RetrogeneDB ID:

retro_hsap_2303

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:107557338..107557941(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000229360
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PPP1R2
Ensembl ID:ENSG00000184203
Aliases:PPP1R2, IPP-2, IPP2
Description:protein phosphatase 1, regulatory (inhibitor) subunit 2 [Source:HGNC Symbol;Acc:9288]


Retrocopy-Parental alignment summary:






>retro_hsap_2303
GCAATGGCAGCCTCGCACCAGCCCATCAAGGGGATCCTGAAGAACAAGACCTCCAGGACTTCCTCTATGGTGGCGTTGTC
GGAACAGCCCTGCAGAACTGTCCACGAGGAGCTGAGTAAAAAATGCCAGAAGTGTGATGAAATGAACATCCTGTCAACAT
ATCATCCAGCAGACAAAGACTATGGTTTAATGAAAATAGATGAGCCAAGCCCTCCTTACCATGGTATAACGGGTGATGAT
GAAAATGCATGTAGTGATACAGAAACCACTGAAACCATGGTATCAGATATCTTAGCTAAGAAATTAGCTGCTGCTGAAGG
CTTAGAGCCAAAATATTGGGTTCAGGAACAAGAAAGCAGTGGAGAGGAGGACCTCTTAGCTGAAGAATGAGAAAAAAACA
GACAATTTGAAATGAAAAGGAAGCTTCACTACAGTGAAGGACTCAATATCGAACTAGCTAGACAATTAGTTTCAAAAGAC
CTACATGATGATGACAAAGGTGAAGAAATGTTATAGACTACAGATGGAGAAAGCACGAATACTAAAGAATCAAATTAAGG
ATCTACTGCAAGTGACCAATGGCTAAACAAATCACGAAGTTCA

ORF - retro_hsap_2303 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.83 %
Parental protein coverage: 99.02 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalASTASHRPIKGILKNKTSTTSSMVASAEQPRGNVDEELSKKSQKWDEMNILATYHPADKDYGLMKIDEPS
A..ASH.PIKGILKNKTS.TSSMVA..EQP...V.EELSKK.QK.DEMNIL.TYHPADKDYGLMKIDEPS
RetrocopyAMAASHQPIKGILKNKTSRTSSMVALSEQPCRTVHEELSKKCQKCDEMNILSTYHPADKDYGLMKIDEPS
ParentalTPYHSMMGDDEDACSDTEATEAMAPDILARKLAAAEGLEPKYRIQEQESSGEEDSDLSPEEREKKRQFEM
.PYH...GDDE.ACSDTE.TE.M..DILA.KLAAAEGLEPKY..QEQESSGEE..DL..EE.EK.RQFEM
RetrocopyPPYHGITGDDENACSDTETTETMVSDILAKKLAAAEGLEPKYWVQEQESSGEE--DLLAEE*EKNRQFEM
ParentalKRKLHYNEGLNIKLARQLISKDLHDDDEDEEMLETADGESMNTEESNQGSTPSDQQQNKLRSS
KRKLHY.EGLNI.LARQL.SKDLHDDD..EEML.T.DGES.NT.ESN.GST.SDQ..NK.RSS
RetrocopyKRKLHYSEGLNIELARQLVSKDLHDDDKGEEML*TTDGESTNTKESN*GSTASDQWLNKSRSS

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 94 .62 RPM
bodymap2_adrenal 0 .00 RPM 136 .84 RPM
bodymap2_brain 0 .35 RPM 101 .59 RPM
bodymap2_breast 0 .00 RPM 83 .00 RPM
bodymap2_colon 0 .00 RPM 61 .55 RPM
bodymap2_heart 0 .00 RPM 44 .75 RPM
bodymap2_kidney 0 .00 RPM 52 .63 RPM
bodymap2_liver 0 .00 RPM 18 .50 RPM
bodymap2_lung 0 .00 RPM 85 .30 RPM
bodymap2_lymph_node 0 .00 RPM 94 .04 RPM
bodymap2_ovary 0 .00 RPM 68 .74 RPM
bodymap2_prostate 0 .00 RPM 75 .48 RPM
bodymap2_skeletal_muscle 0 .00 RPM 88 .94 RPM
bodymap2_testis 0 .00 RPM 136 .57 RPM
bodymap2_thyroid 0 .00 RPM 113 .89 RPM
bodymap2_white_blood_cells 0 .00 RPM 99 .70 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2303 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2303 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2303 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2303 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2303 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1705
Pongo abelii retro_pabe_1979
Callithrix jacchus retro_cjac_1252
Parental genes homology:
Parental genes homology involve 23 parental genes, and 58 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000094102 retrocopies
retro_amel_1164, retro_amel_53,
Canis familiaris ENSCAFG000000326481 retrocopy
retro_cfam_44,
Choloepus hoffmanni ENSCHOG000000132102 retrocopies
retro_chof_1353, retro_chof_2148,
Callithrix jacchus ENSCJAG000000138762 retrocopies
retro_cjac_1252, retro_cjac_2429,
Cavia porcellus ENSCPOG000000220062 retrocopies
retro_cpor_1144, retro_cpor_82,
Dasypus novemcinctus ENSDNOG000000236191 retrocopy
retro_dnov_1698,
Equus caballus ENSECAG000000180501 retrocopy
retro_ecab_3,
Felis catus ENSFCAG000000247491 retrocopy
retro_fcat_55,
Homo sapiens ENSG00000184203 7 retrocopies
retro_hsap_1262, retro_hsap_1271, retro_hsap_2303 , retro_hsap_2505, retro_hsap_3258, retro_hsap_3576, retro_hsap_3800,
Gorilla gorilla ENSGGOG000000259085 retrocopies
retro_ggor_1563, retro_ggor_1705, retro_ggor_2412, retro_ggor_2554, retro_ggor_992,
Loxodonta africana ENSLAFG000000120101 retrocopy
retro_lafr_85,
Macaca mulatta ENSMMUG000000193962 retrocopies
retro_mmul_1314, retro_mmul_1666,
Mustela putorius furoENSMPUG000000037532 retrocopies
retro_mputfur_1269, retro_mputfur_172,
Mus musculus ENSMUSG000000477148 retrocopies
retro_mmus_1540, retro_mmus_1610, retro_mmus_1611, retro_mmus_1868, retro_mmus_2760, retro_mmus_3350, retro_mmus_3428, retro_mmus_3580,
Nomascus leucogenys ENSNLEG000000083716 retrocopies
retro_nleu_123, retro_nleu_1435, retro_nleu_1943, retro_nleu_2147, retro_nleu_2315, retro_nleu_2740,
Oryctolagus cuniculus ENSOCUG000000141232 retrocopies
retro_ocun_188, retro_ocun_942,
Otolemur garnettii ENSOGAG000000025971 retrocopy
retro_ogar_10,
Procavia capensis ENSPCAG000000136141 retrocopy
retro_pcap_397,
Pongo abelii ENSPPYG000000144296 retrocopies
retro_pabe_105, retro_pabe_1056, retro_pabe_1979, retro_pabe_3025, retro_pabe_3105, retro_pabe_96,
Pteropus vampyrus ENSPVAG000000116381 retrocopy
retro_pvam_18,
Rattus norvegicus ENSRNOG000000017332 retrocopies
retro_rnor_245, retro_rnor_2860,
Sus scrofa ENSSSCG000000118301 retrocopy
retro_sscr_1191,
Sus scrofa ENSSSCG000000304551 retrocopy
retro_sscr_1161,

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 .03 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 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 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 .03 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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