RetrogeneDB ID:

retro_hsap_163

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:62654851..62655141(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000234204
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:PIGP
Ensembl ID:ENSG00000185808
Aliases:PIGP, DCRC, DCRC-S, DSCR5, DSRC
Description:phosphatidylinositol glycan anchor biosynthesis, class P [Source:HGNC Symbol;Acc:3046]


Retrocopy-Parental alignment summary:






>retro_hsap_163
AGACTGTCTAAAGCCGTAGGATAGTCATGGAGAATTCACCATTACATCTGCCAGAAAGAGCAATGTATGGCTCTGTTCTT
TTCTTAAACTCCCAATTTGGCTTCATGCCTTGTCTACTATGGACTTTGGCTCCTGAATCTTGGCAAAATTCTTCATGCTT
AAATTATTGGCTTCAAAAATACTGGGCAGTTGCATTACCTGTCTACCTCCTTAGTACTATAGTAACCAGTTATGTACTCT
TTTTTGGCACTAAAGTAATGAGTATCTCTCTCTCCACTCAACTCCATTCG

ORF - retro_hsap_163 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.24 %
Parental protein coverage: 61.39 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRLSKAPG-KMVENSPSPLPERAIYGFVLFLSSQFGFILYLVWAFIPESWLNSLGLTYWPQKYWAVALPVY
RLSKA.G....ENSP..LPERA.YG.VLFL.SQFGF...L.W...PESW.NS..L.YW.QKYWAVALPVY
RetrocopyRLSKAVG<IVMENSPLHLPERAMYGSVLFLNSQFGFMPCLLWTLAPESWQNSSCLNYWLQKYWAVALPVY
ParentalLLIAIVIGYVLLFGINMMSTSPLDSIHT
LL..IV..YVL.FG...MS.S.....H.
RetrocopyLLSTIVTSYVLFFGTKVMSISLSTQLHS

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 10 .81 RPM
bodymap2_adrenal 0 .00 RPM 9 .15 RPM
bodymap2_brain 0 .00 RPM 9 .00 RPM
bodymap2_breast 0 .00 RPM 16 .56 RPM
bodymap2_colon 0 .00 RPM 23 .38 RPM
bodymap2_heart 0 .00 RPM 17 .06 RPM
bodymap2_kidney 0 .00 RPM 10 .48 RPM
bodymap2_liver 0 .00 RPM 12 .51 RPM
bodymap2_lung 0 .00 RPM 9 .34 RPM
bodymap2_lymph_node 0 .00 RPM 9 .67 RPM
bodymap2_ovary 0 .00 RPM 10 .18 RPM
bodymap2_prostate 0 .00 RPM 35 .51 RPM
bodymap2_skeletal_muscle 0 .00 RPM 25 .04 RPM
bodymap2_testis 0 .00 RPM 24 .13 RPM
bodymap2_thyroid 0 .00 RPM 16 .85 RPM
bodymap2_white_blood_cells 0 .00 RPM 11 .89 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_163 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_163 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_163 retrocopy 5' end.

