RetrogeneDB ID:

retro_mmus_187

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:8:78505545..78506712(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000037070
Aliases:Rbmxl1, Hnrpg, Rbmx, Rbmxrt
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Rbmx
Ensembl ID:ENSMUSG00000031134
Aliases:Rbmx, hnRNP G
Description:RNA binding motif protein, X chromosome [Source:MGI Symbol;Acc:MGI:1343044]


Retrocopy-Parental alignment summary:






>retro_mmus_187
ATGGTTGAAGCAGATCGCCCAGGAAAGCTCTTCATTGGTGGGCTTAATACAGAAACAAATGAGAAAGCCCTTGAAGCAGT
ATTTGGCAAGTATGGACGAATAGTGGAAATACTTTTGATGAAAGACCGGGAAACCAACAAATCAAGAGGATTTGCTTTTG
TTACCTTCGAAAGCCCAGCAGATGCTAAAGATGCAGCTAGAGATATGAATGGAAAGTCCTTGGATGGAAAAGCCATCAAG
GTGGAGCAAGCTACCAAACCATCTTTTGAAAGTGGCAGGCGTGGACCACCTCCACCTCCAAGAAGCAGGGGCCCTCCCAG
AGGTCTTCGAGGAGGAAGTGGAGGAACTAGGGGACCCCCTTCACGTGGAGGATACATGGATGATGGTGGTTATTCCATGA
ACTTTAACATGAGTTCTTCCAGGGGACCACTTCCAGTAAAGAGAGGACCACCACCACGAAGCGGGGGTCCCCCTCCTAAA
AGATCAACACCTTCCGGACCAGTTCGAAGCAGCAGTGGAATGGGCGGAAGAACACCAGTGTCCCGTGGAAGAGATAGCTA
CGGGGGTCCACCACGAAGGGAACCCCTGCCATCTCGCAGAGATGTTTATTTGTCCCCAAGAGATGATGGATATTCTACAA
AAGATAGCTATTCAAGCAGAGATTACCCAAGCTCCCGAGACACCAGAGATTATGCACCGCCACCAAGAGATTATACTTAC
CGTGATTACAGTCATTCCAGTTCCCGTGATGACTATCCATCAAGAGGCTACGGTGATAGAGATGGATATGGTCGGGATCG
TGACTATTCAGATCATCCAAGTGGAGGTTCCTACAGAGATTCATATGAGAGTTATGGAAACTCACGCAGTGCACCCCCTA
CACGAGGGCCACCACCATCTTATGGAGGAAGCAGTCGCTATGATGATTACAGCAGCTCACGTGATGGCTACGGTGGAAGT
CGAGACAGTTACTCAAGCAGCAGAAGTGATCTCTACTCAAGTGGCCGTGATCGAGTTGGCAGACAAGAACGAGGGCTTCC
CCCTTCTATGGAAAGGGGGTACCCTCCTCCACGTGATTCCTACAGCAGTTCAAGCCGAGGAGCGCCAAGAGGAGGTGGCC
GTGGAGGGAGCCGATCTGATAGAGGGGGAGGCAGAAGCAGATATTAG

ORF - retro_mmus_187 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 96.42 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
MVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVE.LLMKDRETNKSRGFAFVTFESPADAKDAARDMN
RetrocopyMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEILLMKDRETNKSRGFAFVTFESPADAKDAARDMN
ParentalGKSLDGKAIKVEQATKPSFESGRRGLPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFTM
GKSLDGKAIKVEQATKPSFESGRRG.PPPPRSRGPPRGL...RGGSGGTRGPPSRGG.MDDGGYSMNF.M
RetrocopyGKSLDGKAIKVEQATKPSFESGRRGPPPPPRSRGPPRGL---RGGSGGTRGPPSRGGYMDDGGYSMNFNM
ParentalSSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGLGGRAPVSRGRDGYGGPPRREPLPSRRDVYLSPR
SSSRGPLPVKRGPPPRSGGPPPKRS.PSGPVRSSSG.GGR.PVSRGRD.YGGPPRREPLPSRRDVYLSPR
RetrocopySSSRGPLPVKRGPPPRSGGPPPKRSTPSGPVRSSSGMGGRTPVSRGRDSYGGPPRREPLPSRRDVYLSPR
ParentalDDGYSTKDSYSSREYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGYGRDRDYSDHPSGGS
DDGYSTKDSYSSR.YPSSRDTRDYAPPPRDYTYRDY.HSSSRDDYPSRGY.DRDGYGRDRDYSDHPSGGS
RetrocopyDDGYSTKDSYSSRDYPSSRDTRDYAPPPRDYTYRDYSHSSSRDDYPSRGYGDRDGYGRDRDYSDHPSGGS
ParentalYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLP
YRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLP
RetrocopyYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDYSSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERGLP
ParentalPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY
PSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY
RetrocopyPSMERGYPPPRDSYSSSSRGAPRGGGRGGSRSDRGGGRSRY

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
SRP007412_brain 5 .75 RPM 55 .88 RPM
SRP007412_cerebellum 5 .69 RPM 61 .75 RPM
SRP007412_heart 2 .71 RPM 35 .52 RPM
SRP007412_kidney 3 .14 RPM 43 .47 RPM
SRP007412_liver 2 .51 RPM 14 .86 RPM
SRP007412_testis 2 .84 RPM 5 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_187 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001YJZ POLR2A 8:78507538..78510519
ENCFF001YKA POLR2A 8:78506799..78510620

EST - click to see more details

No EST(s) were mapped for retro_mmus_187 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_187 retrocopy 5' end.

Lab - click to see more details

retro_mmus_187 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_187 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 28 parental genes, and 65 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 ENSG000001472747 retrocopies
retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
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 ENSMUSG000000228586 retrocopies
retro_mmus_1187, retro_mmus_2253, retro_mmus_2313, retro_mmus_3139, retro_mmus_3617, retro_mmus_756,
Mus musculus ENSMUSG00000031134 2 retrocopies
retro_mmus_170, retro_mmus_187 ,
Mus musculus ENSMUSG000000311674 retrocopies
retro_mmus_2044, retro_mmus_2963, retro_mmus_3019, retro_mmus_501,
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,
Pongo abelii ENSPPYG000000207713 retrocopies
retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus ENSRNOG000000008661 retrocopy
retro_rnor_268,
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,


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