RetrogeneDB ID:

retro_hsap_2288

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:85568403..85568961(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000270532
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PEBP1
Ensembl ID:ENSG00000089220
Aliases:PEBP1, HCNP, HCNPpp, HEL-210, HEL-S-34, PBP, PEBP, PEBP-1, RKIP
Description:phosphatidylethanolamine binding protein 1 [Source:HGNC Symbol;Acc:8630]


Retrocopy-Parental alignment summary:






>retro_hsap_2288
ATGCCGGTGGACCTCAGCAAGTGGTCCGGGCCCTTGAGCCTGCGAGAAATGGACGAGCGGTCACAGCACCTGCTGCATGT
CACCTACGCCCGGGCGGTGGTGGACGAGCTGGGCAAAGTGCTGACGCCCACCCAGGTTAAGAATAGACCCACCAGCATTT
AGTGGGATGGTCTTGATTCAGGGAAGCTCTACACCTTGGTCCTGACAGACCCTGATGCTCCCAGCAGGAAGGATCCCAAA
TACAGAGAATGGCATCATTTCCTGGTGGTCAACATGAAGGGCAATGACATCAGCAGTGACACACTCCTCTCCGATTATGT
GGGCTCGGGGCCTCCCAAGGGCACAGGTCTCCACCGCTATGTCTGGCTGGTTTATGAGCAGGACAGGCCACTAAAGTGTG
ACGAGCCCATCCTCAGCAACCGATCTGGAGACCACCGTGGCAAATTTGAGGTGGTGTCCTTCCGTAAAAAGTACGAGCTC
GGGGCCCCGGTGGCTGGCACGTGTTACCAGGCTGAGTGGGACGACTATGTGCCCAAACTGTACGAGCAACTCTCTGGG

ORF - retro_hsap_2288 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.01 %
Parental protein coverage: 99.47 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMPVDLSKWSGPLSLQEVDEQPQHPLHVTYAGAAVDELGKVLTPTQVKNRPTSISWDGLDSGKLYTLVLTD
MPVDLSKWSGPLSL.E.DE..QH.LHVTYA.A.VDELGKVLTPTQVKNRPTSI.WDGLDSGKLYTLVLTD
RetrocopyMPVDLSKWSGPLSLREMDERSQHLLHVTYARAVVDELGKVLTPTQVKNRPTSI*WDGLDSGKLYTLVLTD
ParentalPDAPSRKDPKYREWHHFLVVNMKGNDISSGTVLSDYVGSGPPKGTGLHRYVWLVYEQDRPLKCDEPILSN
PDAPSRKDPKYREWHHFLVVNMKGNDISS.T.LSDYVGSGPPKGTGLHRYVWLVYEQDRPLKCDEPILSN
RetrocopyPDAPSRKDPKYREWHHFLVVNMKGNDISSDTLLSDYVGSGPPKGTGLHRYVWLVYEQDRPLKCDEPILSN
ParentalRSGDHRGKFKVASFRKKYELRAPVAGTCYQAEWDDYVPKLYEQLSG
RSGDHRGKF.V.SFRKKYEL.APVAGTCYQAEWDDYVPKLYEQLSG
RetrocopyRSGDHRGKFEVVSFRKKYELGAPVAGTCYQAEWDDYVPKLYEQLSG

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 .04 RPM 127 .06 RPM
bodymap2_adrenal 0 .00 RPM 163 .94 RPM
bodymap2_brain 0 .02 RPM 525 .97 RPM
bodymap2_breast 0 .14 RPM 250 .72 RPM
bodymap2_colon 0 .00 RPM 201 .96 RPM
bodymap2_heart 0 .00 RPM 253 .73 RPM
bodymap2_kidney 0 .00 RPM 510 .56 RPM
bodymap2_liver 0 .00 RPM 985 .00 RPM
bodymap2_lung 0 .04 RPM 176 .00 RPM
bodymap2_lymph_node 0 .09 RPM 132 .76 RPM
bodymap2_ovary 0 .08 RPM 223 .32 RPM
bodymap2_prostate 0 .05 RPM 313 .46 RPM
bodymap2_skeletal_muscle 0 .04 RPM 154 .32 RPM
bodymap2_testis 0 .00 RPM 215 .40 RPM
bodymap2_thyroid 0 .00 RPM 550 .25 RPM
bodymap2_white_blood_cells 0 .00 RPM 86 .27 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2288 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CUP POLR2A 2:85568798..85569114
ENCFF002CUP POLR2A 2:85569380..85569696

