RetrogeneDB ID:

retro_hsap_2901

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:191670144..191670558(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000237653
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PERP
Ensembl ID:ENSG00000112378
Aliases:PERP, KCP1, KRTCAP1, PIGPC1, THW, dJ496H19.1
Description:PERP, TP53 apoptosis effector [Source:HGNC Symbol;Acc:17637]


Retrocopy-Parental alignment summary:






>retro_hsap_2901
CAGGATGGCGGCAGCAGGCCCCCCGCAGGATGGCTGCCAGAGCCTCGTGGAGTACGTAGGAGGAAGAGCAGCCGCTGCCA
TGCTCTTCTGTGGCTGTATCATGCTGGTGACCTGTTTCATCCTCACCTTCTTTGCCCTCTGTGCACCCCTGACGCTAGTC
CTCCTAAGAGTGAGTTGGAGGCCTCCCTACCCTGGCTGCTGTGTTGCAGGTCATCTCCCTGGTAATCAACCCTGTGAAGT
ATACCCATACCTTCAATCTTCATGCCAACCCCGCCGTCACATCACATGTGTCACTGGACCCGTGGCTTCCCGTGGGTGGC
CACAATTATCCTGATTGGCTGTCCTTTCTCCTTCTGCTGCGGCCCGAAGGGCGAAGACAACCTCCTGGGAGGCGCCAAGC
CCAGGTACTTCCAC

ORF - retro_hsap_2901 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.57 %
Parental protein coverage: 70.98 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalEGGGS-GSYEEGCQSLMEYAWGRAAAAMLFCGFIILVICFILSFFALCGPQMLVFLRV-IGGLLALAAVF
..GGS.G....GCQSL.EY..GRAAAAMLFCG.I.LV.CFIL.FFALC.P..LV.LRV..GGL..LAAV.
RetrocopyQDGGS>GPPQDGCQSLVEYVGGRAAAAMLFCGCIMLVTCFILTFFALCAPLTLVLLRV>VGGLPTLAAVL
ParentalQIISLVIYPVKYTQTFTLHANPAVT-YIYNWAYGFGWAATIILIGCAFFFCCLPNYEDDLLGNAKPRYFY
Q.ISLVI.PVKYT.TF.LHANPAVT.....W..GF.W.ATIILIGC.F.FCC.P..ED.LLG.AKPRYF.
RetrocopyQVISLVINPVKYTHTFNLHANPAVT>HMCHWTRGFPWVATIILIGCPFSFCCGPKGEDNLLGGAKPRYFH

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 96 .33 RPM
bodymap2_adrenal 0 .00 RPM 24 .09 RPM
bodymap2_brain 0 .00 RPM 12 .10 RPM
bodymap2_breast 0 .00 RPM 158 .76 RPM
bodymap2_colon 0 .00 RPM 170 .62 RPM
bodymap2_heart 0 .00 RPM 101 .81 RPM
bodymap2_kidney 0 .00 RPM 66 .72 RPM
bodymap2_liver 0 .00 RPM 156 .06 RPM
bodymap2_lung 0 .00 RPM 124 .72 RPM
bodymap2_lymph_node 0 .00 RPM 35 .41 RPM
bodymap2_ovary 0 .00 RPM 46 .17 RPM
bodymap2_prostate 0 .00 RPM 221 .02 RPM
bodymap2_skeletal_muscle 0 .00 RPM 11 .73 RPM
bodymap2_testis 0 .00 RPM 41 .01 RPM
bodymap2_thyroid 0 .00 RPM 93 .72 RPM
bodymap2_white_blood_cells 0 .00 RPM 7 .19 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2901 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2901 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2901 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2901 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2901 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_2400
Parental genes homology:
Parental genes homology involve 12 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000200971 retrocopy
retro_btau_165,
Callithrix jacchus ENSCJAG000000190241 retrocopy
retro_cjac_3992,
Homo sapiens ENSG00000112378 2 retrocopies
retro_hsap_1523, retro_hsap_2901 ,
Gorilla gorilla ENSGGOG000000283401 retrocopy
retro_ggor_1165,
Macropus eugenii ENSMEUG000000048721 retrocopy
retro_meug_845,
Microcebus murinus ENSMICG000000139791 retrocopy
retro_mmur_353,
Myotis lucifugus ENSMLUG000000014731 retrocopy
retro_mluc_2287,
Macaca mulatta ENSMMUG000000009971 retrocopy
retro_mmul_2156,
Nomascus leucogenys ENSNLEG000000149302 retrocopies
retro_nleu_1934, retro_nleu_631,
Oryctolagus cuniculus ENSOCUG000000042381 retrocopy
retro_ocun_170,
Otolemur garnettii ENSOGAG000000116691 retrocopy
retro_ogar_631,
Pongo abelii ENSPPYG000000170433 retrocopies
retro_pabe_1267, retro_pabe_2400, retro_pabe_2416,

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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