RetrogeneDB ID:

retro_hsap_570

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:47396222..47396775(+)
Located in intron of:ENSG00000189014
Retrocopy
information
Ensembl ID:ENSG00000226964
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RHEB
Ensembl ID:ENSG00000106615
Aliases:RHEB, RHEB2
Description:Ras homolog enriched in brain [Source:HGNC Symbol;Acc:10011]


Retrocopy-Parental alignment summary:






>retro_hsap_570
ATGCCGCAGTCAAAGTCCCGGAAGATCGCGATCCTGGGCTACCGGTCTGTGGGGAAATCCTCATTGACGATTCAATTTGT
TGAAGGCCAATTTGTGGACTCCTACGATCCAACCATAGAAAACACTTTTACAAAGTTGATCACAGTAAATGGACAAGAAT
ATCATCTTTAACTTGTAGACACAGCCGGGCAAGATGAATATTCTATCTTTCCTCAGACATACTCCATAGATATTAATGGC
TATATTCTTGTGTATTCTGTTACATCAATCAAAAGTTTTGAAGTGATTAAAGTTATCCATGGCAAATTGTTGGATATGGT
GGGGAAAGTACAAATACCTATTATGTTGGTTGGAAATAAGAAAGACCTGCATATGGAAAGGGTGATCAGTTATGAAGAAG
GGAAAGCTTTGGCAGAATCTTGGAATGCAGCTTTTTTGGAATCTTCTGCTAAAGAAAATCAGACTGCTGTTGATGTTTTT
CGAAGGATGATTTTGGAGGCAGAAAAAATGGACGGGGGCAGCTTCACAAGGCAAGTCTTCATGCTCGGTGATG

ORF - retro_hsap_570 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.38 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIF
MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHL.LVDTAGQDEYSIF
RetrocopyMPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHL*LVDTAGQDEYSIF
ParentalPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES
PQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES
RetrocopyPQTYSIDINGYILVYSVTSIKSFEVIKVIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGKALAES
ParentalWNAAFLESSAKENQTAVDVFRRIILEAEKMD-GAASQGKSSCSVM
WNAAFLESSAKENQTAVDVFRR.ILEAEKMD.GAASQGKSSCSVM
RetrocopyWNAAFLESSAKENQTAVDVFRRMILEAEKMD>GAASQGKSSCSVM

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 .24 RPM 71 .54 RPM
bodymap2_adrenal 0 .63 RPM 54 .49 RPM
bodymap2_brain 0 .05 RPM 113 .97 RPM
bodymap2_breast 0 .21 RPM 57 .02 RPM
bodymap2_colon 0 .06 RPM 120 .95 RPM
bodymap2_heart 0 .00 RPM 56 .77 RPM
bodymap2_kidney 0 .45 RPM 82 .31 RPM
bodymap2_liver 0 .72 RPM 41 .99 RPM
bodymap2_lung 0 .09 RPM 105 .57 RPM
bodymap2_lymph_node 0 .07 RPM 57 .53 RPM
bodymap2_ovary 0 .27 RPM 72 .13 RPM
bodymap2_prostate 0 .10 RPM 147 .05 RPM
bodymap2_skeletal_muscle 0 .00 RPM 106 .89 RPM
bodymap2_testis 2 .73 RPM 71 .70 RPM
bodymap2_thyroid 0 .32 RPM 111 .18 RPM
bodymap2_white_blood_cells 0 .30 RPM 38 .92 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_570 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 10:47395817..47396247
ENCFF002CFX POLR2A 10:47395996..47396096

EST - click to see more details

No EST(s) were mapped for retro_hsap_570 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_570 retrocopy 5' end.

Lab - click to see more details

retro_hsap_570 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_570 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_568
Pan troglodytes retro_ptro_115
Parental genes homology:
Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000318611 retrocopy
retro_btau_373,
Cavia porcellus ENSCPOG000000075412 retrocopies
retro_cpor_287, retro_cpor_787,
Dasypus novemcinctus ENSDNOG000000164931 retrocopy
retro_dnov_2542,
Homo sapiens ENSG00000106615 2 retrocopies
retro_hsap_568, retro_hsap_570 ,
Gorilla gorilla ENSGGOG000000146751 retrocopy
retro_ggor_149,
Loxodonta africana ENSLAFG000000006911 retrocopy
retro_lafr_471,
Macropus eugenii ENSMEUG000000117741 retrocopy
retro_meug_172,
Myotis lucifugus ENSMLUG000000043092 retrocopies
retro_mluc_2140, retro_mluc_857,
Mus musculus ENSMUSG000000289451 retrocopy
retro_mmus_1779,
Oryctolagus cuniculus ENSOCUG000000131731 retrocopy
retro_ocun_1309,
Ictidomys tridecemlineatus ENSSTOG000000045442 retrocopies
retro_itri_1251, retro_itri_1357,
Tarsius syrichta ENSTSYG000000012862 retrocopies
retro_tsyr_1174, retro_tsyr_1848,

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 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .02 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .03 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 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .03 RPM
TSI_NA20538 0 .05 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 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .02 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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