RetrogeneDB ID:

retro_mmus_2955

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:7:99945375..99945728(+)
Located in intron of:ENSMUSG00000058761
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:U2af1
Ensembl ID:ENSMUSG00000061613
Aliases:U2af1, 2010107D16Rik, 35kDa
Description:U2 small nuclear ribonucleoprotein auxiliary factor (U2AF) 1 [Source:MGI Symbol;Acc:MGI:98884]


Retrocopy-Parental alignment summary:






>retro_mmus_2955
GAGGAGGATGCAGAGAAAGCCGTGATCGACTTGAATAACCGTTGGTTTAATGGACAGCCGATCCATGCAGAGCTGTCCTC
AGTAACTGACTTCAGGGAAGCCTGCTGCCGCCAGTATGAAATGGGAGAGTGCACAAGAGGGGGCTTCTGCAACTTCATGC
ATTTGAAGTCCATCTCAAGAGAGCTACGACGGGAGCTGTATGGGCGCCAGCGCAAGAAGCATAGATCCAGGTCCCGATCC
AGGGAACGGAGTTCCCGATCCAGAGACCGTGGACGCGGTGGTGGAGGTGGAGGTGGCGGAGGAAGGAGCGTGACAGGAGG
CGGTCAAGAGACCGGGAGAGATCTGGACGATTC

ORF - retro_mmus_2955 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.21 %
Parental protein coverage: 50.21 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalEEDAEKAVIDLNNRWFNGQPIHAELSPVTDFREACCRQYEMGECTRGGFCNFMHLKPISRELRRELYGRR
EEDAEKAVIDLNNRWFNGQPIHAELS.VTDFREACCRQYEMGECTRGGFCNFMHLK.ISRELRRELYGR.
RetrocopyEEDAEKAVIDLNNRWFNGQPIHAELSSVTDFREACCRQYEMGECTRGGFCNFMHLKSISRELRRELYGRQ
ParentalRKKHRSRSRSRERRSRSRDRGRGGGGGGGGGGGR-ERDRRRSRDRERSGRF
RKKHRSRSRSRER.SRSRDRGR..GGGGGGGGGR.ERDRRRSRDRERSGRF
RetrocopyRKKHRSRSRSRERSSRSRDRGR--GGGGGGGGGR<ERDRRRSRDRERSGRF

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 .07 RPM 17 .66 RPM
SRP007412_cerebellum 0 .09 RPM 23 .36 RPM
SRP007412_heart 0 .03 RPM 14 .72 RPM
SRP007412_kidney 0 .17 RPM 22 .33 RPM
SRP007412_liver 0 .19 RPM 18 .98 RPM
SRP007412_testis 0 .00 RPM 13 .86 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_2955 was not detected
No EST(s) were mapped for retro_mmus_2955 retrocopy.
No TSS is located nearby retro_mmus_2955 retrocopy 5' end.
retro_mmus_2955 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2955 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG000000155581 retrocopy
Homo sapiens ENSG000001602012 retrocopies
Loxodonta africana ENSLAFG000000114601 retrocopy
Macaca mulatta ENSMMUG000000227692 retrocopies
Mus musculus ENSMUSG000000313701 retrocopy
Mus musculus ENSMUSG00000061613 3 retrocopies
retro_mmus_1602, retro_mmus_1787, retro_mmus_2955 ,
Mus musculus ENSMUSG000000787651 retrocopy
Nomascus leucogenys ENSNLEG000000147371 retrocopy
Otolemur garnettii ENSOGAG000000165041 retrocopy
Pongo abelii ENSPPYG000000114632 retrocopies



Copyright © RetrogeneDB 2014-2017