EST - click to see more details

No EST(s) were mapped for retro_hsap_2288 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1256631035 libraries678 libraries112 libraries3 libraries1 library

The graphical summary, for retro_hsap_2288 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1829 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_hsap_2288 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2288 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1621
Gorilla gorilla retro_ggor_1701
Parental genes homology:
Parental genes homology involve 20 parental genes, and 51 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161432 retrocopies
retro_amel_1355, retro_amel_754,
Bos taurus ENSBTAG000000181152 retrocopies
retro_btau_1183, retro_btau_705,
Canis familiaris ENSCAFG000000099101 retrocopy
retro_cfam_526,
Callithrix jacchus ENSCJAG000000093142 retrocopies
retro_cjac_1410, retro_cjac_818,
Erinaceus europaeus ENSEEUG000000036891 retrocopy
retro_eeur_292,
Felis catus ENSFCAG000000022773 retrocopies
retro_fcat_1317, retro_fcat_1360, retro_fcat_299,
Homo sapiens ENSG00000089220 3 retrocopies
retro_hsap_1456, retro_hsap_2288 , retro_hsap_492,
Gorilla gorilla ENSGGOG000000132813 retrocopies
retro_ggor_1121, retro_ggor_1701, retro_ggor_461,
Myotis lucifugus ENSMLUG000000022597 retrocopies
retro_mluc_103, retro_mluc_1612, retro_mluc_1742, retro_mluc_2357, retro_mluc_2373, retro_mluc_984, retro_mluc_998,
Macaca mulatta ENSMMUG000000050984 retrocopies
retro_mmul_1621, retro_mmul_2272, retro_mmul_328, retro_mmul_442,
Mustela putorius furoENSMPUG000000028613 retrocopies
retro_mputfur_1228, retro_mputfur_1361, retro_mputfur_223,
Mus musculus ENSMUSG000000329594 retrocopies
retro_mmus_138, retro_mmus_1857, retro_mmus_2314, retro_mmus_542,
Oryctolagus cuniculus ENSOCUG000000083952 retrocopies
retro_ocun_1329, retro_ocun_1900,
Otolemur garnettii ENSOGAG000000017401 retrocopy
retro_ogar_2750,
Pongo abelii ENSPPYG000000050112 retrocopies
retro_pabe_1202, retro_pabe_241,
Pan troglodytes ENSPTRG000000055123 retrocopies
retro_ptro_1621, retro_ptro_371, retro_ptro_992,
Rattus norvegicus ENSRNOG000000011363 retrocopies
retro_rnor_1223, retro_rnor_46, retro_rnor_541,
Ictidomys tridecemlineatus ENSSTOG000000040852 retrocopies
retro_itri_1603, retro_itri_961,
Tupaia belangeri ENSTBEG000000001772 retrocopies
retro_tbel_272, retro_tbel_2728,
Tursiops truncatus ENSTTRG000000006581 retrocopy
retro_ttru_1164,

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 = 0.2 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .09 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .07 RPM
CEU_NA12760 0 .13 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .05 RPM
CEU_NA12873 0 .06 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .04 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .03 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .20 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .05 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .06 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .09 RPM
TSI_NA20756 0 .06 RPM
TSI_NA20765 0 .08 RPM
TSI_NA20771 0 .03 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .08 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .04 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).



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