RetrogeneDB ID:

retro_hsap_2966

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:103883285..103884252(+)
Located in intron of:ENSG00000164037
Retrocopy
information
Ensembl ID:ENSG00000249283
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTR3B
Ensembl ID:ENSG00000133627
Aliases:ACTR3B, ARP11, ARP3BETA
Description:ARP3 actin-related protein 3 homolog B (yeast) [Source:HGNC Symbol;Acc:17256]


Retrocopy-Parental alignment summary:






>retro_hsap_2966
TATTCTGAGCTTGGCTATGCAGGCAACACTGAGCCATAGTTTACTATTCTTTCTTGCATTTCTATCAGAGAGTCAGCAAA
GGTAGTTGACAAAGCCCAAAGGAGAATGTTGAGGGGAGTTGATGACCTTGACTTTTTCATACAGGATGAAGCCATTGATA
AATCTATGTATGCTACAAAGTGGTCAATATGACTGGAATCACTGAAGACTGGGATATTATGGAAAGGTTCATGGAGCAAG
TGGTTTTTAAATATCTTTGAGCAGAATCTGAGGACCATTATTTTTTAATGACAGAACTTCCACTGAATACACTAGAAAAT
ACAGAGCATTTTTGCAGAAATTATGTTTGAATTATTTAATGTACCAGGATTCTACATTGCAGTTCAGGAGGTACTGGCCT
TGGCAGTATCTTGGACATCTCAACAAGTGGGTGAATGTATGTTAATGAGTATAGTCATTGACAAAGGAGATGGAGTCACC
CATGTTCTCCCAGTTGTAGAAGGTTATGTAATTGGGAGCTGCATCAATCACATCCTGATTGTAGGTGATACTGTGTATTT
CACTCAACAGCTGCTAAGGGAGAGGGAGGTAGGAATCCCTCTTGAGCAGTCACTGGAGACCACAAAAGCCATTAAGGAGA
AATACTGTTACATTTGCCCTGATACAGTCAAGGAATTTGCTAAGCATGATGTGGATTCCTGGAAGTGGATCAAACAATAC
ACAGGTATCAATGTGATCAACCAGGAGAAGTTCATAATAGATGTTGGTTACAAAAGGTTCCTGCAACCTGAAATATTTTT
TTACCCAGAGTTTGCCAACCCAGACTTTATGGAATCCATCTTGAATGTTGTTGATGAATACAAAACTGTCCCATTGATGT
GCATGGTCCACTGTATAAGAATGTTGTTCTTTCAAGGGGTTTGACCATATTCGGGGATTTGAACCTCAACTACAGAGAGA
TTTGAAG

ORF - retro_hsap_2966 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.2 %
Parental protein coverage: 77.75 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalYTKLGYAGNTEPQFIIPSCIAIRESAKVVDQAQRRVLRGVDDLDFFIGDEAIDKPTYATKWPI-RHGIIE
Y..LGYAGNTEP.F.I.SCI.IRESAKVVD.AQRR.LRGVDDLDFFI.DEAIDK..YATKW.I...GI.E
RetrocopyYSELGYAGNTEP*FTILSCISIRESAKVVDKAQRRMLRGVDDLDFFIQDEAIDKSMYATKWSI<MTGITE
ParentalDWDLMERFMEQVVFKYLRAEPEDHYFLMTEPPLNTPENREYL-AEIMFESFNVPGLYIAVQAVLALAASW
DWD.MERFMEQVVFKYL.AE.EDHYFLMTE.PLNT.EN.E...AEIMFE.FNVPG.YIAVQ.VLALA.SW
RetrocopyDWDIMERFMEQVVFKYL*AESEDHYFLMTELPLNTLENTEHF>AEIMFELFNVPGFYIAVQEVLALAVSW
ParentalTSRQVGERTLTGIVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLREREVGIPPEQSLET
TS.QVGE..L..IVID.GDGVTHV.PV.EGYVIGSCI.HI.I.G.D..YF.QQLLREREVGIP.EQSLET
RetrocopyTSQQVGECMLMSIVIDKGDGVTHVLPVVEGYVIGSCINHILIVG-DTVYFTQQLLREREVGIPLEQSLET
ParentalAKAIKEKYCYICPDIVKEFAKYDVDPRKWIKQYTGINAINQKKFVIDVGYERFLGPEIFFHPEFANPDFM
.KAIKEKYCYICPD.VKEFAK.DVD..KWIKQYTGIN.INQ.KF.IDVGY.RFL.PEIFF.PEFANPDFM
RetrocopyTKAIKEKYCYICPDTVKEFAKHDVDSWKWIKQYTGINVINQEKFIIDVGYKRFLQPEIFFYPEFANPDFM
ParentalESISDVVDEVIQNCPI-DVRRPLYKNVVLSGGSTMF-RDFGRRLQRDLK
ESI..VVDE.....P..DV..PLYKNVVLS.G.T.F.R.F...LQRDLK
RetrocopyESILNVVDE-YKTVPL<DVHGPLYKNVVLSRGLTIF<RGFEPQLQRDLK