Lab - click to see more details

retro_hsap_163 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_163 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_156
Pongo abelii retro_pabe_464
Macaca mulatta retro_mmul_377
Parental genes homology:
Parental genes homology involve 22 parental genes, and 61 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000097024 retrocopies
retro_cfam_1022, retro_cfam_1559, retro_cfam_1976, retro_cfam_238,
Callithrix jacchus ENSCJAG000000026832 retrocopies
retro_cjac_1276, retro_cjac_2587,
Cavia porcellus ENSCPOG000000071562 retrocopies
retro_cpor_426, retro_cpor_680,
Equus caballus ENSECAG000000193491 retrocopy
retro_ecab_348,
Felis catus ENSFCAG000000284008 retrocopies
retro_fcat_1269, retro_fcat_1286, retro_fcat_1408, retro_fcat_1495, retro_fcat_1671, retro_fcat_181, retro_fcat_1859, retro_fcat_729,
Homo sapiens ENSG00000185808 4 retrocopies
retro_hsap_163 , retro_hsap_1909, retro_hsap_2110, retro_hsap_2423,
Gorilla gorilla ENSGGOG000000102753 retrocopies
retro_ggor_1397, retro_ggor_1508, retro_ggor_1639,
Macaca mulatta ENSMMUG000000162112 retrocopies
retro_mmul_377, retro_mmul_624,
Monodelphis domestica ENSMODG000000209881 retrocopy
retro_mdom_1807,
Mustela putorius furoENSMPUG000000083125 retrocopies
retro_mputfur_1069, retro_mputfur_1388, retro_mputfur_421, retro_mputfur_642, retro_mputfur_826,
Mus musculus ENSMUSG000000229401 retrocopy
retro_mmus_2841,
Nomascus leucogenys ENSNLEG000000045234 retrocopies
retro_nleu_1235, retro_nleu_1276, retro_nleu_1558, retro_nleu_2444,
Oryctolagus cuniculus ENSOCUG000000224513 retrocopies
retro_ocun_586, retro_ocun_664, retro_ocun_881,
Otolemur garnettii ENSOGAG000000110971 retrocopy
retro_ogar_2382,
Pongo abelii ENSPPYG000000114093 retrocopies
retro_pabe_1787, retro_pabe_1993, retro_pabe_464,
Pan troglodytes ENSPTRG000000138973 retrocopies
retro_ptro_1397, retro_ptro_1547, retro_ptro_156,
Pteropus vampyrus ENSPVAG000000008573 retrocopies
retro_pvam_1100, retro_pvam_1182, retro_pvam_682,
Sarcophilus harrisii ENSSHAG000000142841 retrocopy
retro_shar_548,
Sus scrofa ENSSSCG000000120611 retrocopy
retro_sscr_1085,
Ictidomys tridecemlineatus ENSSTOG000000109435 retrocopies
retro_itri_1237, retro_itri_1258, retro_itri_1869, retro_itri_616, retro_itri_897,
Tarsius syrichta ENSTSYG000000098991 retrocopy
retro_tsyr_47,
Tursiops truncatus ENSTTRG000000077113 retrocopies
retro_ttru_1043, retro_ttru_677, retro_ttru_883,

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 ) 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 .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 .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 .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 .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_163 across human populations is associated with 3 indels. The percentage values indicate the frequencies of retro_hsap_163 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. 1:62654000..62657100 98.36 100 97.94 81.82 95.45 90 96.47 100 97.19 96.24 96.94 61.8 65.46 66
2. 1:62654661..62657800 100 100 97.94 86.36 96.36 90.83 96.47 100 97.75 96.24 96.94 71.91 76.29 75
3. 1:62654736..62657200 98.36 100 97.94 81.82 95.45 90 96.47 100 97.19 96.24 96.94 60.11 65.46 65.5

Indel #1, located at the genomic coordinates 1:62654000..62657100.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 81.82 % Puerto Ricansfrom Puerto Rico PUR 95.45 % Colombians fromMedellin, Colombia CLM 90 % Americans of AfricanAncestry in SW USA ASW 98.36 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 97.94 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 96.47 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 97.19 % Finnish in Finland FIN 96.24 % Toscani in Italia TSI 96.94 % Han Chinese in Bejing,China CHB 65.46 % Japanese in Tokyo,Japan 61.8 % Southern Han Chinese CHS 66 % JPT EUROPE AMERICAS AFRICA EAST ASIA


Indel #2, located at the genomic coordinates 1:62654661..62657800.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 86.36 % Puerto Ricansfrom Puerto Rico PUR 96.36 % Colombians fromMedellin, Colombia CLM 90.83 % Americans of AfricanAncestry in SW USA ASW 100 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 97.94 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 96.47 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 97.75 % Finnish in Finland FIN 96.24 % Toscani in Italia TSI 96.94 % Han Chinese in Bejing,China CHB 76.29 % Japanese in Tokyo,Japan 71.91 % Southern Han Chinese CHS 75 % JPT EUROPE AMERICAS AFRICA EAST ASIA


Indel #3, located at the genomic coordinates 1:62654736..62657200.

image/svg+xml Mexican Ancestryfrom Los Angeles USA MXL 81.82 % Puerto Ricansfrom Puerto Rico PUR 95.45 % Colombians fromMedellin, Colombia CLM 90 % Americans of AfricanAncestry in SW USA ASW 98.36 % Yoruba in Ibadan,Nigeria YRI 100 % Luhya in Webuye,Kenya LWK 97.94 % Utah Residents (CEPH)with Northern andWestern European Ancestry CEU 96.47 % Iberian Populationin Spain IBS 100 % British in Englandand Scotland GBR 97.19 % Finnish in Finland FIN 96.24 % Toscani in Italia TSI 96.94 % Han Chinese in Bejing,China CHB 65.46 % Japanese in Tokyo,Japan 60.11 % Southern Han Chinese CHS 65.5 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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