RetrogeneDB ID:

retro_hsap_3

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:9:104356690..104357212(-)
Located in intron of:ENSG00000198785
Retrocopy
information
Ensembl ID:ENSG00000188386
Aliases:PPP3R2, PPP3RL
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:PPP3R1
Ensembl ID:ENSG00000221823
Aliases:PPP3R1, CALNB1, CNB, CNB1
Description:protein phosphatase 3, regulatory subunit B, alpha [Source:HGNC Symbol;Acc:9317]


Retrocopy-Parental alignment summary:






>retro_hsap_3
ATGTCCACAATGGGAAACGAGGCCAGTTACCCGGCGGAGATGTGCTCCCACTTTGACAATGATGAAATTAAAAGGCTGGG
CAGGAGGTTTAAGAAGTTGGACTTGGACAAATCAGGGTCTCTGAGCGTGGAGGAGTTCATGTCCCTGCCGGAGCTGCGCC
ACAACCCGTTGGTGCGGCGAGTGATCGACGTCTTCGACACCGACGGTGATGGAGAAGTGGACTTCAAGGAATTCATCCTG
GGGACCTCCCAGTTCAGCGTCAAGGGCGACGAGGAGCAGAAGTTGAGGTTTGCGTTCAGCATTTACGACATGGATAAAGA
TGGCTACATTTCCAACGGGGAGCTCTTCCAGGTGCTGAAGATGATGGTGGGCAACAACCTGACGGACTGGCAGCTCCAGC
AGCTGGTCGACAAAACCATCATCATCCTGGACAAGGATGGCGATGGGAAGATATCCTTTGAGGAATTCAGTGCTGTGGTC
AGAGACCTGGAGATCCACAAGAAGCTGGTCCTCATCGTATGA

ORF - retro_hsap_3 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.71 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEV
MGNEASYP.EMCSHFD.DEIKRLG.RFKKLDLD.SGSLSVEEFMSLPEL..NPLV.RVID.FDTDG.GEV
RetrocopyMGNEASYPAEMCSHFDNDEIKRLGRRFKKLDLDKSGSLSVEEFMSLPELRHNPLVRRVIDVFDTDGDGEV
ParentalDFKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINA
DFKEFI.G.SQFSVKGD.EQKLRFAF.IYDMDKDGYISNGELFQVLKMMVGNNL.D.QLQQ.VDKTII..
RetrocopyDFKEFILGTSQFSVKGDEEQKLRFAFSIYDMDKDGYISNGELFQVLKMMVGNNLTDWQLQQLVDKTIIIL
ParentalDKDGDGRISFEEFCAVVGGLDIHKKMVVDV
DKDGDG.ISFEEF.AVV..L.IHKK.V..V
RetrocopyDKDGDGKISFEEFSAVVRDLEIHKKLVLIV

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 147 .51 RPM
bodymap2_adrenal 0 .00 RPM 93 .20 RPM
bodymap2_brain 0 .00 RPM 534 .76 RPM
bodymap2_breast 0 .00 RPM 132 .14 RPM
bodymap2_colon 0 .00 RPM 99 .42 RPM
bodymap2_heart 0 .00 RPM 42 .85 RPM
bodymap2_kidney 0 .00 RPM 72 .84 RPM
bodymap2_liver 0 .00 RPM 44 .78 RPM
bodymap2_lung 0 .00 RPM 113 .75 RPM
bodymap2_lymph_node 0 .00 RPM 94 .62 RPM
bodymap2_ovary 0 .00 RPM 128 .29 RPM
bodymap2_prostate 0 .00 RPM 104 .68 RPM
bodymap2_skeletal_muscle 0 .00 RPM 92 .47 RPM
bodymap2_testis 55 .94 RPM 118 .34 RPM
bodymap2_thyroid 0 .00 RPM 85 .83 RPM
bodymap2_white_blood_cells 0 .00 RPM 216 .55 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3 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_1880161815 libraries10 libraries1 library0 libraries3 libraries
TSS #2 TSS_1880171824 libraries1 library1 library1 library2 libraries
TSS #3 TSS_1880181824 libraries2 libraries3 libraries0 libraries0 libraries

The graphical summary, for retro_hsap_3 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_3 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3 has 7 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2909
Macaca mulatta retro_mmul_1141
Callithrix jacchus retro_cjac_624
Oryctolagus cuniculus retro_ocun_272
Bos taurus retro_btau_1660
Sus scrofa retro_sscr_86
Equus caballus retro_ecab_651
Parental genes homology:
Parental genes homology involve 22 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000106191 retrocopy
retro_btau_1660,
Choloepus hoffmanni ENSCHOG000000028931 retrocopy
retro_chof_2602,
Callithrix jacchus ENSCJAG000000064981 retrocopy
retro_cjac_624,
Dipodomys ordii ENSDORG000000197601 retrocopy
retro_dord_404,
Equus caballus ENSECAG000000096271 retrocopy
retro_ecab_651,
Felis catus ENSFCAG000000284821 retrocopy
retro_fcat_1639,
Homo sapiens ENSG000001874462 retrocopies
retro_hsap_3334, retro_hsap_3541,
Homo sapiens ENSG00000221823 1 retrocopy
retro_hsap_3 ,
Loxodonta africana ENSLAFG000000226821 retrocopy
retro_lafr_1014,
Macaca mulatta ENSMMUG000000174601 retrocopy
retro_mmul_1141,
Mustela putorius furoENSMPUG000000062501 retrocopy
retro_mputfur_537,
Nomascus leucogenys ENSNLEG000000265381 retrocopy
retro_nleu_1049,
Oryctolagus cuniculus ENSOCUG000000275621 retrocopy
retro_ocun_272,
Otolemur garnettii ENSOGAG000000348761 retrocopy
retro_ogar_1011,
Pan troglodytes ENSPTRG000000419411 retrocopy
retro_ptro_2909,
Rattus norvegicus ENSRNOG000000432101 retrocopy
retro_rnor_1932,
Sus scrofa ENSSSCG000000223621 retrocopy
retro_sscr_86,
Ictidomys tridecemlineatus ENSSTOG000000259851 retrocopy
retro_itri_1569,
Tarsius syrichta ENSTSYG000000195312 retrocopies
retro_tsyr_326, retro_tsyr_41,
Tursiops truncatus ENSTTRG000000213951 retrocopy
retro_ttru_382,
Vicugna pacos ENSVPAG000000155221 retrocopy
retro_vpac_3,
Drosophila melanogaster FBgn00156141 retrocopy
retro_dmel_53,

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 = 0.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .04 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 .03 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 .03 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 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 .04 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .03 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .03 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 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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