RetrogeneDB ID:

retro_mmus_108

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:12:73545277..73546339(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000034435
Aliases:Tmem30b, 9130011B11Rik
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Tmem30a
Ensembl ID:ENSMUSG00000032328
Aliases:Tmem30a, 2010200I23Rik, AW540225, Cdc50a, D9Wsu20e
Description:transmembrane protein 30A [Source:MGI Symbol;Acc:MGI:106402]


Retrocopy-Parental alignment summary:






>retro_mmus_108
ATGACCTGGAGCGCCACGGCGCGGGGCGCGCACCAGCCCGACAACACCGCCTTCACTCAGCAGCGCCTCCCCGCCTGGCA
GCCGCTGCTGTCGGCGGGCATCGCGCTGCCGCTCTTCTTCTGCGCCGGCCTGGCGTTCATCGGCCTGGGCCTGGGCCTCT
TCTACTCCTCCAACGGCATCAAGGAGCTGGAGTACGACTACACCGGCAACCCCGGCACCGGCGATTGCTCGGTGTGCGCC
GCCAAGGGCCAGGGCCGCGCTCCGCCGCCCGGCTGCGCTTGCTCCTGGAGCTTTACGCTGCCCGAGCTCTTCCCGGGCCC
CGTGTACCTCTACTACGAGCTGTCCAACTTCTACCAGAACAACCGGCGCTACGGCGTGTCCCGCGACGACGCGCAGCTCA
GCGGCCTGGCCAGCGCGCTGCGCCACCCGGCCAACGAGTGCGCCCCCTACCAGTTCCGCTCCGACGGTCTGCCTATCGCA
CCGTGCGGCGCCATCGCCAACAGCCTCTTCAACGACTCCTTCTCGCTCTGGCACCAGCGCCAGCCCTCGGACCCCTTCGT
CGAGGTGCCGCTCGATCGCACCGCCATCGCCTGGTGGACCGACTACCACGTCAAGTTCCGCAACCCGCCGCTGGTGAACG
GCAGCCTGGCGCTGGCCTTCCGCGGCACGGCGCCGCCGCCCAACTGGCACCGGCCGGTTTATGAGCTCAGCCCGGATCCC
AACAACACCGGCTTCATCAACCAGGACTTCGTGGTGTGGATGCGCACCGCGGCGCTGCCCACGTTCCGCAAGCTCTATGC
GCGCATCCGCCAGGGCAACTACTCCGCCGGTCTGCCCCGGGGCACCTACCGTGTCAACATCACCTACAACTACCCGGTGC
GCGCCTTCGGCGGCCACAAGCTCATCATTCTTAGCAACATCTCTTGGATGGGTGGCAAGAACCCTTTCCTGGGCATCGCC
TACCTGGTCGTTGGCTCCCTCTGCATCGTCATGGGCTTTGTCATGCTGGTCGTCTACATTCGCTACCAGGACCAGGACGA
CGACGACAACGATGATGAGTGA

ORF - retro_mmus_108 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.14 %
Parental protein coverage: 70.6 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalCACTINFTLKQSFEGNVFMYYGLSNFYQNHRRYVKSRDDSQLNGDPSALLNPSKECEPYR-RNEDRPIAP
CAC...FTL...F.G.V..YY.LSNFYQN.RRY..SRDD.QL.G..SAL..P..EC.PY..R....PIAP
RetrocopyCACSWSFTLPELFPGPVYLYYELSNFYQNNRRYGVSRDDAQLSGLASALRHPANECAPYQFRSDGLPIAP
ParentalCGAIANSMFNDTLELYLVANESDPKPIPIPLKKKGIAWWTDKNVKFRNPP-GKESLEEKFKDTIKPVNWH
CGAIANS.FND...L......SDP.....PL....IAWWTD..VKFRNPP....SL...F..T..P.NWH
RetrocopyCGAIANSLFNDSFSLWHQRQPSDPF-VEVPLDRTAIAWWTDYHVKFRNPPLVNGSLALAFRGTAPPPNWH
ParentalKAVYELDPEDESNNGFINEDFIVWMRTAALPTFRKLYRLIERRDDLHPTLPAGQYFLNITYNYPVHSFDG
..VYEL.P.D..N.GFIN.DF.VWMRTAALPTFRKLY..I.R.......LP.G.Y..NITYNYPV..F.G
RetrocopyRPVYELSP-DPNNTGFINQDFVVWMRTAALPTFRKLYARI-RQGNYSAGLPRGTYRVNITYNYPVRAFGG
ParentalRKRMILSTISWMGGKNPFLGIAYITIGSISFLLGVVLLVINHKYRNSSN
.K..ILS.ISWMGGKNPFLGIAY...GS.....G.V.LV....Y.....
RetrocopyHKLIILSNISWMGGKNPFLGIAYLVVGSLCIVMGFVMLVVYIRYQDQDD

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 .02 RPM 303 .44 RPM
SRP007412_cerebellum 0 .13 RPM 193 .92 RPM
SRP007412_heart 0 .09 RPM 68 .74 RPM
SRP007412_kidney 5 .22 RPM 129 .84 RPM
SRP007412_liver 8 .52 RPM 138 .56 RPM
SRP007412_testis 0 .05 RPM 70 .30 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_108 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_108 retrocopy.

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_24312753 libraries187 libraries82 libraries36 libraries14 libraries
TSS #2 TSS_24313889 libraries139 libraries43 libraries1 library0 libraries
TSS #3 TSS_24314594 libraries122 libraries115 libraries63 libraries178 libraries
TSS #4 TSS_24315602 libraries111 libraries111 libraries49 libraries199 libraries

The graphical summary, for retro_mmus_108 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_108 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_108 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 15 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000051001 retrocopy
retro_btau_72,
Canis familiaris ENSCAFG000000027081 retrocopy
retro_cfam_26,
Callithrix jacchus ENSCJAG000000103251 retrocopy
retro_cjac_801,
Cavia porcellus ENSCPOG000000207121 retrocopy
retro_cpor_23,
Homo sapiens ENSG000001126971 retrocopy
retro_hsap_12,
Myotis lucifugus ENSMLUG000000119231 retrocopy
retro_mluc_1871,
Monodelphis domestica ENSMODG000000185021 retrocopy
retro_mdom_287,
Mus musculus ENSMUSG00000032328 1 retrocopy
retro_mmus_108 ,
Nomascus leucogenys ENSNLEG000000049621 retrocopy
retro_nleu_69,
Otolemur garnettii ENSOGAG000000157181 retrocopy
retro_ogar_22,
Pongo abelii ENSPPYG000000167821 retrocopy
retro_pabe_204,
Pelodiscus sinensis ENSPSIG000000071741 retrocopy
retro_psin_61,
Rattus norvegicus ENSRNOG000000108951 retrocopy
retro_rnor_399,
Ictidomys tridecemlineatus ENSSTOG000000025431 retrocopy
retro_itri_50,
Tarsius syrichta ENSTSYG000000082111 retrocopy
retro_tsyr_928,




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