RetrogeneDB ID:

retro_hsap_4694

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:67991164..67992192(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000232267
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTR3
Ensembl ID:ENSG00000115091
Aliases:ACTR3, ARP3
Description:ARP3 actin-related protein 3 homolog (yeast) [Source:HGNC Symbol;Acc:170]


Retrocopy-Parental alignment summary:






>retro_hsap_4694
ATGGTGGGAGGGCTGCAGGCCTGTGTGGTGGACTGTAGCATGGGGTATACAAAACTAGGATATGCCAGAAATATAGAACC
ACAGTTGATCATCCTTTCCTGTATTGCTACTAAGGAGTCACCAAAAGTGGGTGATCAATCTCAAAGGAGGGTGATGAAAA
GTATTGATGACCAAGACTTCTTCATTGGTGATGAAGCAGTAGAAAAAACCTACATATGCAACAAAGTGGCCAATCCGCCA
TGGTATAGTTGAAGTTGGACCTGACAAAAAGTTTTATAGAGCAAGTCATCTTAAATATTTAAGGGCAGAAACTGAAGACC
GTTATTTTATTTTGTCTGAACCTCGACTTAATACTCCAGAAAACAGGGAATATACTGCTGAAGTAATGTTTGAGTCCTTC
AGTGTTCCAGGCTTGTACATTGCTGTGCAGGCTGTTCTTGCCTTAGCTGCATCTTGGACCTCCAGACAAGTAGGAGGACG
GACATTTACAGGTACAGTAATAGACAGTGGAGATGGTGTCACTCATGTCATTGCTATGGCTGAAGGGTATTTGATTGCCA
ACTGTATTAAACACATTCCAATCCCAGGACGAAATATAACATATTTTATTCCGCAACTGCTGAGAGACCAAGAAGTAGGA
ATCCCTCAAAAACAATCCCTGGAAACTGCTAAGACAATAAAGGAGCACTATAGTTATGTCTGCCCAGATTTAGTAAAGGA
ATTTAACAAGTATGACACAGATGGGTCAAAATGGATTAAGCAGTATACCAGAATCAATGCTATCTCAAAGAAAGAATTTT
CCATTGGTGTTGTTTCTGAGAGACTTTTGGGATTTGAAATCTTTTTTTCATCTAGAGTTTGCCAATCCAGACTTTACATA
ACCTATCTCAGAAATTGTAGGTGAAGTAATTCAGAATTGTCCTATTGATGTCAGACGGCCTCTCTATAAGAATATGGTCC
TCTCTGTAGGTTCAACCATGTTCAGTGACTTTGGATATCACTTGCAAAGAGATTTGAAAAGAACTGTA

ORF - retro_hsap_4694 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.32 %
Parental protein coverage: 82.06 %
Number of stop codons detected: 1
Number of frameshifts detected: 5


Retrocopy - Parental Gene Alignment:

