RetrogeneDB ID:

retro_hsap_3574

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:31255975..31256741(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000231402
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:WASF3
Ensembl ID:ENSG00000132970
Aliases:WASF3, Brush-1, SCAR3, WAVE3
Description:WAS protein family, member 3 [Source:HGNC Symbol;Acc:12734]


Retrocopy-Parental alignment summary:






>retro_hsap_3574
ATGCCTCCCGTGAAGAGGAGCATCTAATCCCAGCATTTGCACCAGGGAACTCTGCCTGAAGGGATTACCAGTGACTTGAA
AGTGTAACCAACAACAATCTTGTCACTATTACGCACCAGCTAAGCAATCTGAACATACATGCTGAAGACATATTTGGTGA
GCTATTTAAGGAGGCTAACTACTTCCACATTAGATCAAATTCTCTTAGAATTTGTTGCCTCATGGTCAAAGTCACTCAGC
TGGATTCAGCAGTGGAAGAGGTGTCACCACAGGACATCAACATGGAAAAAGCCCTCAAAAGTTCCCCAGCCCAAGACCAG
CAAGCAGTTTCAAAGAGCAGCATTCCTACTCCTGCTGCTGACATTTACAATCAGAGTGATTGACCACCTCCCCTGAATAG
CATGAGAGCACATGGAGATGATAAAGACAGGCTGAAGTTCTATACTGATCCTTCCCATTTATTTGACCTCTGGAAAGAAG
AAGTGCTGCAGGACACAGAAGACAAAAGGAAAGACAGAAGGCATCAAAAGTAGCAAAACCACATAGATGGCACCACTTAT
GATGTGAAAAGGATTACAAAAGCCAGAAACAAGCACCATGAGTGGAATATGATGGCATATGACAAAGAGCTTAGACCCAG
CAACAGGTTGTCTCAGTGTGTACCATGGAGCATCCTGCAAGAACCCCTGTCCCTAGACAGCAGGTCCCATACAATGGATG
TTAGGGATGCTCTTATCGAGCTACTCCAAACCATTCTCACGACCCT

ORF - retro_hsap_3574 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.18 %
Parental protein coverage: 51.79 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMPLVKRNIEPRHLCRGALPEGITSEL-ECVTNSTLAAIIRQLSSLSKHAEDIFGELFNEANNFYIRANSL
MP.VKR.I...HL..G.LPEGITS.L.E.VTN..L..I..QLS.L..HAEDIFGELF.EAN.F.IR.NSL
RetrocopyMPPVKRSI*SQHLHQGTLPEGITSDL<ESVTNNNLVTITHQLSNLNIHAEDIFGELFKEANYFHIRSNSL
ParentalQDRIDRLAVKVTQLDSTVEEVSLQDINMKKAFKSSTVQDQQVVSKNSIPNPVADIYNQSDKPPPLNILTP
..RI..L.VKVTQLDS.VEEVS.QDINM.KA.KSS..QDQQ.VSK.SIP.P.ADIYNQSD.PPPLN....
Retrocopy--RICCLMVKVTQLDSAVEEVSPQDINMEKALKSSPAQDQQAVSKSSIPTPAADIYNQSD*PPPLNSMRA
ParentalYRDDKKDGLKFYTDPSYFFDLWKEKMLQDTEDKRKEKRRQKEQKRIDGTTREVKKVRKARNRRQEWNMMA
..DDK.D.LKFYTDPS..FDLWKE..LQDTEDKRK..R.QK.Q..IDGTT..VK...KARN...EWNMMA
RetrocopyHGDDK-DRLKFYTDPSHLFDLWKEEVLQDTEDKRKDRRHQK*QNHIDGTTYDVKRITKARNKHHEWNMMA
ParentalYDKELRPDNRLSQSVYHGASSEGSLSPDTRSHASDVTD-YSYPATPNHSLHP
YDKELRP.NRLSQ.V......E..LS.D.RSH..DV.D..SY.ATPNHS..P
RetrocopyYDKELRPSNRLSQCVPWSILQE-PLSLDSRSHTMDVRD<CSYRATPNHSHDP

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 44 .35 RPM
bodymap2_adrenal 0 .00 RPM 18 .95 RPM
bodymap2_brain 0 .00 RPM 184 .12 RPM
bodymap2_breast 0 .00 RPM 80 .53 RPM
bodymap2_colon 0 .00 RPM 26 .80 RPM
bodymap2_heart 0 .00 RPM 20 .62 RPM
bodymap2_kidney 0 .06 RPM 20 .56 RPM
bodymap2_liver 0 .00 RPM 19 .96 RPM
bodymap2_lung 0 .00 RPM 19 .92 RPM
bodymap2_lymph_node 0 .00 RPM 28 .16 RPM
bodymap2_ovary 0 .00 RPM 50 .22 RPM
bodymap2_prostate 0 .00 RPM 39 .23 RPM
bodymap2_skeletal_muscle 0 .00 RPM 12 .71 RPM
bodymap2_testis 0 .06 RPM 55 .82 RPM
bodymap2_thyroid 0 .06 RPM 98 .11 RPM
bodymap2_white_blood_cells 0 .00 RPM 6 .16 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3574 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3574 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3574 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3574 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3574 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 4 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000132970 1 retrocopy
retro_hsap_3574 ,
Homo sapiens ENSG000001581951 retrocopy
retro_hsap_4682,
Gorilla gorilla ENSGGOG000000125181 retrocopy
retro_ggor_2411,
Tarsius syrichta ENSTSYG000000051843 retrocopies
retro_tsyr_1561, retro_tsyr_366, retro_tsyr_407,

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 = 0.14 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 .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 .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 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .02 RPM
GBR_HG00137 0 .14 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 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 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 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

The presence of retro_hsap_3574 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_3574 presence in various populations. Based on Kabza et al. 2015 (PubMed).


# Indel coordinates AFR, African AMR, Ad Mixed American EUR, European EAS, East Asian
ASW YRI LWK MXL PUR CLM CEU IBS GBR FIN TSI JPT CHB CHS
1. 6:31220481..31312900 99.18 100 100 100 100 100 100 100 99.44 100 100 100 100 100

Indel #1, located at the genomic coordinates 6:31220481..31312900.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 100 % Puerto Ricansfrom Puerto Rico PUR 100 % Colombians fromMedellin, Colombia CLM 100 % Americans of AfricanAncestry in SW USA ASW 99.18 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 100 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 99.44 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




Copyright © RetrogeneDB 2014-2017