RetrogeneDB ID:

retro_mmus_170

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:7:107209509..107210667(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000073894
Aliases:Rbmxl2, 1700012H05Rik, Hnrnpg-t
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_170
ATGGTTGAAGCCGACCGTCCAGGGAAGCTCTTCATCGGCGGTCTCAACCTCGAGACCGACGAGAAGGGCCTCGAAACCGC
TTTCGGCAAGTATGGCCGCATCATCGAGGTGCTCCTGATGAAGGACCGGGAAACCTCCAAGTCCAGAGGCTTCGCCTTCG
TCACCTTCGAGAACCCCGCGGACGCCAAGGCCGCAGCCCGAGACATGAACGGCAAGTCCCTGGATGGTAAGGCCATCAAA
GTGGCCCAAGCCACCAAGCCGGTGTTCGAGAGCGGCCGGCGCGGGCCCCCTCCTCCCCGAAGCCGCGGCCGCCCGAGGGG
CCTGCGCGGGACCCGTGGCGGCGGCCCGAGGCGCCCTCCCTCCCGGGGCGGGTCGGCCGACGAAGGCGGCTACACGGGGG
ATTTCGACCTGCGGCCTTCGCGGGCCCCCATGCCACTGAAGCGCGGGCCGCCGCCGCGCCGGGCCGGGCCTCCGCCCAAA
AGAGCAGCGCCGTCGGGCCCCGCGCGCAGCGGCGCGGGAATTCGCGGGCGGGCGGCGGGCTCCCGGGGACGAGACGGCTA
CGGGGGCCCGCCGCGCCGGGAGCTGCCACCGCCGCGCCGCGACCCGTACCTGGGCCCGCGCGACGAGGGCTACTCGCCCC
GGGAGAGCTATTCGAGCCGCGACTACCCGAGCGCCCGGGACCCGCGCGACTTCGCGCCCTCGCCCCGCGACTACACCTAC
CGCGACTATGGCCACTCGAGCGCGCGAGACGAATGCCCTTCCCGGGGCTACTGTGAGCGCGACGGCTACGGCGGCCGCGA
GCGCGACTACGAGCATCCTAGCGGAGGCTCCTACCGCGACCCCTTCGACAGCTACGGGGACCCGCGTGGCGCCGGTCCTG
CCCGAGGGCCACCGCCATCTTACGGCGGGGGCCGCTATGACGAGTACCGAGGCTGCTCGCCCGACGGCTATGGCGGCCGC
GACAGCTACCGCAGCGAGCGCTACTCGAGTGGCCGTGAGCGCGTGGGTAGGCCGGAGCGCGGGCTGCCGCCGTCTGTAGA
ACGAAACTGCCCGGCGCCGCGGGATTCCTACAGCCGCTCGGGCCGCCGGGCGCCCCCGAGGGGCGGAGGCCGCGTGGGAA
GCCGCCTGGAGCGAGGGGGAGGCCGGAGCAGGTACTGA

