodymap2_brain 1 .08 RPM 45 .83 RPM
bodymap2_breast 0 .00 RPM 71 .15 RPM
bodymap2_colon 0 .02 RPM 69 .78 RPM
bodymap2_heart 0 .00 RPM 52 .72 RPM
bodymap2_kidney 0 .00 RPM 65 .02 RPM
bodymap2_liver 0 .00 RPM 33 .27 RPM
bodymap2_lung 0 .00 RPM 82 .21 RPM
bodymap2_lymph_node 0 .00 RPM 84 .42 RPM
bodymap2_ovary 0 .10 RPM 67 .76 RPM
bodymap2_prostate 0 .10 RPM 88 .83 RPM
bodymap2_skeletal_muscle 0 .00 RPM 60 .71 RPM
bodymap2_testis 0 .62 RPM 79 .79 RPM
bodymap2_thyroid 0 .11 RPM 53 .63 RPM
bodymap2_white_blood_cells 0 .00 RPM 140 .12 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4765 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4765 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4765 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4765 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4765 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3172
Gorilla gorilla retro_ggor_2968
Pongo abelii retro_pabe_163
Mus musculus retro_mmus_3460
Rattus norvegicus retro_rnor_156
Sus scrofa retro_sscr_1177
Canis familiaris retro_cfam_147
Equus caballus retro_ecab_1091
Parental genes homology:
Parental genes homology involve 17 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000107192 retrocopies
retro_amel_1715, retro_amel_88,
Canis familiaris ENSCAFG000000189811 retrocopy
retro_cfam_147,
Cavia porcellus ENSCPOG000000109251 retrocopy
retro_cpor_101,
Dasypus novemcinctus ENSDNOG000000158933 retrocopies
retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus ENSECAG000000094301 retrocopy
retro_ecab_1091,
Homo sapiens ENSG00000182831 1 retrocopy
retro_hsap_4765 ,
Gorilla gorilla ENSGGOG000000107441 retrocopy
retro_ggor_2968,
Monodelphis domestica ENSMODG000000053782 retrocopies
retro_mdom_1716, retro_mdom_299,
Mustela putorius furoENSMPUG000000147071 retrocopy
retro_mputfur_44,
Mus musculus ENSMUSG000000225071 retrocopy
retro_mmus_3460,
Nomascus leucogenys ENSNLEG000000101061 retrocopy
retro_nleu_2348,
Otolemur garnettii ENSOGAG000000039091 retrocopy
retro_ogar_74,
Pongo abelii ENSPPYG000000070881 retrocopy
retro_pabe_163,
Pan troglodytes ENSPTRG000000077511 retrocopy
retro_ptro_3172,
Rattus norvegicus ENSRNOG000000025452 retrocopies
retro_rnor_156, retro_rnor_1928,
Sus scrofa ENSSSCG000000284541 retrocopy
retro_sscr_1177,
Ictidomys tridecemlineatus ENSSTOG000000093241 retrocopy
retro_itri_137,

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 = 0.09 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 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .02 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 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .05 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 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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