RetrogeneDB ID:

retro_hsap_1678

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:16:34455999..34456314(-)
Located in intron of:ENSG00000260958
Retrocopy
information
Ensembl ID:ENSG00000260967
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RARRES2
Ensembl ID:ENSG00000106538
Aliases:RARRES2, HP10433, TIG2
Description:retinoic acid receptor responder (tazarotene induced) 2 [Source:HGNC Symbol;Acc:9868]


Retrocopy-Parental alignment summary:






>retro_hsap_1678
CACCCGCCTGTGCAGTGGCCTTCTGGGAGACCAGTGTGTACGGCACCATGGACACGGCCTTCCCAGCTGGAACATTTGTG
AGGCTGTAATTTAAGCTCAGGCATACAAGCGGCCAGAAGGTGGACTGGATGCAATCTGAGCGCAAAGTCCAACCTAGCGG
GAGTAAGCGGAAATGCCTGGCCTGCGTCAAACTGGGCTCTTAGGATAAGGCTCTAGGCTAGATGGCCACTGCCTTATAGA
GACTCAGGCTCGGCGGGAGCCTGAGGAGCACCAGGGACCCAGTGCAGCAGGGCGCAGTGGGCAGCGACAGCCCCA

ORF - retro_hsap_1678 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.3 %
Parental protein coverage: 65.03 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalHPPVQW-AFQETSVESAVDTPFPAGIFVRLEFKLQQTSCRKRDWKKPECKVRPNGRKRKCLACIKLGSED
HPPVQW.AF.ETSV....DT.FPAG.FVRL.FKL..TS..K.DW...E.KV.P.G.KRKCLAC.KLGS.D
RetrocopyHPPVQW<AFWETSVYGTMDTAFPAGTFVRL*FKLRHTSGQKVDWMQSERKVQPSGSKRKCLACVKLGS*D
ParentalKVLGRLV-HCPIETQVLREAEEHQ-ETQCLRVQRAGEDP
K.LG....HC.IETQ..RE.EEHQ..TQC.R.Q.A...P
RetrocopyKALG*MA<HCLIETQARREPEEHQ<GTQCSRAQWAATAP

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 38 .90 RPM
bodymap2_adrenal 0 .00 RPM 78 .66 RPM
bodymap2_brain 0 .00 RPM 7 .83 RPM
bodymap2_breast 0 .00 RPM 230 .96 RPM
bodymap2_colon 0 .00 RPM 81 .81 RPM
bodymap2_heart 0 .00 RPM 2 .88 RPM
bodymap2_kidney 0 .00 RPM 44 .61 RPM
bodymap2_liver 0 .00 RPM 190 .66 RPM
bodymap2_lung 0 .00 RPM 209 .11 RPM
bodymap2_lymph_node 0 .00 RPM 72 .40 RPM
bodymap2_ovary 0 .00 RPM 81 .50 RPM
bodymap2_prostate 0 .00 RPM 97 .53 RPM
bodymap2_skeletal_muscle 0 .00 RPM 1 .93 RPM
bodymap2_testis 0 .00 RPM 34 .11 RPM
bodymap2_thyroid 0 .00 RPM 29 .24 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .04 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1678 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1678 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1678 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1678 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1678 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1100
Parental genes homology:
Parental genes homology involve 7 parental genes, and 79 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000103225 retrocopies
retro_cjac_2100, retro_cjac_2706, retro_cjac_3874, retro_cjac_3904, retro_cjac_4141,
Homo sapiens ENSG00000106538 13 retrocopies
retro_hsap_1678 , retro_hsap_1679, retro_hsap_1680, retro_hsap_1681, retro_hsap_1682, retro_hsap_1683, retro_hsap_2665, retro_hsap_3134, retro_hsap_4327, retro_hsap_4330, retro_hsap_4332, retro_hsap_4792, retro_hsap_743,
Gorilla gorilla ENSGGOG000000111581 retrocopy
retro_ggor_2984,
Macaca mulatta ENSMMUG000000052324 retrocopies
retro_mmul_1555, retro_mmul_1993, retro_mmul_2378, retro_mmul_2554,
Nomascus leucogenys ENSNLEG0000000136218 retrocopies
retro_nleu_1108, retro_nleu_1744, retro_nleu_2079, retro_nleu_2944, retro_nleu_2978, retro_nleu_2999, retro_nleu_3000, retro_nleu_3001, retro_nleu_3034, retro_nleu_3036, retro_nleu_3067, retro_nleu_3071, retro_nleu_3072, retro_nleu_3076, retro_nleu_3089, retro_nleu_3092, retro_nleu_3119, retro_nleu_3128,
Pongo abelii ENSPPYG0000001816628 retrocopies
retro_pabe_1382, retro_pabe_1383, retro_pabe_1384, retro_pabe_1386, retro_pabe_1387, retro_pabe_1423, retro_pabe_1424, retro_pabe_1425, retro_pabe_1426, retro_pabe_2404, retro_pabe_2591, retro_pabe_2593, retro_pabe_2595, retro_pabe_2596, retro_pabe_2597, retro_pabe_2600, retro_pabe_2604, retro_pabe_2605, retro_pabe_2606, retro_pabe_2608, retro_pabe_3540, retro_pabe_3558, retro_pabe_3559, retro_pabe_3604, retro_pabe_3727, retro_pabe_638, retro_pabe_639, retro_pabe_666,
Pan troglodytes ENSPTRG0000001985410 retrocopies
retro_ptro_1095, retro_ptro_1096, retro_ptro_1097, retro_ptro_1098, retro_ptro_1099, retro_ptro_1100, retro_ptro_1795, retro_ptro_2942, retro_ptro_3067, retro_ptro_3188,

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_1678 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1678 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. 16:34455678..34457700 100 100 100 100 100 100 100 100 100 100 100 100 99.48 100

Indel #1, located at the genomic coordinates 16:34455678..34457700.

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 100 % 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 100 % Finnish in Finland FIN 100 % Toscani in Italia TSI 100 % Han Chinese in Bejing,China CHB 99.48 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




Copyright © RetrogeneDB 2014-2017