RetrogeneDB ID:

retro_hsap_2263

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:2:60962027..60962672(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000271707
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP1B3
Ensembl ID:ENSG00000069849
Aliases:ATP1B3, ATPB-3, CD298
Description:ATPase, Na+/K+ transporting, beta 3 polypeptide [Source:HGNC Symbol;Acc:806]


Retrocopy-Parental alignment summary:






>retro_hsap_2263
CTCAACGATGAGGTTCCAAAATACCGTGACCAGATTCTTAACCCAGGACTGATGGTTTTTCCAAAACCAGTCACTGCATT
GGAATATGCATTCAGTAGGTCTGATCTAACTTCGTATGCAGGGTACACTGAAGACCTTAAGAAGTTTCTAAAACCATATA
CTTTAGAAGAACAGAAAAACCTCACAGTCTGTCCTGATGGAGCACTTTTTGAACAGAAGGGTCCAGTTTATGTTGCTTGT
CAATCTCCCATTTCGTTACTTCAAGCATGCCGTGGTATGAATGATCTTGATTTCGGCTATTCTCAAAGAAACCCTTGTAT
TCTTGTGAAAATGAACAGAATAATTGGATTAAAGTCTGAAGGAGTGCCAAGGATAGATTGTGTTTCGAAGAATGAAGATA
TACCAAATGTAGCAGTTTATCCTCATAATGGAATTATAGACTTAAAATATTTCCCATATTATGGGGAAAAACTGCATGTG
GGGTATCTACAGCCATTGGTTGCTGTTCAGGTCAGCTTTGCTCCTAACGATACTGGGAAAGAAGTAACAGTTGAATGCAA
GATTGATGGATCAGCCAACCTTAAAAGTCAGGATGATCGTGACAAGTTTTTGGGACGAGTTATGTTCAAAATCACAGCAT
GTGCA

ORF - retro_hsap_2263 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.49 %
Parental protein coverage: 77.06 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLNDEVPKYRDQIPSPGLMVFPKPVTALEYTFSRSDPTSYAGYIEDLKKFLKPYTLEEQKNLTVCPDGALF
LNDEVPKYRDQI..PGLMVFPKPVTALEY.FSRSD.TSYAGY.EDLKKFLKPYTLEEQKNLTVCPDGALF
RetrocopyLNDEVPKYRDQILNPGLMVFPKPVTALEYAFSRSDLTSYAGYTEDLKKFLKPYTLEEQKNLTVCPDGALF
ParentalEQKGPVYVACQFPISLLQACSGMNDPDFGYSQGNPCILVKMNRIIGLKPEGVPRIDCVSKNEDIPNVAVY
EQKGPVYVACQ.PISLLQAC.GMND.DFGYSQ.NPCILVKMNRIIGLK.EGVPRIDCVSKNEDIPNVAVY
RetrocopyEQKGPVYVACQSPISLLQACRGMNDLDFGYSQRNPCILVKMNRIIGLKSEGVPRIDCVSKNEDIPNVAVY
ParentalPHNGMIDLKYFPYYGKKLHVGYLQPLVAVQVSFAPNNTGKEVTVECKIDGSANLKSQDDRDKFLGRVMFK
PHNG.IDLKYFPYYG.KLHVGYLQPLVAVQVSFAPN.TGKEVTVECKIDGSANLKSQDDRDKFLGRVMFK
RetrocopyPHNGIIDLKYFPYYGEKLHVGYLQPLVAVQVSFAPNDTGKEVTVECKIDGSANLKSQDDRDKFLGRVMFK
ParentalITARA
ITA.A
RetrocopyITACA

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 82 .71 RPM
bodymap2_adrenal 0 .02 RPM 110 .17 RPM
bodymap2_brain 0 .00 RPM 69 .69 RPM
bodymap2_breast 0 .00 RPM 77 .14 RPM
bodymap2_colon 0 .00 RPM 103 .74 RPM
bodymap2_heart 0 .00 RPM 47 .92 RPM
bodymap2_kidney 0 .00 RPM 139 .24 RPM
bodymap2_liver 0 .00 RPM 12 .23 RPM
bodymap2_lung 0 .02 RPM 280 .10 RPM
bodymap2_lymph_node 0 .00 RPM 176 .10 RPM
bodymap2_ovary 0 .00 RPM 97 .10 RPM
bodymap2_prostate 0 .02 RPM 68 .26 RPM
bodymap2_skeletal_muscle 0 .00 RPM 14 .62 RPM
bodymap2_testis 0 .08 RPM 135 .44 RPM
bodymap2_thyroid 0 .09 RPM 115 .10 RPM
bodymap2_white_blood_cells 0 .02 RPM 91 .35 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_hsap_2263 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002CFW POLR2A 2:60962792..60963222

EST - click to see more details

No EST(s) were mapped for retro_hsap_2263 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_124024889 libraries787 libraries150 libraries2 libraries1 library

The graphical summary, for retro_hsap_2263 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_2263 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2263 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1603
Pongo abelii retro_pabe_1953
Parental genes homology:
Parental genes homology involve 18 parental genes, and 35 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000141405 retrocopies
retro_btau_1136, retro_btau_1322, retro_btau_1743, retro_btau_318, retro_btau_920,
Choloepus hoffmanni ENSCHOG000000075154 retrocopies
retro_chof_1000, retro_chof_1421, retro_chof_2393, retro_chof_2445,
Callithrix jacchus ENSCJAG000000019811 retrocopy
retro_cjac_309,
Cavia porcellus ENSCPOG000000037394 retrocopies
retro_cpor_1181, retro_cpor_1468, retro_cpor_1506, retro_cpor_222,
Equus caballus ENSECAG000000198852 retrocopies
retro_ecab_1084, retro_ecab_468,
Homo sapiens ENSG00000069849 2 retrocopies
retro_hsap_1387, retro_hsap_2263 ,
Homo sapiens ENSG000001431531 retrocopy
retro_hsap_2924,
Loxodonta africana ENSLAFG000000105531 retrocopy
retro_lafr_815,
Mus musculus ENSMUSG000000324122 retrocopies
retro_mmus_2174, retro_mmus_3427,
Otolemur garnettii ENSOGAG000000086621 retrocopy
retro_ogar_2284,
Procavia capensis ENSPCAG000000139271 retrocopy
retro_pcap_350,
Pan troglodytes ENSPTRG000000154762 retrocopies
retro_ptro_1603, retro_ptro_951,
Rattus norvegicus ENSRNOG000000115012 retrocopies
retro_rnor_2571, retro_rnor_789,
Sus scrofa ENSSSCG000000116763 retrocopies
retro_sscr_889, retro_sscr_945, retro_sscr_95,
Ictidomys tridecemlineatus ENSSTOG000000132351 retrocopy
retro_itri_1663,
Tupaia belangeri ENSTBEG000000010041 retrocopy
retro_tbel_3620,
Tarsius syrichta ENSTSYG000000002221 retrocopy
retro_tsyr_330,
Tursiops truncatus ENSTTRG000000120381 retrocopy
retro_ttru_333,

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 = 0.04 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .03 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .02 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 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 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 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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