RetrogeneDB ID:

retro_hsap_1451

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:89756688..89757700(-)
Located in intron of:ENSG00000053254
Retrocopy
information
Ensembl ID:ENSG00000259151
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CAP2
Ensembl ID:ENSG00000112186
Aliases:None
Description:CAP, adenylate cyclase-associated protein, 2 (yeast) [Source:HGNC Symbol;Acc:20039]


Retrocopy-Parental alignment summary:






>retro_hsap_1451
AGGGCTTTCCTTCTGATGGCATCTCATGACCAACAACCCCGAGAGAATGCGTGGCTGCATTTCTGAAACCCAAATCAGAA
AAGATTCAGAAGTCCAAACCTTCAAAGAGAGAAACCGAGGGAGTAACATGTTTAGTCATCTCTCGGATGTCAGCAAAAGC
CTCCCTGCCCTTGGCTGCATAACTGTGCCCCCCAACTTGGGTACTTACGTCAACGAGATGTGTGATGCTGCCACCTTTTA
CACTAACAGGGTCTTAAAGGGCTACAAACATGATTTACACCGTGTGGATTGGGTGAGGTCATATGTGAACATTTGGAGTG
AGTTTCAAGCATGAGTCAAGGAGCACCACACCACGGGCCTCACGTGGAGCAGAACAGGTCCGCAGCACCCACATCAGCGC
TTTCTGTTCTCTCCTGAGGGCCTGACCTTTCTCCACATCCTCCTCACCTCCTCCAGGGCCCCTCCACTTTTTGAGAATGA
AGACACAAAAGAAAAGTCCTCTCCTTCATGCTCAGCTTTATTTGCCCGGTTTAACCAGGGAGAAGCCTAACCCTGCAGAA
CCAGGGCTCTGGCACATCACTGATGACCAGAAGGCCTATATAAGAATCCCAGCCTGCAGGCTCACGGAGGGCAAAGTACG
TCTCCCCACAGAAGCTACATTCCAAGTCCCACATCTCCCAAACCTCATCCTTCCCAGCAACATGCACCCGTGTTCAAGTT
GGAAGGAAGTAAATGGAGAGCAGAGTACCAAGAAGACAGGAATGACCTTGTGATTTCAGAGACTGAGCTGAAACAAGTGG
CTTACATTTTCAATTGTGAAAAATCAGCTCTCCCGATGAAAGGGAAAGTAAACTCCATTCCAGTGGAAAACTGTAAGAAG
TTTGGTCTGGTCTTTGACAGTTTGGTGGGCATTGGGGAAATGACCAACTCCAAGTACATTCAAATCCAGGTAATGGGGAG
AGTACCAGCAATTTCCACTAATAAGACAGAAGGTTGCCACACATACCTAACT

