RetrogeneDB ID:

retro_hsap_3221

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:97073597..97074203(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000251193
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ZDHHC3
Ensembl ID:ENSG00000163812
Aliases:None
Description:zinc finger, DHHC-type containing 3 [Source:HGNC Symbol;Acc:18470]


Retrocopy-Parental alignment summary:






>retro_hsap_3221
ATGGTGCTGGTCCCCACCCACCACTTCAGAGACTTTGAGAGGAAACCAGAGTACCCATAGCTGGAGATGCCTGTCCGACC
TCCCTACCCTGGTCCTATGAGAACCATGTGGCTTATCCACGATGGCTGTGGCATCGCCTGTGCCATCATCACCTGGTTTC
TGGTCCTCTATGCGGAGTTTGTGGTCCTCTTTTTCATGCTGATTCCATCCGGAGACTATGCTTACAGCACCATCAATGGA
ATTGTGTTCAACCTGCTGACTTTCTTGGCCCTGGCCTCCCACTGCCAGGCCATGCTGACAGACACCGGAGCAGTGCCCAA
ATGAAATGCCACAAATAATTCATCCAGAGTTTACAGATGAAGCCCAGGCATGTGGTATACTCGTGTCCCAGTGCTGCAGC
CTCAAGCCTGACCCAGCCTGCCGCTGCAGTGTTTGTAAGGGGTGCATTCGTAGGGTGGACCCCCACTGTCCCTGGGTCAA
CATCTGCATCGAAGAGAACAACCAGAAGTGCTTTGTCCTGCCTATCATGTGCACAGCTCTCATTTCCTTGCCTGCCCTCA
TCATGGTGGATTACACTTCCTGGATTGTTGTGAAGAAGATTACTCA

ORF - retro_hsap_3221 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.3 %
Parental protein coverage: 67.89 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMMLIPTHHFRNIERKPEYLQPEKCVPPPYPGPVGTMWFIRDGCGIACAIVTWFLVLYAEFVVLFVMLIPS
M.L.PTHHFR..ERKPEY...E..V.PPYPGP..TMW.I.DGCGIACAI.TWFLVLYAEFVVLF.MLIPS
RetrocopyMVLVPTHHFRDFERKPEYP*LEMPVRPPYPGPMRTMWLIHDGCGIACAIITWFLVLYAEFVVLFFMLIPS
ParentalRDYVYSIINGIVFNLLAFLALASHCRAMLTDPGAVPKGNAT-KEFIESLQLKPGQVVYKCP-KCCSIKPD
.DY.YS.INGIVFNLL.FLALASHC.AMLTD.GAVPK.NAT.K.FI.SLQ.KP..VVY.CP..CCS.KPD
RetrocopyGDYAYSTINGIVFNLLTFLALASHCQAMLTDTGAVPK*NAT<K*FIQSLQMKPRHVVYSCP<QCCSLKPD
ParentalRAHHCSVCKRCIRKMDHHCPWVNNCVGENNQKYFVLFTMYIALISLHALIMV-GFHFLHCFEEDWT
.A..CSVCK.CIR..D.HCPWVN.C..ENNQK.FVL..M..ALISL.ALIMV.G.HFL.C.EED..
RetrocopyPACRCSVCKGCIRRVDPHCPWVNICIEENNQKCFVLPIMCTALISLPALIMV<GLHFLDCCEEDYS

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 63 .57 RPM
bodymap2_adrenal 0 .00 RPM 48 .12 RPM
bodymap2_brain 0 .00 RPM 30 .82 RPM
bodymap2_breast 0 .00 RPM 98 .64 RPM
bodymap2_colon 0 .00 RPM 44 .22 RPM
bodymap2_heart 0 .00 RPM 45 .43 RPM
bodymap2_kidney 0 .00 RPM 59 .21 RPM
bodymap2_liver 0 .00 RPM 26 .68 RPM
bodymap2_lung 0 .00 RPM 52 .23 RPM
bodymap2_lymph_node 0 .00 RPM 51 .62 RPM
bodymap2_ovary 0 .00 RPM 55 .00 RPM
bodymap2_prostate 0 .00 RPM 56 .88 RPM
bodymap2_skeletal_muscle 0 .00 RPM 28 .12 RPM
bodymap2_testis 0 .00 RPM 102 .77 RPM
bodymap2_thyroid 0 .00 RPM 52 .09 RPM
bodymap2_white_blood_cells 0 .00 RPM 59 .97 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3221 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3221 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3221 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3221 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3221 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2171
Gorilla gorilla retro_ggor_2187
Pongo abelii retro_pabe_2668
Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000163812 1 retrocopy
retro_hsap_3221 ,
Homo sapiens ENSG000001807761 retrocopy
retro_hsap_1211,
Pongo abelii ENSPPYG000000139501 retrocopy
retro_pabe_2668,
Pan troglodytes ENSPTRG000000148291 retrocopy
retro_ptro_2171,

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 = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 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 .02 RPM
FIN_HG00338 0 .00 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 .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 .03 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 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

The presence of retro_hsap_3221 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_3221 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. 5:97047854..97096200 100 100 100 99.24 95.45 99.17 97.06 100 97.75 93.55 96.94 100 100 100

Indel #1, located at the genomic coordinates 5:97047854..97096200.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 99.24 % Puerto Ricansfrom Puerto Rico PUR 95.45 % Colombians fromMedellin, Colombia CLM 99.17 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 100 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 97.06 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 97.75 % Finnish in Finland FIN 93.55 % Toscani in Italia TSI 96.94 % Han Chinese in Bejing,China CHB 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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