RetrogeneDB ID:

retro_hsap_75

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:18:11851510..11852110(+)
Located in intron of:ENSG00000141404
Retrocopy
information
Ensembl ID:ENSG00000255112
Aliases:CHMP1B, C10orf2, C18-ORF2, C18orf2, CHMP1.5, Vps46-2, Vps46B, hVps46-2
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CHMP1A
Ensembl ID:ENSG00000131165
Aliases:CHMP1A, CHMP1, PCH8, PCOLN3, PRSM1, VPS46-1, VPS46A
Description:charged multivesicular body protein 1A [Source:HGNC Symbol;Acc:8740]


Retrocopy-Parental alignment summary:






>retro_hsap_75
ATGTCTAACATGGAGAAACACCTGTTCAACCTGAAGTTCGCGGCCAAAGAACTGAGTAGGAGTGCCAAAAAATGCGATAA
GGAGGAAAAGGCCGAAAAGGCCAAAATTAAAAAGGCCATTCAGAAGGGCAACATGGAAGTTGCGAGGATACACGCCGAAA
ATGCCATCCGCCAGAAGAACCAGGCGGTGAATTTCTTGAGAATGAGTGCGCGAGTCGATGCAGTGGCTGCCAGGGTCCAG
ACGGCGGTGACGATGGGCAAGGTGACCAAGTCGATGGCTGGTGTGGTTAAGTCGATGGATGCGACATTGAAGACCATGAA
TCTGGAGAAGATTTCTGCTTTGATGGACAAATTCGAGCACCAGTTTGAGACTCTGGACGTCCAGACGCAGCAAATGGAAG
ACACGATGAGCAGCACGACGACGCTCACCACTCCCCAGAACCAAGTGGATATGCTGCTCCAGGAAATGGCAGATGAGGCG
GGCCTCGACCTCAACATGGAGCTGCCGCAGGGCCAGACCGGCTCCGTGGGCACGAGCGTGGCTTCGGCGGAGCAGGATGA
ACTGTCTCAGAGACTGGCCCGCCTTCGGGATCAAGTGTGA

ORF - retro_hsap_75 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 55.61 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMDDTLFQLKFTAKQLEKLAKKAEKDSKAEQAKVKKALLQKNVECARVYAENAIRKKNEGVNWLRMASRVD
M...LF.LKF.AK.L...AKK..K..KAE.AK.KKA....N.E.AR..AENAIR.KN..VN.LRM..RVD
RetrocopyMEKHLFNLKFAAKELSRSAKKCDKEEKAEKAKIKKAIQKGNMEVARIHAENAIRQKNQAVNFLRMSARVD
ParentalAVASKVQTAVTMKGVTKNMAQVTKALDKALSTMDLQKVSSVMDRFEQQVQNLDVHTSVMEDSMSSATTLT
AVA..VQTAVTM..VTK.MA.V.K..D..L.TM.L.K.S..MD.FE.Q...LDV.T..MED.MSS.TTLT
RetrocopyAVAARVQTAVTMGKVTKSMAGVVKSMDATLKTMNLEKISALMDKFEHQFETLDVQTQQMEDTMSSTTTLT
ParentalTPQEQVDSLIMQIAEENGLEVLDQLSQLPEGASAVGESSVRSQEDQLSRRLAALRN
TPQ.QVD.L....A.E.GL.....L.Q...G...VG.S......D.LS.RLA.LR.
RetrocopyTPQNQVDMLLQEMADEAGLDLNMELPQGQTG--SVGTSVASAEQDELSQRLARLRD

