RetrogeneDB ID:

retro_mmus_117

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:3:124321192..124322284(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000044528
Aliases:Tram1l1, A830091N21Rik
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Tram1
Ensembl ID:ENSMUSG00000025935
Aliases:Tram1, 1810049E02Rik, TRAMP
Description:translocating chain-associating membrane protein 1 [Source:MGI Symbol;Acc:MGI:1919515]


Retrocopy-Parental alignment summary:






>retro_mmus_117
ATGGGGCTCCGCAAGAAGAACGCCAGGAACCCCCCGGTGTTGAGCCACGAATTCATGGTGCAGAACCACGCGGATATGGT
CTCCTGCGTGGGCATGTTCTTCGTGCTGGGGCTTATGTTCGAGGGCACCTCCGAGATGTCGATCGCGTTCCTCACTCTGC
AGCATGGAGTCGTTGTCCCAGCGGAAGGGCTGCCCTCCGGGTCCAGGACCCTGTACCATTATGGGGTCAAAGATCTGGCC
ACAGTGTTCTTCTACATGCTGGTGGCCATCATCATCCACGCCACCATTCAGGAGTACGTGCTAGATAAGCTCAGCAGGAG
ACTGCAGCTCACCAAAGGCAAACAAAACAAACTGAATGAGGCCGGGCAGCTGAGTGTGTTCTATATAGTGTCCGGGATCT
GGGGCATGATCATTCTGGCCTCTGAGAACTGCCTGTCAGACCCTACACTCTTGTGGAAGTCTCAGCCCCACAACATGATG
ACATTTCAGATGAAATTTTTCTACATTTCACAGTTGGCTTACTGGTTTCATAGCTTTCCGGAGCTTTACTTCCAGAAAGT
CAGGAAGCAAGATATCCCGGGTCAGCTCATCTACATTGGCCTCCACCTCTTCCACATTGGAGGGGCCTATCTCTTGTACT
TGAACCACTTGGGCCTGCTGCTGCTGATGCTGCACTACGCCGTAGAGCTCCTCTCCAGCGTGTGCAGCCTGCTTTACTTT
GGTGATGAGCGGTACCAGAAAGGGTTGTCTCTGTGGCCTATCGTGTTTATATCCGGGAGACTCGTGACATTGATTGTCTC
GGTGGTTACAGTAGGGCTTCACCTGGCCGGGACAAATCGGAATGGCAATGCACTCTCTGGTAATGTCAATGTGCTGGCAG
CTAAAATCGCTGTTCTGTCCTCGAGTTGCAGTATCCAGGTGTACATAACATGGACCTTGACTACTGTCTGGCTTCAGAGA
TGGTTAGAAGACGCGAACCTTCATGTTTGTGGAAGGAAGAGACGGTCCAGGGCGAGAAAAGGCACAGAAAATGGAGTGGA
GAATCCGAATAGAATAGACTCTCCACCAAAGAAGAAAGAGAAGGCTCCTTAA

ORF - retro_mmus_117 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 58.52 %
Parental protein coverage: 94.12 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAIRKKSNKNPPLLSHEFLLQNHADIVSCLAMLFLLGLMFEVTAKGAIIFVALQYNVTRPATEEQATESA
M..RKK...NPP.LSHEF..QNHAD.VSC..M.F.LGLMFE.T....I.F..LQ..V..PA.E.....S.
RetrocopyMGLRKKNARNPPVLSHEFMVQNHADMVSCVGMFFVLGLMFEGTSEMSIAFLTLQHGVVVPA-EGLPSGSR
ParentalSLYHYGIKDLATVLFYMLVAIIIHAIIQEYVLDKINRRMHFSKTKHSKFNESGQLSAFYLFACVWGTFIL
.LYHYG.KDLATV.FYMLVAIIIHA.IQEYVLDK..RR....K.K..K.NE.GQLS.FY.....WG..IL
RetrocopyTLYHYGVKDLATVFFYMLVAIIIHATIQEYVLDKLSRRLQLTKGKQNKLNEAGQLSVFYIVSGIWGMIIL
ParentalISENYISDPTILWRAYPHNLMTFQTKFFYISQLAYWLHAFPELYFQKTKKEDIPRQLVYIGLYLFHIAGA
.SEN..SDPT.LW...PHN.MTFQ.KFFYISQLAYW.H.FPELYFQK..K.DIP.QL.YIGL.LFHI.GA
RetrocopyASENCLSDPTLLWKSQPHNMMTFQMKFFYISQLAYWFHSFPELYFQKVRKQDIPGQLIYIGLHLFHIGGA
ParentalYLLNLNHLGLVLLVLHYFVEFLFHISRLFYFSDEKYQKGFSLWAVLFVLGRLLTLILSVLTVGFGLARAE
YLL.LNHLGL.LL.LHY.VE.L.....L.YF.DE.YQKG.SLW...F..GRL.TLI.SV.TVG..LA...
RetrocopyYLLYLNHLGLLLLMLHYAVELLSSVCSLLYFGDERYQKGLSLWPIVFISGRLVTLIVSVVTVGLHLA-GT
ParentalNQKLDFSTGNFNVLAVRIAVLASICITQAFMMWKFINFQLRRWREHSAFQAPPVKRKPAVTKGRSSRKGT
N.......GN.NVLA..IAVL.S.C..Q....W......L.RW.E.........KR.....KG.....G.
RetrocopyNRNGNALSGNVNVLAAKIAVLSSSCSIQVYITWTLTTVWLQRWLEDANLHVCGRKRRSRARKG--TENGV
ParentalEN
EN
RetrocopyEN

