RetrogeneDB ID:

retro_hsap_2738

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:3:186490485..186491017(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000230951
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:GPS2
Ensembl ID:ENSG00000132522
Aliases:GPS2, AMF-1
Description:G protein pathway suppressor 2 [Source:HGNC Symbol;Acc:4550]


Retrocopy-Parental alignment summary:






>retro_hsap_2738
TCACCAGAGGAGACCGAAGGAACAAATTTTGACTTTGCAGGAGAAGCTGTGGGCCAGGCAGAAAGAAAAGGACCAGCTTT
TTCTGCAGCTGAAGAAAGTTTCCATGAGGAAGAAAAACGGAGGCGAAAGGAGCAGAGCGACCTGACCTTCTGACATCCGC
TGTGAGCCGGCGGAGCCCGATTATTCACGTGGGGACTCGCTTCCTCCTCGGCATGCAGGCAGCGCTGGAGGGCACGATCG
CCCGGGCATTGTCATAGCAGCTGACCCAGCCAAGCAGATGTTCAGGCCCCACGTGCTTACGACCCGGAAGTCCGTGGGCT
CAGCGGCGGCTTTTGCAGGGACCCCAGAGCAGGCAGCCTGGGCGGTGCCGCTGGGACTGCTCAGCCCCTACCTCAATATG
GGCCCACATAGCTAGCCTATGGCCCTAGTCGGCAGCTCAGAGCAGTTCAGTGCTCCCTGGGGTGCATTCATGTCCCAGCC
ACAACCTTATGTTCTGCTGGGCCACTTTCAGCACACCCAGACAGGGTTCCTC

ORF - retro_hsap_2738 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.62 %
Parental protein coverage: 56.27 %
Number of stop codons detected: 1
Number of frameshifts detected 7


Retrocopy - Parental Gene Alignment:

ParentalSLEET-KEQILKLEEKLLALQEEKHQLFLQLKKV-LHEEEKRRRKEQSDLT-TLTSAAYQQSLTVHTGTH
S.EET.KEQIL.L.EKL.A.Q.EK.QLFLQLKKV..HEEEKRRRKEQSDLT..LTSA....S...H.GT.
RetrocopySPEET>KEQILTLQEKLWARQKEKDQLFLQLKKV<FHEEEKRRRKEQSDLT<LLTSAVSRRSPIIHVGTR
Parental-LLSMQ-GSPGGHNRPGTLMAADRAKQMFGPQVLTTRHYVGSAAAFAGTPEH-GQFQGSPGGAYGTAQPP
.LL.MQ.GS.GGH.RPG...AAD.AKQMF.P.VLTTR..VGSAAAFAGTPE..G...G..G....TAQP.
RetrocopyFLLGMQ<GSAGGHDRPGIVIAADPAKQMFRPHVLTTRKSVGSAAAFAGTPEQ<GSLGGAAG----TAQPL
ParentalPHYGPTQPAYSPSQQLRA-PSAFPAVQ-YLSQPQPQPYAVHGHFQPTQTGFL
P.YGPT..AY.PS.QLRA..S..P.V....SQ..PQPY...GHFQ.TQTGFL
RetrocopyPQYGPT*LAYGPSRQLRA<SSVLPGVH<FMSQ--PQPYVLLGHFQHTQTGFL

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 0 .72 RPM
bodymap2_adrenal 0 .00 RPM 6 .37 RPM
bodymap2_brain 0 .00 RPM 1 .80 RPM
bodymap2_breast 0 .00 RPM 1 .83 RPM
bodymap2_colon 0 .00 RPM 0 .99 RPM
bodymap2_heart 0 .00 RPM 1 .77 RPM
bodymap2_kidney 0 .00 RPM 4 .36 RPM
bodymap2_liver 0 .00 RPM 0 .55 RPM
bodymap2_lung 0 .00 RPM 2 .39 RPM
bodymap2_lymph_node 0 .00 RPM 12 .19 RPM
bodymap2_ovary 0 .00 RPM 3 .16 RPM
bodymap2_prostate 0 .00 RPM 2 .98 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .29 RPM
bodymap2_testis 0 .11 RPM 2 .87 RPM
bodymap2_thyroid 0 .00 RPM 2 .73 RPM
bodymap2_white_blood_cells 0 .00 RPM 1 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2738 in 15 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CIH POLR2A 3:186490551..186490804
ENCFF002CIO POLR2A 3:186490526..186490824
ENCFF002CPG POLR2A 3:186490428..186490918
ENCFF002CQA POLR2A 3:186490365..186490935
ENCFF002CQA POLR2A 3:186490566..186491136
ENCFF002CQC POLR2A 3:186490538..186490881
ENCFF002CQE POLR2A 3:186490567..186490902
ENCFF002CQG POLR2A 3:186490590..186490744
ENCFF002CQG POLR2A 3:186490630..186491154
ENCFF002CQI POLR2A 3:186490592..186490787
ENCFF002CQK POLR2A 3:186490605..186490802
ENCFF002CQM POLR2A 3:186490610..186490780
ENCFF002CQO POLR2A 3:186490543..186490703
ENCFF002CQO POLR2A 3:186490617..186491147
ENCFF002CZQ POLR2A 3:186490483..186490933
ENCFF002CZY POLR2A 3:186490527..186491012
ENCFF002DAK POLR2A 3:186490445..186490945
ENCFF002DBO POLR2A 3:186490533..186490917

EST - click to see more details

No EST(s) were mapped for retro_hsap_2738 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2738 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2738 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2738 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1852
Gorilla gorilla retro_ggor_1907
Macaca mulatta retro_mmul_1487
Parental genes homology:
Parental genes homology involve 11 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000165762 retrocopies
retro_amel_1236, retro_amel_362,
Equus caballus ENSECAG000000106352 retrocopies
retro_ecab_124, retro_ecab_480,
Homo sapiens ENSG00000132522 2 retrocopies
retro_hsap_2738 , retro_hsap_4222,
Gorilla gorilla ENSGGOG000000016721 retrocopy
retro_ggor_1907,
Macropus eugenii ENSMEUG000000106452 retrocopies
retro_meug_1327, retro_meug_182,
Myotis lucifugus ENSMLUG000000261691 retrocopy
retro_mluc_1045,
Mus musculus ENSMUSG000000231701 retrocopy
retro_mmus_1476,
Nomascus leucogenys ENSNLEG000000093642 retrocopies
retro_nleu_2477, retro_nleu_600,
Pan troglodytes ENSPTRG000000230461 retrocopy
retro_ptro_1852,
Pteropus vampyrus ENSPVAG000000050521 retrocopy
retro_pvam_35,
Sus scrofa ENSSSCG000000179401 retrocopy
retro_sscr_742,

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 = 0.12 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .08 RPM
FIN_HG00277 0 .07 RPM
FIN_HG00315 0 .08 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .09 RPM
FIN_HG00375 0 .12 RPM
FIN_HG00377 0 .05 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .08 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .07 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .05 RPM
YRI_NA19114 0 .05 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .02 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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