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 19 .96 RPM 43 .71 RPM
bodymap2_adrenal 15 .58 RPM 44 .56 RPM
bodymap2_brain 12 .61 RPM 19 .27 RPM
bodymap2_breast 14 .55 RPM 38 .68 RPM
bodymap2_colon 10 .33 RPM 32 .64 RPM
bodymap2_heart 14 .01 RPM 14 .93 RPM
bodymap2_kidney 16 .40 RPM 39 .50 RPM
bodymap2_liver 6 .00 RPM 16 .43 RPM
bodymap2_lung 21 .92 RPM 31 .45 RPM
bodymap2_lymph_node 19 .86 RPM 34 .85 RPM
bodymap2_ovary 10 .60 RPM 46 .77 RPM
bodymap2_prostate 24 .49 RPM 43 .79 RPM
bodymap2_skeletal_muscle 174 .42 RPM 32 .25 RPM
bodymap2_testis 12 .67 RPM 47 .21 RPM
bodymap2_thyroid 64 .69 RPM 46 .76 RPM
bodymap2_white_blood_cells 36 .30 RPM 60 .30 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_75 in 52 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001VKU POLR2A 18:11851077..11851777
ENCFF002CFW POLR2A 18:11851099..11851621
ENCFF002CFX POLR2A 18:11851107..11851591
ENCFF002CGN POLR2A 18:11851124..11851479
ENCFF002CHO POLR2A 18:11851045..11851674
ENCFF002CIH POLR2A 18:11851328..11851583
ENCFF002CIO POLR2A 18:11851111..11851616
ENCFF002CJE POLR2A 18:11851049..11851671
ENCFF002CJZ POLR2A 18:11850833..11851665
ENCFF002CKX POLR2A 18:11851090..11851577
ENCFF002CLM POLR2A 18:11851129..11851312
ENCFF002CMI POLR2A 18:11851058..11851656
ENCFF002COJ POLR2A 18:11851045..11851481
ENCFF002CPG POLR2A 18:11851122..11851379
ENCFF002CPG POLR2A 18:11851385..11851540
ENCFF002CPH POLR2A 18:11851058..11851448
ENCFF002CQA POLR2A 18:11851059..11851421
ENCFF002CQA POLR2A 18:11851171..11851741
ENCFF002CQC POLR2A 18:11851104..11851574
ENCFF002CQE POLR2A 18:11851087..11851588
ENCFF002CQG POLR2A 18:11851124..11851432
ENCFF002CQG POLR2A 18:11851349..11851561
ENCFF002CQI POLR2A 18:11851098..11851570
ENCFF002CQK POLR2A 18:11851066..11851591
ENCFF002CQM POLR2A 18:11851106..11851606
ENCFF002CQO POLR2A 18:11851088..11851615
ENCFF002CRK POLR2A 18:11850979..11851503
ENCFF002CRO POLR2A 18:11851049..11851469
ENCFF002CSY POLR2A 18:11850838..11852303
ENCFF002CUP POLR2A 18:11851360..11851461
ENCFF002CUQ POLR2A 18:11851109..11851421
ENCFF002CUQ POLR2A 18:11851386..11851588
ENCFF002CUQ POLR2A 18:11850015..11850519
ENCFF002CVF POLR2A 18:11851324..11851617
ENCFF002CVJ POLR2A 18:11850013..11852230
ENCFF002CXM POLR2A 18:11851110..11851408
ENCFF002CXN POLR2A 18:11851101..11851382
ENCFF002CXO POLR2A 18:11851126..11851391
ENCFF002CXO POLR2A 18:11851247..11851671
ENCFF002CXP POLR2A 18:11851082..11851432
ENCFF002CXP POLR2A 18:11851356..11851578
ENCFF002CXR POLR2A 18:11851106..11851579
ENCFF002CZC POLR2A 18:11850601..11852757
ENCFF002CZC POLR2A 18:11850042..11850623
ENCFF002CZD POLR2A 18:11850884..11851832
ENCFF002CZQ POLR2A 18:11851105..11851492
ENCFF002CZQ POLR2A 18:11851105..11851518
ENCFF002CZW POLR2A 18:11850887..11851793
ENCFF002CZY POLR2A 18:11851060..11851610
ENCFF002DAE POLR2A 18:11851106..11851416
ENCFF002DAH POLR2A 18:11851201..11851340
ENCFF002DAK POLR2A 18:11851023..11851523
ENCFF002DAS POLR2A 18:11851181..11851657
ENCFF002DAV POLR2A 18:11851113..11851402
ENCFF002DAV POLR2A 18:11851458..11851596
ENCFF002DAV POLR2A 18:11850055..11850599
ENCFF002DAY POLR2A 18:11851212..11851371
ENCFF002DBB POLR2A 18:11851161..11851361
ENCFF002DBE POLR2A 18:11851104..11851564
ENCFF002DBO POLR2A 18:11851152..11851380
ENCFF002DBO POLR2A 18:11851344..11851565
ENCFF002DBP POLR2A 18:11851164..11851359
ENCFF002DBP POLR2A 18:11851356..11851559
ENCFF002DBQ POLR2A 18:11851165..11851333
ENCFF002DBT POLR2A 18:11851069..11851439

EST - click to see more details

2 EST(s) were mapped to retro_hsap_75 retrocopy
EST ID Start End Identity Match Mis-match Score
BG011449 11851582 11851729 98 144 3 141
R58238 11851491 11851811 99.7 316 1 312

