RetrogeneDB ID:

retro_mmus_65

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:10:86731986..86732388(-)
Located in intron of:ENSMUSG00000044937
Retrocopy
information
Ensembl ID:ENSMUSG00000056366
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Fabp3
Ensembl ID:ENSMUSG00000028773
Aliases:None
Description:fatty acid binding protein 3, muscle and heart [Source:MGI Symbol;Acc:MGI:95476]


Retrocopy-Parental alignment summary:






>retro_mmus_65
ATGGCGGACGCCTTTGTCGGTACCTGGAAGCTAGTGGACTGCAAGAATTTTGATGACTACATGAAGTCACTCGGTGTGGG
CTTTGCCACCAGGCAGGTGGCTAGCATGACCAAGCCTACTACCATCATCGAGAAGAACGGGGATACTATCACCATAAAGA
CACAAAGTACCTTCAAGAACACAGAGATCAACTTTCAGCTGGGAATAGAGTTCGACGAGGTGACAGCAGATGACCGGAAG
GTCAAGTCACTGGTGACGCTGGACGGAGGCAAACTCATCCATGTGCAGAAGTGGAATGGGCAGGAGACAACACTAACTAG
GGAGCTAGTTGACAGGAAACTCATCCTGACTCTCACTCATGGCAGTGTGGTGAGCACTCGGACTTATGAGAAGGAGGCGT
GA

ORF - retro_mmus_65 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 98.5 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMADAFVGTWKLVDSKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDTITIKTQSTFKNTEINFQLGIE
MADAFVGTWKLVD.KNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDTITIKTQSTFKNTEINFQLGIE
RetrocopyMADAFVGTWKLVDCKNFDDYMKSLGVGFATRQVASMTKPTTIIEKNGDTITIKTQSTFKNTEINFQLGIE
ParentalFDEVTADDRKVKSLVTLDGGKLIHVQKWNGQETTLTRELVDGKLILTLTHGSVVSTRTYEKEA
FDEVTADDRKVKSLVTLDGGKLIHVQKWNGQETTLTRELVD.KLILTLTHGSVVSTRTYEKEA
RetrocopyFDEVTADDRKVKSLVTLDGGKLIHVQKWNGQETTLTRELVDRKLILTLTHGSVVSTRTYEKEA

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .21 RPM 17 .38 RPM
SRP007412_cerebellum 0 .17 RPM 14 .24 RPM
SRP007412_heart 11 .05 RPM 1238 .89 RPM
SRP007412_kidney 1 .58 RPM 279 .45 RPM
SRP007412_liver 0 .03 RPM 0 .05 RPM
SRP007412_testis 0 .87 RPM 24 .79 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_65 was not detected
No EST(s) were mapped for retro_mmus_65 retrocopy.


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_6858867 libraries142 libraries55 libraries1 library7 libraries

The graphical summary, for retro_mmus_65 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)

retro_mmus_65 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_65 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 17 parental genes, and 38 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000168192 retrocopies
Danio rerio ENSDARG000000232901 retrocopy
Dasypus novemcinctus ENSDNOG000000005112 retrocopies
Equus caballus ENSECAG000000248521 retrocopy
Homo sapiens ENSG000001217691 retrocopy
Gorilla gorilla ENSGGOG000000144321 retrocopy
Macropus eugenii ENSMEUG000000125016 retrocopies
Microcebus murinus ENSMICG000000093594 retrocopies
Myotis lucifugus ENSMLUG000000136092 retrocopies
Mus musculus ENSMUSG000000275334 retrocopies
Mus musculus ENSMUSG00000028773 3 retrocopies
retro_mmus_2804, retro_mmus_3204, retro_mmus_65 ,
Nomascus leucogenys ENSNLEG000000015861 retrocopy
Otolemur garnettii ENSOGAG000000137574 retrocopies
Pongo abelii ENSPPYG000000016161 retrocopy
Pan troglodytes ENSPTRG000000004571 retrocopy
Rattus norvegicus ENSRNOG000000128791 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000038423 retrocopies



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