RetrogeneDB ID:

retro_hsap_896

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:75622243..75622585(-)
Located in intron of:ENSG00000198382
Retrocopy
information
Ensembl ID:ENSG00000255255
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PPP1R1A
Ensembl ID:ENSG00000135447
Aliases:PPP1R1A, I1, IPP1
Description:protein phosphatase 1, regulatory (inhibitor) subunit 1A [Source:HGNC Symbol;Acc:9286]


Retrocopy-Parental alignment summary:






>retro_hsap_896
AACACGGATCCTCGACCCACTTTGGTAATGTCTCCACAGTGACAGAAGATGACAAGGATCACACCCACAACGAGAGAGCT
CCAGATGATGGCTGAACATCACCTGGGGCAACAGCACCAAGGAGAGGTGCCTGAGAAAGCTTCTGAGAGCACAGGGACCC
AGGAAACGTGCCCACCCAGGATCAAAGACACGGAAGTGGAGTCAAGGCTGGGCACCTTTGGGCTAGCACAAGAGCCTGCA
GAATCTATCCCGACAACTCAGGAGAGAGGCAGTAAAAAATGCAGCACAAAGGAACCCTCGATCCATGTACCACCACTGGA
TTCCCAGGAAGCCAGCTCGGTT

ORF - retro_hsap_896 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.7 %
Parental protein coverage: 67.25 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalNPHLKSTLAMSPRQRKKMTRITPTMKELQMMVEHHLGQQQQGEEPEGAAESTETQESRPPGIPDTEVESR
N.....TL.MSP.Q..KMTRITPT..ELQMM.EHHLGQQ.QGE.PE.A.EST.TQE..PP.I.DTEVESR
RetrocopyNTDPRPTLVMSP-Q*QKMTRITPTTRELQMMAEHHLGQQHQGEVPEKASESTGTQETCPPRIKDTEVESR
ParentalLGTSGTAKKTAECIPKTHERGSKEPSTKEPSTHIPPLDSKGANSV
LGT.G.A...AE.IP.T.ERGSK..STKEPS.H.PPLDS..A.SV
RetrocopyLGTFGLAQEPAESIPTTQERGSKKCSTKEPSIHVPPLDSQEASSV

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 369 .09 RPM
bodymap2_adrenal 0 .00 RPM 2 .15 RPM
bodymap2_brain 0 .05 RPM 22 .74 RPM
bodymap2_breast 0 .00 RPM 272 .05 RPM
bodymap2_colon 0 .00 RPM 29 .93 RPM
bodymap2_heart 0 .00 RPM 65 .04 RPM
bodymap2_kidney 0 .00 RPM 243 .95 RPM
bodymap2_liver 0 .00 RPM 94 .36 RPM
bodymap2_lung 0 .00 RPM 1 .65 RPM
bodymap2_lymph_node 0 .00 RPM 9 .89 RPM
bodymap2_ovary 0 .00 RPM 5 .47 RPM
bodymap2_prostate 0 .00 RPM 27 .19 RPM
bodymap2_skeletal_muscle 0 .00 RPM 274 .89 RPM
bodymap2_testis 0 .00 RPM 6 .50 RPM
bodymap2_thyroid 0 .00 RPM 26 .48 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_896 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_896 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_896 retrocopy 5' end.

Lab - click to see more details

retro_hsap_896 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_896 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_619
Pongo abelii retro_pabe_774
Parental genes homology:
Parental genes homology involve 6 parental genes, and 27 retrocopies.

Species Parental gene accession Retrocopies number
Felis catus ENSFCAG000000101591 retrocopy
retro_fcat_1131,
Homo sapiens ENSG00000135447 2 retrocopies
retro_hsap_1633, retro_hsap_896 ,
Gorilla gorilla ENSGGOG000000083801 retrocopy
retro_ggor_1231,
Pongo abelii ENSPPYG000000046081 retrocopy
retro_pabe_774,
Pan troglodytes ENSPTRG000000050442 retrocopies
retro_ptro_1138, retro_ptro_619,
Tupaia belangeri ENSTBEG0000000119320 retrocopies
retro_tbel_1191, retro_tbel_1233, retro_tbel_1251, retro_tbel_1264, retro_tbel_138, retro_tbel_1881, retro_tbel_2036, retro_tbel_2437, retro_tbel_2574, retro_tbel_2720, retro_tbel_3243, retro_tbel_3316, retro_tbel_3377, retro_tbel_3380, retro_tbel_3414, retro_tbel_3426, retro_tbel_4551, retro_tbel_537, retro_tbel_669, retro_tbel_899,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .04 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 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 .03 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 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .04 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 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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