RetrogeneDB ID:

retro_hsap_1256

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:13:41861879..41862456(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000231404
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RAC1
Ensembl ID:ENSG00000136238
Aliases:RAC1, Rac-1, TC-25, p21-Rac1
Description:ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1) [Source:HGNC Symbol;Acc:9801]


Retrocopy-Parental alignment summary:






>retro_hsap_1256
GTGCAAGCCATCAAGTGTGTGGTGGTTGGAGATGGAGCTACAAGTAAAACTTGCCTACTAATCAGTGTTACACCCAATGC
ATTTCCCAATGCATTATCACTATTGTCTTTGACAATTATTCTGCTGCCAATGTTAAGGTAGATGGAAAGCCAGTGAATCT
GGGCTTATGGGATACATCTGGACAAGAAGATTATGACAGATTATGCCCCCATTCTATCTGTAAACAGACATATTTTTAAT
ATGCTTCTCCCTTGTGAGTCTTGCATCATTTGAAAATGTCTGTGCAGAGTGGCATCCTGAAATGCAGCACCATTTTCCCA
ACACTCCCATCATTCTTGTGGGAAGTAAACTTGATCTTAATGTTGTTAAAGACACGATTGAGAAACTGAAGGAGAAGAAG
CTGACTCCCATCACCTATCTGCAGTTTTTAGCCAGGAATAAGGAGATTGGCGCTTTAAAATACCTGAAGTGCTTGGCTCT
CACATAGCGAGGGTTCAAAACGGTGTTTGACAAAGCTATCTGAGCAGTTCTCTGCCCACCTCCTGTGAAGAAGAGGAAGA
GAAAATGCCTGCTGTTG

ORF - retro_hsap_1256 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.46 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEY-IPTVFDNYSA-NVMVDGKPVNLGLWDTAGQEDYDRLR
.QAIKCVVVGDGA..KTCLLIS.T.NAFP....I..VFDNYSA.NV.VDGKPVNLGLWDT.GQEDYDRL.
RetrocopyVQAIKCVVVGDGATSKTCLLISVTPNAFPNAL<ITIVFDNYSAANVKVDGKPVNLGLWDTSGQEDYDRLC
ParentalPLS-YPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPI
P.S.Y..TD.FLICFSLVS.ASFENV.A.W.PE..HH.PNTPIILVG.KLDL...KDTIEKLKEKKLTPI
RetrocopyPHS<YL*TDIFLICFSLVSLASFENVCAEWHPEMQHHFPNTPIILVGSKLDLNVVKDTIEKLKEKKLTPI
ParentalTYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL
TY.Q.LA..KEIGA.KYL.C.ALT.RG.KTVFD.AI.AVLCPPPVKKRKRKCLLL
RetrocopyTYLQFLARNKEIGALKYLKCLALT*RGFKTVFDKAI*AVLCPPPVKKRKRKCLLL

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 299 .08 RPM
bodymap2_adrenal 0 .00 RPM 316 .19 RPM
bodymap2_brain 0 .00 RPM 421 .92 RPM
bodymap2_breast 0 .00 RPM 323 .35 RPM
bodymap2_colon 0 .00 RPM 312 .24 RPM
bodymap2_heart 0 .00 RPM 153 .30 RPM
bodymap2_kidney 0 .00 RPM 226 .02 RPM
bodymap2_liver 0 .00 RPM 109 .86 RPM
bodymap2_lung 0 .00 RPM 367 .58 RPM
bodymap2_lymph_node 0 .00 RPM 226 .96 RPM
bodymap2_ovary 0 .00 RPM 345 .11 RPM
bodymap2_prostate 0 .00 RPM 336 .25 RPM
bodymap2_skeletal_muscle 0 .00 RPM 296 .79 RPM
bodymap2_testis 0 .00 RPM 223 .28 RPM
bodymap2_thyroid 0 .00 RPM 299 .27 RPM
bodymap2_white_blood_cells 0 .00 RPM 226 .06 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1256 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1256 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1256 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1256 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1256 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_3044
Pongo abelii retro_pabe_1047
Parental genes homology:
Parental genes homology involve 11 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000708316 retrocopies
retro_hsap_2775, retro_hsap_2968, retro_hsap_3028, retro_hsap_3404, retro_hsap_3848, retro_hsap_4013,
Homo sapiens ENSG000001197293 retrocopies
retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Homo sapiens ENSG00000136238 6 retrocopies
retro_hsap_1256 , retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Gorilla gorilla ENSGGOG000000267332 retrocopies
retro_ggor_2110, retro_ggor_217,
Mus musculus ENSMUSG000000018472 retrocopies
retro_mmus_1372, retro_mmus_234,
Pan troglodytes ENSPTRG000000189104 retrocopies
retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus ENSRNOG000000010681 retrocopy
retro_rnor_230,
Ictidomys tridecemlineatus ENSSTOG000000067841 retrocopy
retro_itri_1503,
Tupaia belangeri ENSTBEG000000072724 retrocopies
retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Tarsius syrichta ENSTSYG000000016182 retrocopies
retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis ENSXETG000000275931 retrocopy
retro_xtro_1,

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 = 0.04 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 .04 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 .03 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 .02 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_1256 across human populations is associated with 1 indel. The percentage values indicate the frequencies of retro_hsap_1256 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. 13:41862020..41873600 100 100 99.48 100 100 100 100 100 100 100 100 100 100 100

Indel #1, located at the genomic coordinates 13:41862020..41873600.

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 99.48 % 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 100 % Japanese in Tokyo,Japan 100 % Southern Han Chinese CHS 100 % JPT EUROPE AMERICAS AFRICA EAST ASIA




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