RetrogeneDB ID:

retro_hsap_23

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:89448336..89449509(-)
Located in intron of:ENSG00000137944
Retrocopy
information
Ensembl ID:ENSG00000213516
Aliases:RBMXL1, RBM1
Status:KNOWN_PROTEIN_CODING
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_23
ATGGTTGAAGCAGATCGCCCAGGAAAGCTCTTCATTGGTGGGCTTAATACGGAAACAAATGAGAAAGCTCTTGAAACAGT
ATTTGGCAAATATGGACGAATAGTGGAAGTACTCTTGATAAAAGACCGTGAAACCAACAAATCAAGAGGATTTGCTTTTG
TCACCTTTGAAAGCCCAGCAGACGCTAAGGATGCAGCCAGAGACATGAATGGAAAGTCATTAGATGGAAAAGCCATCAAG
GTGGAACAAGCCACCAAACCATCATTTGAAAGAGGTAGACATGGACCGCCCCCACCTCCAAGAAGTAGAGGTCCTCCAAG
AGGTTTTGGAGCTGGAAGAGGAGGAAGTGGAGGAACCAGGGGACCTCCTTCACGAGGAGGACACATGGATGATGGTGGAT
ATTCCATGAATTTTAACATGAGTTCTTCCAGGGGACCACTCCCAGTAAAAAGAGGACCACCACCAAGAAGTGGGGGTCCT
TCTCCTAAGAGATCTGCACCTTCAGGACTAGTTCGCAGCAGCAGTGGAATGGGAGGAAGAGCTCCTCTATCACGTGGAAG
AGATAGTTATGGAGGTCCACCTCGAAGGGAACCGCTCCCCTCTCGTAGAGATGTTTATTTGTCCCCAAGAGATGATGGGT
ATTCTACTAAAGACAGCTATTCAAGCAGAGATTACCCAAGTTCTCGTGATACAAGAGATTATGCACCACCACCACGAGAT
TATACTTACCGTGATTATGGTCATTCCAGTTCACGTGATGACTATCCATCAAGAGGCTATGGCGATAGAGATGGATATGG
TCGTGATCGTGACTATTCAGATCATCCAAGTGGAGGTTCCTACAGAGATTCATATGAGAGTTATGGTAACTCACGTAGTG
CTCCACTTACACGAGGGCCCCCGCCATCTTATGGTGGAAGCAGTCGCTATGATGATTATAGCAGCTCACGTGATGGATAT
GGTGGAAGTCGAGACAGTTACTCAAGCAGCCGAAGTGATCTCTACTCAAGTTGTGACAGGGTTGGCAGACAAGAAAGAGG
GCTTCCCCCTTCTGTAGAAAGGGGGTACCCTTCTTCACGTGATTCCTACAGCAGTTCAAGCCGCGGAGCACCAAGAGGTG
CTGGCCCTGGAGGAAGCCGATCTGATAGAGGGGGAGGCAGAAGCAGATACTAG

ORF - retro_hsap_23 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.14 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
MVEADRPGKLFIGGLNTETNEKALE.VFGKYGRIVEVLL.KDRETNKSRGFAFVTFESPADAKDAARDMN
RetrocopyMVEADRPGKLFIGGLNTETNEKALETVFGKYGRIVEVLLIKDRETNKSRGFAFVTFESPADAKDAARDMN
ParentalGKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFNM
GKSLDGKAIKVEQATKPSFE.GR.GPPPPPRSRGPPRG...GRGGSGGTRGPPSRGGHMDDGGYSMNFNM
RetrocopyGKSLDGKAIKVEQATKPSFERGRHGPPPPPRSRGPPRGFGAGRGGSGGTRGPPSRGGHMDDGGYSMNFNM
ParentalSSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRRDVYLSPR
SSSRGPLPVKRGPPPRSGGP.PKRSAPSG.VRSSSGMGGRAP.SRGRDSYGGPPRREPLPSRRDVYLSPR
RetrocopySSSRGPLPVKRGPPPRSGGPSPKRSAPSGLVRSSSGMGGRAPLSRGRDSYGGPPRREPLPSRRDVYLSPR
ParentalDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGS
DDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGY.DRDGYGRDRDYSDHPSGGS
RetrocopyDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYGDRDGYGRDRDYSDHPSGGS
ParentalYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLP
YRDSYESYGNSRSAP.TRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSS..DRVGRQERGLP
RetrocopyYRDSYESYGNSRSAPLTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSS-CDRVGRQERGLP
ParentalPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY
PS.ERGYP..RDSYSSSSRGAPRG.G.GGSRSDRGGGRSRY
RetrocopyPSVERGYPSSRDSYSSSSRGAPRGAGPGGSRSDRGGGRSRY

