RetrogeneDB ID:

retro_mmus_288

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:4328775..4329212(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Rpl17
Ensembl ID:ENSMUSG00000062328
Aliases:None
Description:ribosomal protein L17 [Source:MGI Symbol;Acc:MGI:2448270]


Retrocopy-Parental alignment summary:






>retro_mmus_288
ACTGCCCAGGCCATTAAGGGTATACATATCTAAATGGCAGCCAAATATCTGAATGATTTCTCTTTAAAGAAGCAAAATAT
GCCACTTGACAGTACAGCAGTAGAGCATGTAGGTGTGCCCAATCCAAATACAGCGGGATACAGGGCCAGGGACGCAAAAA
GTGCTGTGAAGTTTTGCTGCACTTGCTAAAAATACAGAGAGTAATGCTGAACTTAAGGGTTTACATGAGGATTCTCTAGT
CATTGAAATAGCCATGTGAACAAAGCACATAAGATGTGGCACTGAGCTTAAAGAGCCCATGGTCATGTTACCCTGTACAC
AAGCTCCTGCCACATGGAGAAATGATCCTCACTGAAAAGGAAAATATCCCAGGGTCATGAAAGGAGAACACAACAGAGAA
AAGGATATCCTAGAAGAAATTGAAGGGAAAAAACTTG

ORF - retro_mmus_288 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.98 %
Parental protein coverage: 80.98 %
Number of stop codons detected: 5
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalTAQAIKGMHIRKATKYLKDVTLKKQCVPFR-RYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHML-KNAE
TAQAIKG.HI..A.KYL.D..LKKQ..P....Y.....RCAQ.K..G..QG...KK..E.LLH.L.KN.E
RetrocopyTAQAIKGIHI*MAAKYLNDFSLKKQNMPLD<QYSSRACRCAQSKYSG-IQGQGRKKCCEVLLHLL<KNTE
ParentalSNAELKGLDVDSLVIE-HIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEM-ILTEKEQIVPKPEEEVAQK
SNAELKGL..DSLVIE....VNKA.KM.....RAHG....Y.SS.CH.E...........P....E....
RetrocopySNAELKGLHEDSLVIE<NSHVNKAHKMWH*A*RAHGHVTLYTSS-CHMEK<MILTEKENIPGS*KENTTE
ParentalKKISQKKLKKQKL
K.IS.KKLK...L
RetrocopyKRIS*KKLKGKNL

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 .00 RPM 98 .22 RPM
SRP007412_cerebellum 0 .04 RPM 73 .21 RPM
SRP007412_heart 0 .00 RPM 85 .48 RPM
SRP007412_kidney 0 .00 RPM 105 .64 RPM
SRP007412_liver 0 .00 RPM 113 .17 RPM
SRP007412_testis 0 .00 RPM 56 .53 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_288 was not detected
No EST(s) were mapped for retro_mmus_288 retrocopy.
No TSS is located nearby retro_mmus_288 retrocopy 5' end.
retro_mmus_288 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_288 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 20 parental genes, and 501 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG0000000787250 retrocopies
Cavia porcellus ENSCPOG0000001933731 retrocopies
Equus caballus ENSECAG000000115479 retrocopies
Echinops telfairi ENSETEG0000001132210 retrocopies
Homo sapiens ENSG000002154721 retrocopy
Latimeria chalumnae ENSLACG000000088351 retrocopy
Macropus eugenii ENSMEUG0000001670926 retrocopies
Microcebus murinus ENSMICG0000001710214 retrocopies
Myotis lucifugus ENSMLUG0000002555422 retrocopies
Myotis lucifugus ENSMLUG0000002926436 retrocopies
Macaca mulatta ENSMMUG0000001883726 retrocopies
Mus musculus ENSMUSG00000062328 80 retrocopies
Oryctolagus cuniculus ENSOCUG000000124852 retrocopies
Procavia capensis ENSPCAG000000031038 retrocopies
Pongo abelii ENSPPYG0000000915143 retrocopies
Pteropus vampyrus ENSPVAG0000000196976 retrocopies
Sarcophilus harrisii ENSSHAG0000000306014 retrocopies
Tarsius syrichta ENSTSYG0000000740220 retrocopies
Tursiops truncatus ENSTTRG0000000579731 retrocopies
Vicugna pacos ENSVPAG000000095681 retrocopy



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