ParentalMAGRLPACVVDCGTGYTKLGYAGNTEPQFIIPSCIAIKESAKVGDQAQRRVMKGVDDLDFFIGDEAIEK-
M.G.L.ACVVDC..GYTKLGYA.N.EPQ.II.SCIA.KES.KVGDQ.QRRVMK..DD.DFFIGDEA.EK.
RetrocopyMVGGLQACVVDCSMGYTKLGYARNIEPQLIILSCIATKESPKVGDQSQRRVMKSIDDQDFFIGDEAVEK>
ParentalPTYATKWPIRHGIVE-DW-DLMERFMEQVIF-KYLRAEPEDHYFLLTEPPLNTPENREYTAEIMFESFNV
PTYATKWPIRHGIVE..W.DL...F.EQVI..KYLRAE.ED.YF.L.EP.LNTPENREYTAE.MFESF.V
RetrocopyPTYATKWPIRHGIVE<SW<DLTKSFIEQVIL<KYLRAETEDRYFILSEPRLNTPENREYTAEVMFESFSV
ParentalPGLYIAVQAVLALAASWTSRQVGERTLTGTVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQ
PGLYIAVQAVLALAASWTSRQVG.RT.TGTVIDSGDGVTHVI..AEGY.I..CIKHIPI.GR.ITYFI.Q
RetrocopyPGLYIAVQAVLALAASWTSRQVGGRTFTGTVIDSGDGVTHVIAMAEGYLIANCIKHIPIPGRNITYFIPQ
ParentalLLRDREVGIPPEQSLETAKAVKERYSYVCPDLVKEFNKYDTDGSKWIKQYTGINAISKKEFSIDVGYERF
LLRD.EVGIP..QSLETAK..KE.YSYVCPDLVKEFNKYDTDGSKWIKQYT.INAISKKEFSI.V..ER.
RetrocopyLLRDQEVGIPQKQSLETAKTIKEHYSYVCPDLVKEFNKYDTDGSKWIKQYTRINAISKKEFSIGVVSERL
ParentalLGPEI-FFHPEFANPDFTQPISEVVDEVIQNCPIDVRRPLYKNIVLSGGSTMFRDFGRRLQRDLKRTV
LG.EI.FFH.EFANPDFT.PISE.V.EVIQNCPIDVRRPLYKN.VLS.GSTMF.DFG..LQRDLKRTV
RetrocopyLGFEI>FFHLEFANPDFT*PISEIVGEVIQNCPIDVRRPLYKNMVLSVGSTMFSDFGYHLQRDLKRTV

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 209 .43 RPM
bodymap2_adrenal 0 .00 RPM 275 .99 RPM
bodymap2_brain 0 .00 RPM 175 .85 RPM
bodymap2_breast 0 .00 RPM 167 .34 RPM
bodymap2_colon 0 .00 RPM 264 .21 RPM
bodymap2_heart 0 .00 RPM 105 .58 RPM
bodymap2_kidney 0 .00 RPM 243 .04 RPM
bodymap2_liver 0 .00 RPM 81 .22 RPM
bodymap2_lung 0 .00 RPM 314 .19 RPM
bodymap2_lymph_node 0 .00 RPM 239 .15 RPM
bodymap2_ovary 0 .00 RPM 227 .97 RPM
bodymap2_prostate 0 .00 RPM 235 .80 RPM
bodymap2_skeletal_muscle 0 .00 RPM 80 .44 RPM
bodymap2_testis 0 .08 RPM 219 .07 RPM
bodymap2_thyroid 0 .02 RPM 178 .54 RPM
bodymap2_white_blood_cells 0 .00 RPM 791 .76 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_hsap_4694 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4694 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4694 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4694 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4694 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2921
Parental genes homology:
Parental genes homology involve 11 parental genes, and 23 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000034011 retrocopy
retro_btau_672,
Callithrix jacchus ENSCJAG000000140914 retrocopies
retro_cjac_3602, retro_cjac_3813, retro_cjac_385, retro_cjac_4005,
Homo sapiens ENSG00000115091 2 retrocopies
retro_hsap_1391, retro_hsap_4694 ,
Homo sapiens ENSG000001336277 retrocopies
retro_hsap_1676, retro_hsap_2126, retro_hsap_2540, retro_hsap_2966, retro_hsap_4334, retro_hsap_4921, retro_hsap_561,
Gorilla gorilla ENSGGOG000000113461 retrocopy
retro_ggor_2921,
Mustela putorius furoENSMPUG000000107171 retrocopy
retro_mputfur_1275,
Mus musculus ENSMUSG000000263411 retrocopy
retro_mmus_3653,
Nomascus leucogenys ENSNLEG000000116192 retrocopies
retro_nleu_1077, retro_nleu_2364,
Pongo abelii ENSPPYG000000127981 retrocopy
retro_pabe_3647,
Pan troglodytes ENSPTRG000000123882 retrocopies
retro_ptro_3118, retro_ptro_955,
Vicugna pacos ENSVPAG000000094791 retrocopy
retro_vpac_468,

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 = 0.19 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 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .03 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 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 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 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 .00 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 .19 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 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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