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 5 .13 RPM 111 .30 RPM
bodymap2_adrenal 2 .95 RPM 161 .12 RPM
bodymap2_brain 7 .59 RPM 90 .38 RPM
bodymap2_breast 3 .02 RPM 94 .77 RPM
bodymap2_colon 4 .80 RPM 124 .83 RPM
bodymap2_heart 3 .75 RPM 77 .33 RPM
bodymap2_kidney 4 .51 RPM 107 .46 RPM
bodymap2_liver 3 .19 RPM 52 .49 RPM
bodymap2_lung 8 .14 RPM 104 .25 RPM
bodymap2_lymph_node 5 .15 RPM 106 .28 RPM
bodymap2_ovary 6 .80 RPM 179 .54 RPM
bodymap2_prostate 8 .83 RPM 183 .35 RPM
bodymap2_skeletal_muscle 4 .20 RPM 175 .20 RPM
bodymap2_testis 7 .28 RPM 113 .87 RPM
bodymap2_thyroid 4 .46 RPM 159 .88 RPM
bodymap2_white_blood_cells 10 .24 RPM 136 .42 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_23 was not detected

EST - click to see more details

3 EST(s) were mapped to retro_hsap_23 retrocopy
EST ID Start End Identity Match Mis-match Score
BE867589 89448440 89449030 99.5 590 0 589
DA237438 89448275 89448861 100 585 0 584
DB384583 89448294 89448841 98.9 540 3 536

TSS - click to see more details

No TSS is located nearby retro_hsap_23 retrocopy 5' end.

Lab - click to see more details

retro_hsap_23 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_23 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_303
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 = 10.06 RPM Legend:


Library Retrogene expression
CEU_NA11831 4 .52 RPM
CEU_NA11843 2 .90 RPM
CEU_NA11930 6 .10 RPM
CEU_NA12004 4 .33 RPM
CEU_NA12400 3 .68 RPM
CEU_NA12751 7 .19 RPM
CEU_NA12760 6 .02 RPM
CEU_NA12827 5 .14 RPM
CEU_NA12872 6 .31 RPM
CEU_NA12873 5 .52 RPM
FIN_HG00183 5 .66 RPM
FIN_HG00277 6 .80 RPM
FIN_HG00315 5 .19 RPM
FIN_HG00321 5 .89 RPM
FIN_HG00328 6 .84 RPM
FIN_HG00338 5 .09 RPM
FIN_HG00349 4 .84 RPM
FIN_HG00375 6 .77 RPM
FIN_HG00377 5 .07 RPM
FIN_HG00378 8 .75 RPM
GBR_HG00099 10 .06 RPM
GBR_HG00111 4 .34 RPM
GBR_HG00114 5 .44 RPM
GBR_HG00119 7 .42 RPM
GBR_HG00131 8 .02 RPM
GBR_HG00133 6 .54 RPM
GBR_HG00134 6 .68 RPM
GBR_HG00137 5 .03 RPM
GBR_HG00142 5 .08 RPM
GBR_HG00143 6 .80 RPM
TSI_NA20512 3 .33 RPM
TSI_NA20513 7 .33 RPM
TSI_NA20518 6 .22 RPM
TSI_NA20532 5 .17 RPM
TSI_NA20538 6 .31 RPM
TSI_NA20756 6 .75 RPM
TSI_NA20765 7 .33 RPM
TSI_NA20771 5 .76 RPM
TSI_NA20786 7 .74 RPM
TSI_NA20798 6 .24 RPM
YRI_NA18870 7 .18 RPM
YRI_NA18907 7 .07 RPM
YRI_NA18916 6 .25 RPM
YRI_NA19093 9 .63 RPM
YRI_NA19099 8 .10 RPM
YRI_NA19114 6 .95 RPM
YRI_NA19118 6 .46 RPM
YRI_NA19213 7 .61 RPM
YRI_NA19214 8 .49 RPM
YRI_NA19223 8 .60 RPM

Indel association:

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





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