RetrogeneDB ID:

retro_hsap_3632

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:92525560..92526131(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000219867
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RHOA
Ensembl ID:ENSG00000067560
Aliases:RHOA, ARH12, ARHA, RHO12, RHOH12
Description:ras homolog family member A [Source:HGNC Symbol;Acc:667]


Retrocopy-Parental alignment summary:






>retro_hsap_3632
ATGGTTCCCGTCCAGAAGAAGCTGGTAATTGTCGGTGACAGAGTCTGTGGCAAGACATGCTTGCTCATTGTCTTCAGCAA
GGACCAGTTCCCAGAGGGGTGAGCACCCTCAGGGTTTCAGAACTATGTGGCCCATATCGAGGTGGATGGGAAAGTGTAGA
GCTGACTTTGTGGGACACAGCCAGGCAGGAAGATTAGGATCGCCTGAGGCCCCTCTTTTACTCGGACACTGATGTTATGT
GTTCTCCGTTGACAACCCTGAGAGTTTAGAAAACATCCCAGAGAAATGGAGCCCAGAAGTCAAGCATTTCTGTCCCAACG
TGCCCACCAGCCTGGTTGGGAACAAGAAGGATCTTCGGAATGATGTGCACACAAGGTGGGAGCTAGCCAGGATGAAGCAG
AAGAGGGTGAGACTCGAAGAGGGCAGAGATATGGTCAAGGGAATTGGCTCTTTGGGGTACATGAAGTGTTCAGCAAAGAC
CAAAGATGGAGTGAGAGAGGTTTTTGAAGTGGCTGCGAAAGCTACTCTGCAAGCCAGATGTGGGAAGAAAAACTCTGGGT
GCCTTGTCTTG

ORF - retro_hsap_3632 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.38 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGK-QVELALWDTAGQEDYDRL
M....KKLVIVGD..CGKTCLLIVFSKDQFPE...P..F.NYVA.IEVDGK..VEL.LWDTA.QED.DRL
RetrocopyMVPVQKKLVIVGDRVCGKTCLLIVFSKDQFPEG*APSGFQNYVAHIEVDGK<SVELTLWDTARQED*DRL
ParentalRPLSYPDTDVILMC-FSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEP
RPL.Y.DTDV..MC.FS.D.P.SLENIPEKW.PEVKHFCPNVP..LVGNKKDLRND.HTR.ELA.MKQ..
RetrocopyRPLFYSDTDV--MC<FSVDNPESLENIPEKWSPEVKHFCPNVPTSLVGNKKDLRNDVHTRWELARMKQKR
ParentalVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRGKKKSGCLVL
V..EEGRDM...IG..GYM.CSAKTKDGVREVFE.A..A.LQAR.GKK.SGCLVL
RetrocopyVRLEEGRDMVKGIGSLGYMKCSAKTKDGVREVFEVAAKATLQARCGKKNSGCLVL

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 757 .45 RPM
bodymap2_adrenal 0 .00 RPM 649 .43 RPM
bodymap2_brain 0 .00 RPM 361 .28 RPM
bodymap2_breast 0 .00 RPM 744 .74 RPM
bodymap2_colon 0 .00 RPM 587 .60 RPM
bodymap2_heart 0 .00 RPM 237 .02 RPM
bodymap2_kidney 0 .00 RPM 493 .85 RPM
bodymap2_liver 0 .00 RPM 198 .94 RPM
bodymap2_lung 0 .00 RPM 799 .91 RPM
bodymap2_lymph_node 0 .00 RPM 569 .64 RPM
bodymap2_ovary 0 .00 RPM 636 .81 RPM
bodymap2_prostate 0 .00 RPM 587 .31 RPM
bodymap2_skeletal_muscle 0 .00 RPM 593 .82 RPM
bodymap2_testis 0 .11 RPM 544 .03 RPM
bodymap2_thyroid 0 .00 RPM 519 .31 RPM
bodymap2_white_blood_cells 0 .00 RPM 1068 .50 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3632 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3632 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3632 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3632 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3632 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2456
Gorilla gorilla retro_ggor_2450
Pongo abelii retro_pabe_2979
Parental genes homology:
Parental genes homology involve 24 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000082971 retrocopy
retro_acar_41,
Anas platyrhynchos ENSAPLG000000146871 retrocopy
retro_apla_10,
Canis familiaris ENSCAFG000000230662 retrocopies
retro_cfam_1652, retro_cfam_186,
Callithrix jacchus ENSCJAG000000039043 retrocopies
retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Cavia porcellus ENSCPOG000000140731 retrocopy
retro_cpor_514,
Dipodomys ordii ENSDORG000000033823 retrocopies
retro_dord_1, retro_dord_18, retro_dord_538,
Homo sapiens ENSG00000067560 2 retrocopies
retro_hsap_108, retro_hsap_3632 ,
Gasterosteus aculeatus ENSGACG000000056701 retrocopy
retro_gacu_9,
Gallus gallus ENSGALG000000038061 retrocopy
retro_ggal_5,
Gadus morhua ENSGMOG000000081881 retrocopy
retro_gmor_18,
Latimeria chalumnae ENSLACG000000169411 retrocopy
retro_lcha_15,
Meleagris gallopavo ENSMGAG000000022801 retrocopy
retro_mgal_2,
Macaca mulatta ENSMMUG000000129621 retrocopy
retro_mmul_977,
Monodelphis domestica ENSMODG000000129812 retrocopies
retro_mdom_19, retro_mdom_294,
Mustela putorius furoENSMPUG000000138405 retrocopies
retro_mputfur_1015, retro_mputfur_140, retro_mputfur_1541, retro_mputfur_1588, retro_mputfur_650,
Mus musculus ENSMUSG000000078159 retrocopies
retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,
Ornithorhynchus anatinus ENSOANG000000138071 retrocopy
retro_oana_7,
Oreochromis niloticus ENSONIG000000188841 retrocopy
retro_onil_32,
Ochotona princeps ENSOPRG000000096381 retrocopy
retro_opri_590,
Pelodiscus sinensis ENSPSIG000000153281 retrocopy
retro_psin_7,
Rattus norvegicus ENSRNOG000000505193 retrocopies
retro_rnor_127, retro_rnor_2899, retro_rnor_408,
Ictidomys tridecemlineatus ENSSTOG000000045612 retrocopies
retro_itri_39, retro_itri_96,
Takifugu rubripes ENSTRUG000000119441 retrocopy
retro_trub_19,
Tursiops truncatus ENSTTRG000000173702 retrocopies
retro_ttru_27, retro_ttru_339,

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 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 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 .03 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:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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