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 3 .36 RPM
bodymap2_adrenal 0 .00 RPM 4 .46 RPM
bodymap2_brain 0 .00 RPM 27 .31 RPM
bodymap2_breast 0 .04 RPM 5 .04 RPM
bodymap2_colon 0 .00 RPM 3 .48 RPM
bodymap2_heart 0 .00 RPM 3 .21 RPM
bodymap2_kidney 0 .00 RPM 7 .80 RPM
bodymap2_liver 0 .00 RPM 4 .25 RPM
bodymap2_lung 0 .00 RPM 4 .82 RPM
bodymap2_lymph_node 0 .00 RPM 2 .94 RPM
bodymap2_ovary 0 .00 RPM 6 .57 RPM
bodymap2_prostate 0 .00 RPM 5 .39 RPM
bodymap2_skeletal_muscle 0 .00 RPM 5 .04 RPM
bodymap2_testis 0 .08 RPM 19 .46 RPM
bodymap2_thyroid 0 .00 RPM 5 .07 RPM
bodymap2_white_blood_cells 0 .00 RPM 8 .54 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2966 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2966 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2966 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2966 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2966 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2007
Pongo abelii retro_pabe_2460
Parental genes homology:
Parental genes homology involve 12 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000077305 retrocopies
retro_chof_1134, retro_chof_1204, retro_chof_1899, retro_chof_208, retro_chof_2171,
Dasypus novemcinctus ENSDNOG000000192882 retrocopies
retro_dnov_1143, retro_dnov_2539,
Homo sapiens ENSG000001150912 retrocopies
retro_hsap_1391, retro_hsap_4694,
Homo sapiens ENSG00000133627 7 retrocopies
retro_hsap_1676, retro_hsap_2126, retro_hsap_2540, retro_hsap_2966 , retro_hsap_4334, retro_hsap_4921, retro_hsap_561,
Macropus eugenii ENSMEUG000000048855 retrocopies
retro_meug_1340, retro_meug_1477, retro_meug_2105, retro_meug_330, retro_meug_899,
Nomascus leucogenys ENSNLEG000000156881 retrocopy
retro_nleu_733,
Oryctolagus cuniculus ENSOCUG000000004591 retrocopy
retro_ocun_320,
Otolemur garnettii ENSOGAG000000032492 retrocopies
retro_ogar_1307, retro_ogar_3388,
Pongo abelii ENSPPYG000000182061 retrocopy
retro_pabe_2460,
Pan troglodytes ENSPTRG000000198978 retrocopies
retro_ptro_1137, retro_ptro_1479, retro_ptro_2007, retro_ptro_2952, retro_ptro_2961, retro_ptro_3052, retro_ptro_3281, retro_ptro_420,
Tupaia belangeri ENSTBEG000000116472 retrocopies
retro_tbel_2820, retro_tbel_932,
Tursiops truncatus ENSTTRG000000163342 retrocopies
retro_ttru_471, retro_ttru_93,

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 = 0.09 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 .03 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .02 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .09 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 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 .03 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 .00 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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