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 17 .31 RPM 24 .95 RPM
SRP007412_cerebellum 13 .20 RPM 24 .32 RPM
SRP007412_heart 0 .16 RPM 25 .87 RPM
SRP007412_kidney 0 .04 RPM 69 .93 RPM
SRP007412_liver 0 .00 RPM 113 .03 RPM
SRP007412_testis 0 .23 RPM 149 .34 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_117 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001XVA POLR2A 3:124320791..124321570

EST - click to see more details

4 EST(s) were mapped to retro_mmus_117 retrocopy
EST ID Start End Identity Match Mis-match Score
BI985062 124321138 124321736 99.2 598 0 596
BY254975 124321130 124321590 98.5 451 7 444
CJ148946 124321121 124321563 95 418 21 394
CX732284 124321163 124321715 100 551 0 550

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_91904529 libraries126 libraries185 libraries80 libraries152 libraries
TSS #2 TSS_91905831 libraries194 libraries47 libraries0 libraries0 libraries

The graphical summary, for retro_mmus_117 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_117 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_117 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Oryctolagus cuniculus retro_ocun_52
Parental genes homology:
Parental genes homology involve 25 parental genes, and 26 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000063251 retrocopy
retro_amel_78,
Bos taurus ENSBTAG000000075621 retrocopy
retro_btau_24,
Canis familiaris ENSCAFG000000078661 retrocopy
retro_cfam_15,
Callithrix jacchus ENSCJAG000000078931 retrocopy
retro_cjac_168,
Dasypus novemcinctus ENSDNOG000000092962 retrocopies
retro_dnov_27, retro_dnov_906,
Dipodomys ordii ENSDORG000000019011 retrocopy
retro_dord_27,
Equus caballus ENSECAG000000183781 retrocopy
retro_ecab_506,
Echinops telfairi ENSETEG000000184471 retrocopy
retro_etel_674,
Felis catus ENSFCAG000000287751 retrocopy
retro_fcat_136,
Homo sapiens ENSG000000671671 retrocopy
retro_hsap_51,
Loxodonta africana ENSLAFG000000116251 retrocopy
retro_lafr_9,
Macaca mulatta ENSMMUG000000015161 retrocopy
retro_mmul_235,
Monodelphis domestica ENSMODG000000073161 retrocopy
retro_mdom_308,
Mustela putorius furoENSMPUG000000106161 retrocopy
retro_mputfur_558,
Mus musculus ENSMUSG00000025935 1 retrocopy
retro_mmus_117 ,
Nomascus leucogenys ENSNLEG000000113761 retrocopy
retro_nleu_73,
Oryctolagus cuniculus ENSOCUG000000087341 retrocopy
retro_ocun_52,
Otolemur garnettii ENSOGAG000000063791 retrocopy
retro_ogar_2932,
Pongo abelii ENSPPYG000000186601 retrocopy
retro_pabe_169,
Pan troglodytes ENSPTRG000000203341 retrocopy
retro_ptro_2081,
Rattus norvegicus ENSRNOG000000078921 retrocopy
retro_rnor_287,
Sus scrofa ENSSSCG000000061931 retrocopy
retro_sscr_980,
Ictidomys tridecemlineatus ENSSTOG000000055371 retrocopy
retro_itri_38,
Tarsius syrichta ENSTSYG000000138871 retrocopy
retro_tsyr_24,
Tursiops truncatus ENSTTRG000000003281 retrocopy
retro_ttru_24,




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