ORF - retro_hsap_1451 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.18 %
Parental protein coverage: 71.07 %
Number of stop codons detected: 5
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalRAFLLMASQYQQPHEND-VAALLKPISEKIQ-EIQTFRERNRGSNMFNHLSAVSESIPALGWIAVSPKPG
RAFLLMAS..QQP.EN..VAA.LKP.SEKIQ.E.QTF.ERNRGSNMF.HLS.VS.S.PALG.I.V.P..G
RetrocopyRAFLLMASHDQQPRENA<VAAFLKPKSEKIQ<EVQTFKERNRGSNMFSHLSDVSKSLPALGCITVPPNLG
ParentalPYVKEMNDAATFYTNRVLKDYKHSDLRHVDWVKSYLNIWSELQAYIKEHHTTGLTWSKTGP-VASTVSAF
.YV.EM.DAATFYTNRVLK.YKH.DL..VDWV.SY.NIWSE.QA..KEHHTTGLTWS.TGP..A.T.SA.
RetrocopyTYVNEMCDAATFYTNRVLKGYKH-DLHRVDWVRSYVNIWSEFQA*VKEHHTTGLTWSRTGP<AAPT-SAL
ParentalSVLSSGPGLPPPPPPL-PPPGP-PPLFENEGKKEESSPSRSALFAQLNQGEA---ITKGLRHVTDDQKTY
SVLS.GP.L.P.PP.L.PP.GP.PPLFENE..KE.SSPS.SALFA..NQGEA....T..L.H.......Y
RetrocopySVLS*GPDLSPHPPHL<PP-GP<PPLFENEDTKEKSSPSCSALFARFNQGEA*PCRTRALAHH**PEGLY
ParentalKNPSLRAQGGQTQSPTKSHTPSPTSPKSYPSQKHAPVLELEGKKWRVEYQEDRNDLVISETELKQVAYIF
KNPSL.A.GGQ..SP..S..PSPTSPK..PSQ.HAPV..LEG.KWR.EYQEDRNDLVISETELKQVAYIF
RetrocopyKNPSLQAHGGQSTSPHRSYIPSPTSPKPHPSQQHAPVFKLEGSKWRAEYQEDRNDLVISETELKQVAYIF
ParentalKCEKSTIQIKGKVNSIIIDNCKKLGLVFDNVVGIVEVINSQDIQIQVMGRVPTISINKTEGCHIYLS
.CEKS....KGKVNSI...NCKK.GLVFD..VGI.E..NS..IQIQVMGRVP.IS.NKTEGCH.YL.
RetrocopyNCEKSALPMKGKVNSIPVENCKKFGLVFDSLVGIGEMTNSKYIQIQVMGRVPAISTNKTEGCHTYLT

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 .14 RPM 4 .47 RPM
bodymap2_adrenal 0 .04 RPM 20 .43 RPM
bodymap2_brain 0 .00 RPM 176 .81 RPM
bodymap2_breast 0 .00 RPM 78 .66 RPM
bodymap2_colon 0 .00 RPM 85 .04 RPM
bodymap2_heart 0 .00 RPM 116 .05 RPM
bodymap2_kidney 0 .00 RPM 22 .33 RPM
bodymap2_liver 0 .00 RPM 2 .77 RPM
bodymap2_lung 0 .00 RPM 11 .13 RPM
bodymap2_lymph_node 0 .00 RPM 15 .53 RPM
bodymap2_ovary 0 .08 RPM 16 .93 RPM
bodymap2_prostate 0 .00 RPM 73 .25 RPM
bodymap2_skeletal_muscle 0 .00 RPM 871 .85 RPM
bodymap2_testis 0 .00 RPM 34 .11 RPM
bodymap2_thyroid 0 .00 RPM 94 .83 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_1451 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1451 retrocopy.

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_412191394 libraries408 libraries25 libraries2 libraries0 libraries

The graphical summary, for retro_hsap_1451 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_1451 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1451 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_987
Macaca mulatta retro_mmul_2271
Parental genes homology:
Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000099771 retrocopy
retro_cfam_1385,
Cavia porcellus ENSCPOG000000088391 retrocopy
retro_cpor_1367,
Homo sapiens ENSG00000112186 1 retrocopy
retro_hsap_1451 ,
Homo sapiens ENSG000001312362 retrocopies
retro_hsap_2666, retro_hsap_664,
Macaca mulatta ENSMMUG000000019901 retrocopy
retro_mmul_2271,
Pan troglodytes ENSPTRG000000177501 retrocopy
retro_ptro_987,

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 = 0.31 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .04 RPM
CEU_NA11843 0 .03 RPM
CEU_NA11930 0 .07 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .09 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .05 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .03 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .06 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .08 RPM
GBR_HG00119 0 .10 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .11 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .06 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .10 RPM
TSI_NA20518 0 .11 RPM
TSI_NA20532 0 .31 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .09 RPM
TSI_NA20786 0 .03 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .10 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .08 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .05 RPM
YRI_NA19223 0 .04 RPM

Indel association:

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



Copyright © RetrogeneDB 2014-2017