RetrogeneDB ID:

retro_hsap_3500

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:100584003..100584536(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213177
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PRDX2
Ensembl ID:ENSG00000167815
Aliases:PRDX2, HEL-S-2a, NKEF-B, NKEFB, PRP, PRX2, PRXII, PTX1, TDPX1, TPX1, TSA
Description:peroxiredoxin 2 [Source:HGNC Symbol;Acc:9353]


Retrocopy-Parental alignment summary:






>retro_hsap_3500
ATGGATAGCGCTTTCAAAGAAGTGAAGCTGTAGGACTACAAAGAGAAATACGTGGTCCTCTTTTTCTACCCTCTGCACTT
CACTTTTGTGTGCCCCACGGAGATCATCGCGTTCAGCGACCATGCCGAGGACTTCCGCAAGCTGGGCTGCGAAGTGCTGG
GCATCTCAGTGGACTCTCAGTTCACCCACCTGGCTTGGATCAACAACCCCCAGAGGGAGGGAGACTTGGGCCCCCTGAAC
ATCCCCCTGCTTGCTGAGGTGGCCAGTGGCTTGTCTGAGGATTACGCCGTGCTGAAAACAGATGCGGGCATTGCCTACAG
GGGCCGCTTTATCAGTGATGGCAAGGGTGTCCTTTCCAGATCACTGTTAATGATTTGCCTGTGGGACGCTCCGTGGATGA
GGCTCTGCGGCTGGTCCAGGCCTTCCAGTACGCAGAAGAGCACGCGGAAGTTTGTCCCGCTGGCTGGAAGCCTGGCACTG
ACACGATTAAGCTCAACGTGGGTGACAGCAAGGAAAATTTATCCAAACACAAT

ORF - retro_hsap_3500 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.24 %
Parental protein coverage: 89.9 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVDGAFKEVKLSDYKGKYVVLFFYPLDFTFVCPTEIIAFSNRAEDFRKLGCEVLGVSVDSQFTHLAWINTP
.D.AFKEVKL.DYK.KYVVLFFYPL.FTFVCPTEIIAFS..AEDFRKLGCEVLG.SVDSQFTHLAWIN.P
RetrocopyMDSAFKEVKL*DYKEKYVVLFFYPLHFTFVCPTEIIAFSDHAEDFRKLGCEVLGISVDSQFTHLAWINNP
ParentalRKEGGLGPLNIPLLADVTRRLSEDYGVLKTDEGIAYRGLFIIDGKGVLR-QITVNDLPVGRSVDEALRLV
..EG.LGPLNIPLLA.V...LSEDY.VLKTD.GIAYRG.FI.DGKGVL..QITVNDLPVGRSVDEALRLV
RetrocopyQREGDLGPLNIPLLAEVASGLSEDYAVLKTDAGIAYRGRFISDGKGVLS<QITVNDLPVGRSVDEALRLV
ParentalQAFQYTDEHGEVCPAGWKPGSDTIKPNVDDSKEYFSKHN
QAFQY..EH.EVCPAGWKPG.DTIK.NV.DSKE..SKHN
RetrocopyQAFQYAEEHAEVCPAGWKPGTDTIKLNVGDSKENLSKHN

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 61 .34 RPM
bodymap2_adrenal 0 .00 RPM 72 .20 RPM
bodymap2_brain 0 .00 RPM 101 .12 RPM
bodymap2_breast 0 .00 RPM 135 .78 RPM
bodymap2_colon 0 .00 RPM 64 .45 RPM
bodymap2_heart 0 .00 RPM 129 .69 RPM
bodymap2_kidney 0 .00 RPM 89 .28 RPM
bodymap2_liver 0 .00 RPM 69 .77 RPM
bodymap2_lung 0 .00 RPM 46 .91 RPM
bodymap2_lymph_node 0 .00 RPM 59 .66 RPM
bodymap2_ovary 0 .00 RPM 103 .79 RPM
bodymap2_prostate 0 .00 RPM 85 .16 RPM
bodymap2_skeletal_muscle 0 .00 RPM 83 .63 RPM
bodymap2_testis 0 .00 RPM 57 .92 RPM
bodymap2_thyroid 0 .00 RPM 86 .42 RPM
bodymap2_white_blood_cells 0 .00 RPM 25 .79 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3500 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3500 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3500 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3500 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3500 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2372
Parental genes homology:
Parental genes homology involve 24 parental genes, and 48 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123073 retrocopies
retro_amel_1188, retro_amel_1710, retro_amel_55,
Canis familiaris ENSCAFG000000171633 retrocopies
retro_cfam_1603, retro_cfam_1624, retro_cfam_1739,
Ciona intestinalis ENSCING000000030021 retrocopy
retro_cint_8,
Callithrix jacchus ENSCJAG000000048824 retrocopies
retro_cjac_1269, retro_cjac_1795, retro_cjac_2356, retro_cjac_2392,
Dipodomys ordii ENSDORG000000090051 retrocopy
retro_dord_176,
Felis catus ENSFCAG000000004731 retrocopy
retro_fcat_1755,
Homo sapiens ENSG000001174501 retrocopy
retro_hsap_4230,
Homo sapiens ENSG000001231311 retrocopy
retro_hsap_3165,
Homo sapiens ENSG000001656723 retrocopies
retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Homo sapiens ENSG00000167815 3 retrocopies
retro_hsap_1184, retro_hsap_3278, retro_hsap_3500 ,
Gorilla gorilla ENSGGOG000000250893 retrocopies
retro_ggor_2366, retro_ggor_2833, retro_ggor_923,
Macaca mulatta ENSMMUG000000056892 retrocopies
retro_mmul_1780, retro_mmul_2061,
Monodelphis domestica ENSMODG000000069781 retrocopy
retro_mdom_1770,
Mustela putorius furoENSMPUG000000045912 retrocopies
retro_mputfur_28, retro_mputfur_660,
Mus musculus ENSMUSG000000051612 retrocopies
retro_mmus_2403, retro_mmus_472,
Nomascus leucogenys ENSNLEG000000128002 retrocopies
retro_nleu_2110, retro_nleu_2883,
Otolemur garnettii ENSOGAG000000249982 retrocopies
retro_ogar_1993, retro_ogar_244,
Pongo abelii ENSPPYG000000096073 retrocopies
retro_pabe_2711, retro_pabe_2892, retro_pabe_988,
Pan troglodytes ENSPTRG000000105413 retrocopies
retro_ptro_2217, retro_ptro_2372, retro_ptro_812,
Rattus norvegicus ENSRNOG000000035202 retrocopies
retro_rnor_2288, retro_rnor_497,
Sorex araneus ENSSARG000000001461 retrocopy
retro_sara_96,
Sarcophilus harrisii ENSSHAG000000155961 retrocopy
retro_shar_305,
Sus scrofa ENSSSCG000000137362 retrocopies
retro_sscr_155, retro_sscr_962,
Ictidomys tridecemlineatus ENSSTOG000000258621 retrocopy
retro_itri_842,

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 = 0.03 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 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 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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