ORF - retro_mmus_170 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.13 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMVEADRPGKLFIGGLNTETNEKALEAVFGKYGRIVEVLLMKDRETNKSRGFAFVTFESPADAKDAARDMN
MVEADRPGKLFIGGLN.ET.EK.LE..FGKYGRI.EVLLMKDRET.KSRGFAFVTFE.PADAK.AARDMN
RetrocopyMVEADRPGKLFIGGLNLETDEKGLETAFGKYGRIIEVLLMKDRETSKSRGFAFVTFENPADAKAAARDMN
ParentalGKSLDGKAIKVEQATKPSFESGRRGLPPPPRSRGPPRGLRGGRGGSGGTRGPPSRGGHMDDGGYSMNFTM
GKSLDGKAIKV.QATKP.FESGRRG.PPPPRSRG.PRGLRG.RGG..G.R.PPSRGG..D.GGY...F..
RetrocopyGKSLDGKAIKVAQATKPVFESGRRG-PPPPRSRGRPRGLRGTRGG--GPRRPPSRGGSADEGGYTGDFDL
ParentalSSSRGPLPVKRGPPPRSGGPPPKRSAPSGPVRSSSGLGGRAPVSRGRDGYGGPPRREPLPSRRDVYLSPR
..SR.P.P.KRGPPPR..GPPPKR.APSGP.RS..G..GRA..SRGRDGYGGPPRRE..P.RRD.YL.PR
RetrocopyRPSRAPMPLKRGPPPRRAGPPPKRAAPSGPARSGAGIRGRAAGSRGRDGYGGPPRRELPPPRRDPYLGPR
ParentalDDGYSTKDSYSSREYPSSRDTRDYAPPPRDYTYRDYGHSSSRDDYPSRGYSDRDGY-GRDRDYSDHPSGG
D.GYS...SYSSR.YPS.RD.RD.AP.PRDYTYRDYGHSS.RD..PSRGY..RDGY.GR.RDY..HPSGG
RetrocopyDEGYSPRESYSSRDYPSARDPRDFAPSPRDYTYRDYGHSSARDECPSRGYCERDGYGGRERDY-EHPSGG
ParentalSYRDSYESYGNSRSAPPTRGPPPSYGGSSRYDDY-SSSRDGYGGSRDSYSSSRSDLYSSGRDRVGRQERG
SYRD...SYG..R.A.P.RGPPPSYGG..RYD.Y...S.DGYGG.RDSY...RS..YSSGR.RVGR.ERG
RetrocopySYRDPFDSYGDPRGAGPARGPPPSYGG-GRYDEYRGCSPDGYGG-RDSY---RSERYSSGRERVGRPERG
ParentalLPPSMERGYPPPRDSYSSSSRGA-PRGGGRGGSRSDRGGGRSRY
LPPS.ER..P.PRDSYS.S.R.A.PRGGGR.GSR..RGGGRSRY
RetrocopyLPPSVERNCPAPRDSYSRSGRRAPPRGGGRVGSRLERGGGRSRY

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 0 .00 RPM 55 .88 RPM
SRP007412_cerebellum 0 .00 RPM 61 .75 RPM
SRP007412_heart 0 .00 RPM 35 .52 RPM
SRP007412_kidney 0 .00 RPM 43 .47 RPM
SRP007412_liver 0 .00 RPM 14 .86 RPM
SRP007412_testis 11 .48 RPM 5 .44 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity near the 5' end of retro_mmus_170 was not detected

EST - click to see more details

15 EST(s) were mapped to retro_mmus_170 retrocopy
EST ID Start End Identity Match Mis-match Score
AV469074 107209477 107209729 99.7 251 1 250
AV471529 107209462 107209813 99.2 347 3 343
AV473722 107209460 107209811 99.8 349 1 347
AV477899 107209459 107209813 100 352 0 350
AV490614 107209486 107209813 100 325 0 324
AV497252 107209459 107209813 100 353 0 352
AV506265 107209486 107209813 100 324 0 322
AV508702 107209463 107209813 99.8 340 0 337
AV574611 107209455 107209813 100 357 0 356
AV575020 107209460 107209813 99.8 351 1 349
AV576406 107209472 107209813 99.8 338 1 335
AV588165 107210025 107210299 99.3 271 2 268
BB624528 107209464 107209990 97.2 516 10 504
BG100571 107209420 107209959 97.6 526 11 512
CF983176 107209421 107209980 98.1 548 11 537

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_1274991061 libraries 7 libraries 2 libraries 0 libraries 2 libraries
TSS #2 TSS_1275001064 libraries 4 libraries 2 libraries 0 libraries 2 libraries
TSS #3 TSS_1275021027 libraries 38 libraries 4 libraries 3 libraries 0 libraries
TSS #4 TSS_1275031006 libraries 20 libraries 14 libraries 26 libraries 6 libraries
TSS #5 TSS_127504996 libraries 19 libraries 13 libraries 6 libraries 38 libraries
TSS #6 TSS_1275051010 libraries 21 libraries 8 libraries 2 libraries 31 libraries

The graphical summary, for retro_mmus_170 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_170 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_170 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_91
Bos taurus retro_btau_36
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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