RetrogeneDB ID:

retro_mmus_1976

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:2:138871984..138872511(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000081009
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Mrpl47
Ensembl ID:ENSMUSG00000037531
Aliases:None
Description:mitochondrial ribosomal protein L47 [Source:MGI Symbol;Acc:MGI:1921850]


Retrocopy-Parental alignment summary:






>retro_mmus_1976
ACACCTTTTCTCCAGGGTGAATTACTTTATATCACATTGTCAGGAGAAGATTAGAAGAATTTTTTGATGACCCAAAGAAT
TGGGGGGTGGAAGGAAGAAAAGTCAAATCTGGAGCTTCACATACCTGGTAGCAACTGAGAAACAAAAGTAATGAAAATTT
ACATAAGCTTTGACATATACTTCTGAAGGAAAGAACCATGCTTCTAACTCTAGAGCAGGAGGCCAAGTGACAGAGATTGC
CAATGCCAAGTCCAGAGTGGTTAGAAAAGGTTGTTGATTCCATGATGCCTTAGATAAAGTTGTCCAGGAGAGAGAAGATG
CTTTGAGGCTTCTTCAGACCAGTCAAGAAAATCCAAGACCTGGTGCTTGGGAGAAGGGACAGCTTTGGCCAAATCATCAG
GTGCAAATTCAAGCAGTGACCTATACCTTGCTATCTAAATAAAAGATATAACAGAAGGCAGTTCTTTGTAATGCCTTATG
TGGATTGCTTTGCCAGACTGAGAGTTGAGAAACATGTCCTCACTGAA

ORF - retro_mmus_1976 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.54 %
Parental protein coverage: 69.05 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalTSFLQCKLLHTTLS-RKGLEEFFDDPKNWGEE--KVKSGASWTCQQLRNKSNEDLHKLWYVLLKERNMLL
T.FLQ..LL..TLS.R..LEEFFDDPKNWG.E..KVKSGAS.T..QLRNKSNE.LHKL...LLKER.MLL
RetrocopyTPFLQGELLYITLS<RRRLEEFFDDPKNWGVEGRKVKSGASHTW*QLRNKSNENLHKL*HILLKERTMLL
ParentalTLEQEAKRQRLPMPSPERLEKVVDSM-DNVDKVVQEREDALRLLQTGQEKPRPGAW-RRDIFGRIVWHKF
TLEQEAK.QRLPMPSPE.LEKVVDSM.D..DKVVQEREDALRLLQT.QE.PRPGAW.RRD.FG.I...KF
RetrocopyTLEQEAK*QRLPMPSPEWLEKVVDSM<DALDKVVQEREDALRLLQTSQENPRPGAW>RRDSFGQIIRCKF
ParentalKQWPIPWYLNKRYNRRRFFAMPYVDRFIRLRIEKHARIE
KQ.PIP.YLNKRYNRR.FF.MPYVD.F.RLR.EKH...E
RetrocopyKQ*PIPCYLNKRYNRRQFFVMPYVDCFARLRVEKHVLTE

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 11 .89 RPM
SRP007412_cerebellum 0 .00 RPM 11 .16 RPM
SRP007412_heart 0 .00 RPM 16 .41 RPM
SRP007412_kidney 0 .00 RPM 12 .24 RPM
SRP007412_liver 0 .00 RPM 8 .93 RPM
SRP007412_testis 0 .00 RPM 30 .46 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_1976 was not detected
No EST(s) were mapped for retro_mmus_1976 retrocopy.
No TSS is located nearby retro_mmus_1976 retrocopy 5' end.
retro_mmus_1976 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1976 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Rattus norvegicus retro_rnor_1829

Parental genes homology:
Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000113801 retrocopy
Cavia porcellus ENSCPOG000000023122 retrocopies
Felis catus ENSFCAG000000315481 retrocopy
Macropus eugenii ENSMEUG000000126492 retrocopies
Monodelphis domestica ENSMODG000000213013 retrocopies
Mustela putorius furoENSMPUG000000172141 retrocopy
Mus musculus ENSMUSG00000037531 3 retrocopies
retro_mmus_1976 , retro_mmus_1986, retro_mmus_2753,
Otolemur garnettii ENSOGAG000000169572 retrocopies
Pteropus vampyrus ENSPVAG000000042841 retrocopy
Rattus norvegicus ENSRNOG000000116392 retrocopies
Sorex araneus ENSSARG000000068982 retrocopies
Tursiops truncatus ENSTTRG000000089091 retrocopy



Copyright © RetrogeneDB 2014-2017