RetrogeneDB ID:

retro_hsap_408

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:76819264..76819777(-)
Located in intron of:ENSG00000184005
Retrocopy
information
Ensembl ID:ENSG00000223905
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PRDX5
Ensembl ID:ENSG00000126432
Aliases:PRDX5, ACR1, AOEB166, B166, HEL-S-55, PLP, PMP20, PRDX6, PRXV, prx-V
Description:peroxiredoxin 5 [Source:HGNC Symbol;Acc:9355]


Retrocopy-Parental alignment summary:






>retro_hsap_408
GGGACCCACGATTTCAGCAGTAACTTTGCAGCCATGGCACCTGTCATGGTGGGAGATGCTATCCTGGCATTAGTGGTGTT
TGAAAGGGAGCCTGGGAACAAGGTGGACCTGACAGAACTATGCCAGGGAAAGAAGGGTGTGCTGTTTAGAATCCCTGGGG
CTTTCACCCCAACTGTCAAAGACCCACCTGCTTGGGTTTGGGGAGTAGGCTGGGGTTCTGAAGGTAAAGGGGGGCCAGAT
CCATGTTTAAGTGCCACTGTCTTTGTGTCTTTGTGACTGGTGAGTGGGGACAGGCCACAGTGCAGAAGGCCAAGGCCAGC
TCATGGGTGGCAGCCCTGGGGCCTCTGGGAAGGAGACTGATTTGTTACTAGATGATTTGCTGTTGCCACTCTTTGAGGAT
GAGAGCTTGAGAGGTTCTTCCTGGTGATAGAGGATGGTGTGGTGAAGGCCTTGCATGAACCTGACCATACAGGCCTCACC
TGCAGCCTGGTCCCCAGTTCTATCTCACAGCTC

ORF - retro_hsap_408 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.11 %
Parental protein coverage: 80.84 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGVRSFSRAAAAMAPIKVGDAIPAVEVFEGEPGNKVNLAELFKGKKGVLFGVPGAFT-PGCSK-THLPGFV
G...FS...AAMAP..VGDAI.A..VFE.EPGNKV.L.EL..GKKGVLF..PGAFT.P.C...THL.GF.
RetrocopyGTHDFSSNFAAMAPVMVGDAILALVVFEREPGNKVDLTELCQGKKGVLFRIPGAFT<PNCQR<THLLGFG
ParentalEQAEALKAKGVQVVACLSVNDAFVTGEWGRAHKAEGKVRLLADPTGAFGKETDLLLDDSLVSIFGNR-RL
E.A..LK.KG.Q................G..H.AEG...L.....GA.GKETDLLLDD.L...F.....L
RetrocopyE*AGVLKVKGGQIHV*VPLSLCLCDW*VGTGHSAEGQGQLMGGSPGASGKETDLLLDDLLLPLFEDE<EL
ParentalKRFSMVVQDGIVKALNVEPDGTGLTCSLAPNIISQL
.RF..V..DG.VKAL..EPD.TGLTCSL.P..ISQL
RetrocopyERFFLVIEDGVVKALH-EPDHTGLTCSLVPSSISQL

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 63 .87 RPM
bodymap2_adrenal 0 .06 RPM 61 .69 RPM
bodymap2_brain 0 .00 RPM 85 .25 RPM
bodymap2_breast 0 .00 RPM 68 .02 RPM
bodymap2_colon 0 .00 RPM 116 .44 RPM
bodymap2_heart 0 .00 RPM 75 .71 RPM
bodymap2_kidney 0 .00 RPM 142 .72 RPM
bodymap2_liver 0 .00 RPM 66 .67 RPM
bodymap2_lung 0 .00 RPM 132 .60 RPM
bodymap2_lymph_node 0 .00 RPM 65 .44 RPM
bodymap2_ovary 0 .00 RPM 104 .85 RPM
bodymap2_prostate 0 .00 RPM 92 .97 RPM
bodymap2_skeletal_muscle 0 .00 RPM 34 .41 RPM
bodymap2_testis 0 .00 RPM 92 .57 RPM
bodymap2_thyroid 0 .00 RPM 143 .16 RPM
bodymap2_white_blood_cells 0 .00 RPM 51 .48 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_408 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_408 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_408 retrocopy 5' end.

Lab - click to see more details

retro_hsap_408 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_408 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_313
Gorilla gorilla retro_ggor_404
Pongo abelii retro_pabe_310
Macaca mulatta retro_mmul_504
Callithrix jacchus retro_cjac_3013
Sus scrofa retro_sscr_888
Canis familiaris retro_cfam_1806
Equus caballus retro_ecab_844
Parental genes homology:
Parental genes homology involve 17 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000179591 retrocopy
retro_amel_753,
Bos taurus ENSBTAG000000086481 retrocopy
retro_btau_1364,
Callithrix jacchus ENSCJAG000000180141 retrocopy
retro_cjac_3013,
Dasypus novemcinctus ENSDNOG000000046471 retrocopy
retro_dnov_2664,
Equus caballus ENSECAG000000177472 retrocopies
retro_ecab_823, retro_ecab_844,
Echinops telfairi ENSETEG000000002643 retrocopies
retro_etel_1821, retro_etel_662, retro_etel_740,
Felis catus ENSFCAG000000288563 retrocopies
retro_fcat_1189, retro_fcat_410, retro_fcat_727,
Homo sapiens ENSG00000126432 1 retrocopy
retro_hsap_408 ,
Gorilla gorilla ENSGGOG000000013371 retrocopy
retro_ggor_404,
Loxodonta africana ENSLAFG000000256612 retrocopies
retro_lafr_132, retro_lafr_250,
Macaca mulatta ENSMMUG000000133971 retrocopy
retro_mmul_504,
Mustela putorius furoENSMPUG000000129071 retrocopy
retro_mputfur_1360,
Nomascus leucogenys ENSNLEG000000050032 retrocopies
retro_nleu_1007, retro_nleu_2228,
Procavia capensis ENSPCAG000000108111 retrocopy
retro_pcap_144,
Pongo abelii ENSPPYG000000031061 retrocopy
retro_pabe_310,
Pan troglodytes ENSPTRG000000038351 retrocopy
retro_ptro_313,
Sus scrofa ENSSSCG000000130302 retrocopies
retro_sscr_1041, retro_sscr_888,

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).



Copyright © RetrogeneDB 2014-2017