RetrogeneDB ID:

retro_mmus_308

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:1:36601801..36602143(+)
Located in intron of:ENSMUSG00000046337
Retrocopy
information
Ensembl ID:ENSMUSG00000089906
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Eif1
Ensembl ID:ENSMUSG00000035530
Aliases:Eif1, Sui1-rs1
Description:eukaryotic translation initiation factor 1 [Source:MGI Symbol;Acc:MGI:105125]


Retrocopy-Parental alignment summary:






>retro_mmus_308
ATGTCCGCTATCCAGAACCTCCACTCTTTCGACCCCTTTGCTGATGCAAGTAAGGGTGGTGACCTGCTTCCTGGTGGCAC
TGAGGATTATATCCATATAAGAATTCAACAGAGAAGCGGCAGGAAGACCCTTACAACAACTGTCCAAGGGATCGCTGATG
ATTACAATAAAAAGAAACTAGTAAAGGCATTTAAGAAGAAATTTGCCTGCAATGGTACTGTAATTGAGCATCCAGAATAT
GGAGAAGTAATTCAGCTACAGGGTGACCAGCGCAAGAACATATGCCAGCTCCTGATAGAGACTGGGCTGCCTAAGGACGA
TCAGCTGAAGGCTCGTGGGTTT

ORF - retro_mmus_308 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.23 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSAIQNLHSFDPFADASKGDDLLPAGTEDYIHIRIQQRNGRKTLTT-VQGIADDYDKKKLVKAFKKKFAC
MSAIQNLHSFDPFADASKG.DLLP.GTEDYIHIRIQQR.GRKTLTT.VQGIADDY.KKKLVKAFKKKFAC
RetrocopyMSAIQNLHSFDPFADASKGGDLLPGGTEDYIHIRIQQRSGRKTLTTTVQGIADDYNKKKLVKAFKKKFAC
ParentalNGTVIEHPEYGEVIQLQGDQRKNICQFLIEIGLAKDDQLKVHGF
NGTVIEHPEYGEVIQLQGDQRKNICQ.LIE.GL.KDDQLK..GF
RetrocopyNGTVIEHPEYGEVIQLQGDQRKNICQLLIETGLPKDDQLKARGF

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 .02 RPM 129 .24 RPM
SRP007412_cerebellum 0 .00 RPM 91 .10 RPM
SRP007412_heart 0 .03 RPM 194 .38 RPM
SRP007412_kidney 0 .04 RPM 123 .04 RPM
SRP007412_liver 0 .00 RPM 113 .49 RPM
SRP007412_testis 1 .56 RPM 149 .52 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_308 was not detected
No EST(s) were mapped for retro_mmus_308 retrocopy.
No TSS is located nearby retro_mmus_308 retrocopy 5' end.
retro_mmus_308 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_308 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 13 parental genes, and 70 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000022821 retrocopy
Callithrix jacchus ENSCJAG000000121206 retrocopies
Cavia porcellus ENSCPOG000000143503 retrocopies
Felis catus ENSFCAG000000244552 retrocopies
Myotis lucifugus ENSMLUG000000050773 retrocopies
Mustela putorius furoENSMPUG000000108836 retrocopies
Mus musculus ENSMUSG000000069411 retrocopy
Mus musculus ENSMUSG00000035530 27 retrocopies
Nomascus leucogenys ENSNLEG000000110133 retrocopies
Pongo abelii ENSPPYG000000296671 retrocopy
Rattus norvegicus ENSRNOG000000327691 retrocopy
Rattus norvegicus ENSRNOG0000003376515 retrocopies
Sarcophilus harrisii ENSSHAG000000057291 retrocopy



Copyright © RetrogeneDB 2014-2017