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_657951586 libraries173 libraries50 libraries14 libraries6 libraries
TSS #2 TSS_657961622 libraries148 libraries39 libraries12 libraries8 libraries
TSS #3 TSS_657971594 libraries161 libraries46 libraries15 libraries13 libraries
TSS #4 TSS_65800103 libraries26 libraries1094 libraries528 libraries78 libraries
TSS #5 TSS_6580124 libraries1 library45 libraries185 libraries1574 libraries
TSS #6 TSS_65802101 libraries142 libraries671 libraries437 libraries478 libraries
TSS #7 TSS_658031306 libraries369 libraries132 libraries17 libraries5 libraries

The graphical summary, for retro_hsap_75 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_75 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_75 has 8 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1278
Gorilla gorilla retro_ggor_1368
Pongo abelii retro_pabe_1581
Callithrix jacchus retro_cjac_1147
Oryctolagus cuniculus retro_ocun_1508
Rattus norvegicus retro_rnor_1361
Canis familiaris retro_cfam_1866
Equus caballus retro_ecab_991
Parental genes homology:
Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000012161 retrocopy
retro_amel_1749,
Bos taurus ENSBTAG000000333311 retrocopy
retro_btau_1048,
Canis familiaris ENSCAFG000000198221 retrocopy
retro_cfam_1866,
Callithrix jacchus ENSCJAG000000108261 retrocopy
retro_cjac_1147,
Homo sapiens ENSG00000131165 2 retrocopies
retro_hsap_359, retro_hsap_75 ,
Macaca mulatta ENSMMUG000000149093 retrocopies
retro_mmul_1325, retro_mmul_476, retro_mmul_706,
Mustela putorius furoENSMPUG000000072811 retrocopy
retro_mputfur_383,
Mus musculus ENSMUSG000000007431 retrocopy
retro_mmus_2260,
Oryctolagus cuniculus ENSOCUG000000233711 retrocopy
retro_ocun_1508,
Otolemur garnettii ENSOGAG000000048831 retrocopy
retro_ogar_170,
Pongo abelii ENSPPYG000000076671 retrocopy
retro_pabe_344,
Pan troglodytes ENSPTRG000000084832 retrocopies
retro_ptro_1278, retro_ptro_283,
Ictidomys tridecemlineatus ENSSTOG000000238131 retrocopy
retro_itri_1311,

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 = 19.72 RPM Legend:


Library Retrogene expression
CEU_NA11831 15 .58 RPM
CEU_NA11843 11 .66 RPM
CEU_NA11930 13 .40 RPM
CEU_NA12004 12 .08 RPM
CEU_NA12400 15 .05 RPM
CEU_NA12751 17 .17 RPM
CEU_NA12760 16 .17 RPM
CEU_NA12827 17 .22 RPM
CEU_NA12872 15 .84 RPM
CEU_NA12873 13 .30 RPM
FIN_HG00183 13 .70 RPM
FIN_HG00277 14 .64 RPM
FIN_HG00315 15 .04 RPM
FIN_HG00321 15 .87 RPM
FIN_HG00328 15 .98 RPM
FIN_HG00338 14 .16 RPM
FIN_HG00349 13 .54 RPM
FIN_HG00375 17 .70 RPM
FIN_HG00377 13 .82 RPM
FIN_HG00378 14 .70 RPM
GBR_HG00099 15 .72 RPM
GBR_HG00111 15 .99 RPM
GBR_HG00114 17 .22 RPM
GBR_HG00119 15 .37 RPM
GBR_HG00131 19 .72 RPM
GBR_HG00133 17 .63 RPM
GBR_HG00134 17 .89 RPM
GBR_HG00137 16 .99 RPM
GBR_HG00142 15 .39 RPM
GBR_HG00143 16 .08 RPM
TSI_NA20512 16 .02 RPM
TSI_NA20513 14 .70 RPM
TSI_NA20518 15 .52 RPM
TSI_NA20532 14 .11 RPM
TSI_NA20538 12 .48 RPM
TSI_NA20756 13 .71 RPM
TSI_NA20765 16 .41 RPM
TSI_NA20771 16 .60 RPM
TSI_NA20786 17 .05 RPM
TSI_NA20798 18 .34 RPM
YRI_NA18870 15 .91 RPM
YRI_NA18907 17 .54 RPM
YRI_NA18916 16 .69 RPM
YRI_NA19093 16 .95 RPM
YRI_NA19099 15 .55 RPM
YRI_NA19114 17 .30 RPM
YRI_NA19118 15 .99 RPM
YRI_NA19213 17 .87 RPM
YRI_NA19214 17 .07 RPM
YRI_NA19223 16 .04 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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