RetrogeneDB ID:

retro_hsap_704

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:82896298..82896991(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000226466
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPA2
Ensembl ID:ENSG00000117748
Aliases:RPA2, REPA2, RPA32
Description:replication protein A2, 32kDa [Source:HGNC Symbol;Acc:10290]


Retrocopy-Parental alignment summary:






>retro_hsap_704
AGGTGTCGAGCCCAGCACATTGTACCCTGTACTATATCTAAGCTGCTTTCTGCCACTTTGATTGACGAAGTGTTTAAAAT
TGGGAATGTTGAGATTTCACAGGTCACTATTGTGGGGGATCATCCAACATACAGAGAAGGCTCCAACAAATATTGTTTAC
AAAATAGATGACATGACAACTGCACCTGTGGATGTTCGCCAGTGGGTTGACACAGATGACACCAGCAGTGAAAACACTGT
CATTCCTCCAGAAAAATATGTCATTGTGGCAGGCGATTTGAGACCTCTTCAGGACAAAAAGAGCCTGGTACCCTTTAAAA
TCATGCCCCTGGAGGATATGAATGAGTTCACCGTACATATTCTGGAAGTGATCAATGTACACATGATACTAAGCAAAGCT
AACAGGCAGCCCTCAGCAGGGAGAGCACCTATCAGCAATCCAGGAATGAGTGAAGCAGGGAAATTTGGTGGGAATAACTT
CATGCCAGCAAAGGACCTACTGTGGCCCAAAACCAGGTGTTGAATTTGATTAAGCGTTGCCCAAGACCGAAAGAATTGAA
CTTTCAGGATCTCAAGAACCAGCTCAACCACATGTCTGTATCCTCAATCAAGCAAGCTGTGGATTTTCTGAGCAATGAGG
GGCACATCTATTCTTCTGTAGATGATTATCATTTTAAATCCACAGATGCAGAA

ORF - retro_hsap_704 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.27 %
Parental protein coverage: 83.09 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalRARAQHIVPCTISQLLSATLVDEVFRIGNVEISQVTIVG-IIRHAEKAPTNIVYKIDDMTAAPMDVRQWV
R.RAQHIVPCTIS.LLSATL.DEVF.IGNVEISQVTIVG.II.H.EKAPTNIVYKIDDMT.AP.DVRQWV
RetrocopyRCRAQHIVPCTISKLLSATLIDEVFKIGNVEISQVTIVG>IIQHTEKAPTNIVYKIDDMTTAPVDVRQWV
ParentalDTDDTSSENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVINAHMVLSKANSQPSA
DTDDTSSENTV.PPE.YV.VAG.LR..Q.KKSLV.FKIMPLEDMNEFT.HILEVIN.HM.LSKAN.QPSA
RetrocopyDTDDTSSENTVIPPEKYVIVAGDLRPLQDKKSLVPFKIMPLEDMNEFTVHILEVINVHMILSKANRQPSA
ParentalGRAPISNPGMSEAGNFGGNSFMPA-NGLTVAQNQVLNLIKACPRPEGLNFQDLKNQLKHMSVSSIKQAVD
GRAPISNPGMSEAG.FGGN.FMPA..G.TVAQNQVLNLIK.CPRP..LNFQDLKNQL.HMSVSSIKQAVD
RetrocopyGRAPISNPGMSEAGKFGGNNFMPA<KGPTVAQNQVLNLIKRCPRPKELNFQDLKNQLNHMSVSSIKQAVD
ParentalFLSNEGHIYSTVDDDHFKSTDAE
FLSNEGHIYS.VDD.HFKSTDAE
RetrocopyFLSNEGHIYSSVDDYHFKSTDAE

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 .77 RPM
bodymap2_adrenal 0 .00 RPM 63 .43 RPM
bodymap2_brain 0 .00 RPM 36 .94 RPM
bodymap2_breast 0 .00 RPM 50 .41 RPM
bodymap2_colon 0 .00 RPM 28 .79 RPM
bodymap2_heart 0 .00 RPM 16 .84 RPM
bodymap2_kidney 0 .00 RPM 33 .13 RPM
bodymap2_liver 0 .00 RPM 11 .17 RPM
bodymap2_lung 0 .00 RPM 23 .28 RPM
bodymap2_lymph_node 0 .00 RPM 40 .37 RPM
bodymap2_ovary 0 .00 RPM 58 .33 RPM
bodymap2_prostate 0 .00 RPM 41 .38 RPM
bodymap2_skeletal_muscle 0 .00 RPM 31 .06 RPM
bodymap2_testis 0 .00 RPM 115 .72 RPM
bodymap2_thyroid 0 .00 RPM 52 .99 RPM
bodymap2_white_blood_cells 0 .00 RPM 79 .64 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_704 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_704 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_704 retrocopy 5' end.

Lab - click to see more details

retro_hsap_704 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_704 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_599
Pongo abelii retro_pabe_523
Parental genes homology:
Parental genes homology involve 14 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000062255 retrocopies
retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus ENSCJAG000000094731 retrocopy
retro_cjac_225,
Homo sapiens ENSG00000117748 2 retrocopies
retro_hsap_704 , retro_hsap_815,
Gorilla gorilla ENSGGOG000000152872 retrocopies
retro_ggor_599, retro_ggor_668,
Loxodonta africana ENSLAFG000000143871 retrocopy
retro_lafr_519,
Macaca mulatta ENSMMUG000000181722 retrocopies
retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys ENSNLEG000000097023 retrocopies
retro_nleu_1409, retro_nleu_250, retro_nleu_2511,
Oryctolagus cuniculus ENSOCUG000000161941 retrocopy
retro_ocun_1180,
Otolemur garnettii ENSOGAG000000155832 retrocopies
retro_ogar_1838, retro_ogar_2066,
Pongo abelii ENSPPYG000000016512 retrocopies
retro_pabe_523, retro_pabe_728,
Pan troglodytes ENSPTRG000000004201 retrocopy
retro_ptro_566,
Pteropus vampyrus ENSPVAG000000014491 retrocopy
retro_pvam_166,
Ictidomys tridecemlineatus ENSSTOG000000044332 retrocopies
retro_itri_1257, retro_itri_773,
Tursiops truncatus ENSTTRG000000075071 retrocopy
retro_ttru_873,

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 ) 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 .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 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 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 .00 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 .00 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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