RetrogeneDB ID:

retro_hsap_4846

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:65176416..65177032(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000217835
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RBMX
Ensembl ID:ENSG00000147274
Aliases:RBMX, HNRNPG, HNRPG, RBMXP1, RBMXRT, RNMX, hnRNP-G
Description:RNA binding motif protein, X-linked [Source:HGNC Symbol;Acc:9910]


Retrocopy-Parental alignment summary:






>retro_hsap_4846
GAAGCAGATCGCCTAGGAAAGTTTTTCATTGGTGGGCTTAATACGGAAACAAATAAGAAAGCTCTTGAAGCAGTATTTGG
CAAATATGGACAAATAGTGGAAGTACACTTGATGAAAGACTGTGAAACCAACAAATCAAGAGGATTTGCTTTTATCACCT
TTGAAAGACCAGCAGACGCTAAGGATGCAGCCAGAGACATGAATGGAAAGTCATTAGATGGAAAAGCCATCAAGGTGGAA
CAAGCCACCAAACCGTCATTTGAAAGTGGTAGACGTGGACCGCCTCCACCTCCAAGAAGTAGAGGCCCTCCAAGAGTTCT
TAGAGGTGGAAGAGGAGGAAGTGGAGGAACCAGGGAACCTCCCTCACGGGGAGGACACATGGATGACTGGTGGATATTCC
ATGAATTTTAACATGAGTTCTTCCAGGGGACCACTCCCAGTAAAAAGAGGACCACCACCAAGAAGTGGGGGTCTTCCTCC
TAAGAGATCTGCACCTTCAGGACCAGTTCGCAGTAGCAGTGGAATGGGAGGAAGAGCTCCTGTATCACGTGGAAGAGATA
GTTACCGAGGTCCACCTCGAAGGGAATCGCTGCCCTCTTGTAGAGAGCTCCACCTA

ORF - retro_hsap_4846 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.41 %
Parental protein coverage: 70.21 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMNGK
EADR.GK.FIGGLNTETN.KALEAVFGKYG.IVEV.LMKD.ETNKSRGFAF.TFE.PADAKDAARDMNGK
RetrocopyEADRLGKFFIGGLNTETNKKALEAVFGKYGQIVEVHLMKDCETNKSRGFAFITFERPADAKDAARDMNGK
ParentalSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDD-GGYSMNFNMS
SLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPR.L..........R.PPSRGGHMDD.GGYSMNFNMS
RetrocopySLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRVLXXXXXXXXXXREPPSRGGHMDD>GGYSMNFNMS
ParentalSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYL
SSRGPLPVKRGPPPRSGG.PPKRSAPSGPVRSSSGMGGRAPVSRGRDSY.GPPRRE.LPS.R...L
RetrocopySSRGPLPVKRGPPPRSGGLPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYRGPPRRESLPSCRELHL

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 111 .30 RPM
bodymap2_adrenal 0 .00 RPM 161 .12 RPM
bodymap2_brain 0 .00 RPM 90 .38 RPM
bodymap2_breast 0 .00 RPM 94 .77 RPM
bodymap2_colon 0 .00 RPM 124 .83 RPM
bodymap2_heart 0 .00 RPM 77 .33 RPM
bodymap2_kidney 0 .00 RPM 107 .46 RPM
bodymap2_liver 0 .00 RPM 52 .49 RPM
bodymap2_lung 0 .14 RPM 104 .25 RPM
bodymap2_lymph_node 0 .00 RPM 106 .28 RPM
bodymap2_ovary 0 .02 RPM 179 .54 RPM
bodymap2_prostate 0 .00 RPM 183 .35 RPM
bodymap2_skeletal_muscle 0 .00 RPM 175 .20 RPM
bodymap2_testis 0 .00 RPM 113 .87 RPM
bodymap2_thyroid 0 .00 RPM 159 .88 RPM
bodymap2_white_blood_cells 0 .00 RPM 136 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4846 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4846 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4846 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4846 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4846 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 26 parental genes, and 53 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000133081 retrocopy
retro_btau_36,
Canis familiaris ENSCAFG000000189624 retrocopies
retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni ENSCHOG000000123693 retrocopies
retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus ENSCPOG000000121641 retrocopy
retro_cpor_778,
Dasypus novemcinctus ENSDNOG000000171993 retrocopies
retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Dipodomys ordii ENSDORG000000154811 retrocopy
retro_dord_793,
Echinops telfairi ENSETEG000000131781 retrocopy
retro_etel_1952,
Felis catus ENSFCAG000000047791 retrocopy
retro_fcat_1903,
Homo sapiens ENSG000001023171 retrocopy
retro_hsap_265,
Homo sapiens ENSG00000147274 7 retrocopies
retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846 , retro_hsap_800, retro_hsap_91,
Homo sapiens ENSG000001645481 retrocopy
retro_hsap_386,
Gorilla gorilla ENSGGOG000000069441 retrocopy
retro_ggor_657,
Loxodonta africana ENSLAFG000000055683 retrocopies
retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus ENSMICG000000068562 retrocopies
retro_mmur_1252, retro_mmur_661,
Myotis lucifugus ENSMLUG000000132095 retrocopies
retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Monodelphis domestica ENSMODG000000140541 retrocopy
retro_mdom_1231,
Mustela putorius furoENSMPUG000000018552 retrocopies
retro_mputfur_1539, retro_mputfur_956,
Mus musculus ENSMUSG000000311342 retrocopies
retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus ENSOCUG000000072201 retrocopy
retro_ocun_3,
Otolemur garnettii ENSOGAG000000078395 retrocopies
retro_ogar_1057, retro_ogar_137, retro_ogar_1586, retro_ogar_2445, retro_ogar_2584,
Ochotona princeps ENSOPRG000000165931 retrocopy
retro_opri_372,
Sorex araneus ENSSARG000000003971 retrocopy
retro_sara_169,
Ictidomys tridecemlineatus ENSSTOG000000062112 retrocopies
retro_itri_1205, retro_itri_1346,
Tupaia belangeri ENSTBEG000000011541 retrocopy
retro_tbel_1919,
Tarsius syrichta ENSTSYG000000095551 retrocopy
retro_tsyr_15,
Tursiops truncatus ENSTTRG000000073221 retrocopy
retro_ttru_1450,

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 = 0.16 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .13 RPM
CEU_NA12004 0 .04 RPM
CEU_NA12400 0 .07 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .03 RPM
CEU_NA12873 0 .03 RPM
FIN_HG00183 0 .16 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .06 RPM
FIN_HG00328 0 .14 RPM
FIN_HG00338 0 .06 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .08 RPM
FIN_HG00378 0 .04 RPM
GBR_HG00099 0 .03 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .07 RPM
GBR_HG00131 0 .11 RPM
GBR_HG00133 0 .10 RPM
GBR_HG00134 0 .04 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .03 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .02 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .06 RPM
TSI_NA20786 0 .08 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .04 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .03 RPM
YRI_NA19114 0 .08 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .05 RPM
YRI_NA19214 0 .07 RPM
YRI_NA19223 0 .08 RPM

Indel association:

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



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