RetrogeneDB ID:

retro_hsap_620

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:105005753..105006437(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000235376
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPE
Ensembl ID:ENSG00000197713
Aliases:None
Description:ribulose-5-phosphate-3-epimerase [Source:HGNC Symbol;Acc:10293]


Retrocopy-Parental alignment summary:






>retro_hsap_620
ATGGCGTCGGGCTGCAAGATTGGCCCGTCCATCCTCAACAGCGACCTGGCCAATTTAGGGGCCAAGTGCCTCCAGATGCT
AGACTCTGGGGCCGATTATCTGCATCTGGATGTAATGGATGGGCATTTTGTTCCCAACATCACCTTTGGTCACCCTGTGG
TAGAAAGCCTTCGAAAGCAGCTAGGCCAGGACCCTTTCTTTGACATGCACATGATGGTGTCCAAGCCAGAACAGTGGGTA
AAGCCAATGGCTGTAGCAGAAGCCAATCAGTACACCTTTCATCTCGAGGCTACTGAGAACCCAGGGACTTTGATTAAAGA
CATTCGGGAGAATGGGATGAAGGTTGGCCTTGCCATCAAACCAGGAACCTCAGTTGAGTATTTGGCACCATGGGCTAATC
AAATAGATATGGCCTTGGTTATGACAGTGGAACCGGGGTTTGGAGAGCAGAAATTCATGGAAGATATGATGCCAAAGGTT
CACTGGTTGAGGACCCAGTTCCCATCTTTGGATATAGAGGGCGATGGTGGAGTAGGTTCTGACACTGTCCATAAGTGTGC
AGAGGCAGGAGCTAACATGACTGTATCTGGCAGTGCTATTATGAGGAGTGAAGACCCCAGATCTGTGATCAACCTATTAA
GAAATATTTGCTCAGAAGCTGCTCAGAAACGTTCTCTTGATCGA

ORF - retro_hsap_620 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.05 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASGCKIGPSILNSDLANLGAECLRMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMH
MASGCKIGPSILNSDLANLGA.CL.MLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMH
RetrocopyMASGCKIGPSILNSDLANLGAKCLQMLDSGADYLHLDVMDGHFVPNITFGHPVVESLRKQLGQDPFFDMH
ParentalMMVSKPEQWVKPMAVAGANQYTFHLEATENPGALIKDIRENGMKVGLAIKPGTSVEYLAPWANQIDMALV
MMVSKPEQWVKPMAVA.ANQYTFHLEATENPG.LIKDIRENGMKVGLAIKPGTSVEYLAPWANQIDMALV
RetrocopyMMVSKPEQWVKPMAVAEANQYTFHLEATENPGTLIKDIRENGMKVGLAIKPGTSVEYLAPWANQIDMALV
ParentalMTVEPGFGGQKFMEDMMPKVHWLRTQFPSLDIEVDGGVGPDTVHKCAEAGANMIVSGSAIMRSEDPRSVI
MTVEPGFG.QKFMEDMMPKVHWLRTQFPSLDIE.DGGVG.DTVHKCAEAGANM.VSGSAIMRSEDPRSVI
RetrocopyMTVEPGFGEQKFMEDMMPKVHWLRTQFPSLDIEGDGGVGSDTVHKCAEAGANMTVSGSAIMRSEDPRSVI
ParentalNLLRNVCSEAAQKRSLDR
NLLRN.CSEAAQKRSLDR
RetrocopyNLLRNICSEAAQKRSLDR

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 27 .35 RPM
bodymap2_adrenal 0 .02 RPM 17 .09 RPM
bodymap2_brain 0 .19 RPM 30 .19 RPM
bodymap2_breast 0 .00 RPM 33 .64 RPM
bodymap2_colon 0 .02 RPM 41 .49 RPM
bodymap2_heart 0 .00 RPM 12 .07 RPM
bodymap2_kidney 0 .00 RPM 43 .84 RPM
bodymap2_liver 0 .02 RPM 19 .75 RPM
bodymap2_lung 0 .00 RPM 25 .74 RPM
bodymap2_lymph_node 0 .02 RPM 32 .18 RPM
bodymap2_ovary 0 .00 RPM 39 .73 RPM
bodymap2_prostate 0 .09 RPM 52 .48 RPM
bodymap2_skeletal_muscle 0 .00 RPM 7 .77 RPM
bodymap2_testis 0 .02 RPM 41 .06 RPM
bodymap2_thyroid 0 .00 RPM 32 .43 RPM
bodymap2_white_blood_cells 0 .02 RPM 28 .63 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_620 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_620 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_620 retrocopy 5' end.

Lab - click to see more details

retro_hsap_620 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_620 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_555
Parental genes homology:
Parental genes homology involve 22 parental genes, and 58 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000049653 retrocopies
retro_amel_1327, retro_amel_1363, retro_amel_827,
Bos taurus ENSBTAG000000478062 retrocopies
retro_btau_343, retro_btau_815,
Canis familiaris ENSCAFG000000138113 retrocopies
retro_cfam_1441, retro_cfam_1596, retro_cfam_1623,
Choloepus hoffmanni ENSCHOG000000011105 retrocopies
retro_chof_1534, retro_chof_2386, retro_chof_392, retro_chof_492, retro_chof_574,
Callithrix jacchus ENSCJAG000000108222 retrocopies
retro_cjac_1199, retro_cjac_1560,
Dasypus novemcinctus ENSDNOG000000031931 retrocopy
retro_dnov_789,
Equus caballus ENSECAG000000000023 retrocopies
retro_ecab_245, retro_ecab_446, retro_ecab_562,
Homo sapiens ENSG00000197713 5 retrocopies
retro_hsap_133, retro_hsap_2553, retro_hsap_2620, retro_hsap_3330, retro_hsap_620 ,
Latimeria chalumnae ENSLACG000000028001 retrocopy
retro_lcha_21,
Microcebus murinus ENSMICG000000099534 retrocopies
retro_mmur_1380, retro_mmur_268, retro_mmur_393, retro_mmur_713,
Macaca mulatta ENSMMUG000000105132 retrocopies
retro_mmul_366, retro_mmul_618,
Monodelphis domestica ENSMODG000000158276 retrocopies
retro_mdom_1181, retro_mdom_1676, retro_mdom_449, retro_mdom_490, retro_mdom_505, retro_mdom_667,
Mustela putorius furoENSMPUG000000079482 retrocopies
retro_mputfur_1066, retro_mputfur_1280,
Nomascus leucogenys ENSNLEG000000071723 retrocopies
retro_nleu_2263, retro_nleu_448, retro_nleu_638,
Otolemur garnettii ENSOGAG000000027781 retrocopy
retro_ogar_2673,
Pongo abelii ENSPPYG000000131324 retrocopies
retro_pabe_1052, retro_pabe_1878, retro_pabe_2340, retro_pabe_555,
Pteropus vampyrus ENSPVAG000000144522 retrocopies
retro_pvam_217, retro_pvam_636,
Sus scrofa ENSSSCG000000161521 retrocopy
retro_sscr_825,
Ictidomys tridecemlineatus ENSSTOG000000103221 retrocopy
retro_itri_1750,
Tarsius syrichta ENSTSYG000000033045 retrocopies
retro_tsyr_113, retro_tsyr_1153, retro_tsyr_1663, retro_tsyr_2129, retro_tsyr_546,
Tursiops truncatus ENSTTRG000000009081 retrocopy
retro_ttru_158,
Vicugna pacos ENSVPAG000000115851 retrocopy
retro_vpac_91,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .00 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 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .03 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 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .03 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 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .03 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 .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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