MmuINT0131652 @ mm9
Intron Retention
Gene
ENSMUSG00000039844 | Rapgef1
Description
Rap guanine nucleotide exchange factor (GEF) 1 [Source:MGI Symbol;Acc:MGI:104580]
Coordinates
chr2:29576163-29577829:+
Coord C1 exon
chr2:29576163-29576258
Coord A exon
chr2:29576259-29577743
Coord C2 exon
chr2:29577744-29577829
Length
1485 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
ACCGTGCTTTCCCTTTGCAGGAA
3' ss Score
14.04
Exon sequences
Seq C1 exon
AGTGAAAAGGCCAGCAGTGAGGAAGCTGGTGGGGATGAGTATGTCAGTCTGTACTCCTCTGGCCAGACCAGCGAGGAGCTGGCTCCCTGTCGAGGA
Seq A exon
GTAAGTAACCTCAGTGGGTGGCCTTGTGCATGGGCCGGCCACTGCCCCCTCAAGGTCACTTCCCTTGCAGCTGCTTCTATTGGCTGAGCCCCTAGAGGCCTGCTGGAAGCCAACCCATCCTATGGGAAAGGACATGGCTTCCAGGTAGAGGTCTGCCCTGCTTTTGCTTCAGTGAGTGTGGCATTTTTCAGAACCTGGCTGAATGAGTGTCCTAGAAACCACTGGACCCTGGCCCAGCCTAGCTGCTCCCTGGAATTTCTTCCCATTCTTCCCTCAATGCTGATCTCTTCTTCCAAGAGATGCTTTTACTCCTGCCCTTCAGTTCTTCCCAGCATGCCCTGCTGCCCTCAGCTAATCCCAAGGAAGTAGGGCAAGTGATGTGCGCCCTGCTGGATATCCACACTTGTCCCTCCTGTGAGCAGACTCCTTGCTGGATTATGGAGGTCCAGACTGTGGCCTCACAGTGCAAACCTTCTATTGAGCATGCAGCTTTTCCAAATTTGGCTTCAGGAAAACAGGGGAAAATTGTGAGACTTCAAAGGTCACTGTCCCATGAGACTGAATGAGAAGCTCTAGGAATGAGGTCGGGTCATCAAGGACAAGGAGCCAGTGCCCTGGAAAGCCCAGCCTGATCATGGTCATCCCATGAGTAATCACACCATAATTCCCTAGGGCTTTCAGATATCTATGTCCAGGCAACCACCCTCCTTAGACATCAGTACAACATCAGCTTCCCTCCAGTGGGATTTTGGTCCTGTTTGTGAGAGCTAAGCCAGTATCCCCAGCCACTGGTGACCTGTGTCACCAGCAGCCTCGAATTCAGGGACTCAATGCCCAGGCCCCACAGCCCTCTCTGCCCTGCAGTGCCAGCTCCACTGTGCTGTCCTTAGTGACAGTCCCTGGATTCACAAGGACTTTTTCTTCACCACCACCTTCTGGACAGCCCAAAAACATTGTAGAGTTGTGTTGTCAGTGGATATAGAGGCAGCAAGTCTGTCCAAGACGGCTCACATTTTTGAGTTTGGGCAGCTGGACTTCTAAACTAGACTGTCACTGATAAAGGGTTGTAATCCTGAAGACTGTAAGAAGTCAGGGAAGTTTGTATGTGGTGGTTAAAGATATAAGCTTTGGAAGCAGATAGCCTCCTCCTATGAGTTCAAGTCTACTCTCTGCCACTGGGCATCCTAGCAGTCAGTTTCTGTAGGGAATGGAGGCGTGGTGGTGGTAGCTTATTGAAGAGAGTGAAGGAGAGGCATGCAGAGTACTCAGTGCTGAACCCCACACTCCTTCAGAGAGGGTACAGTGTCTGTCCCCAGGCTGACACCTCCCCTCTCTCCAAAGGCAAGTGTCAGTCTCCAGGGAGCTTGTGTTTCTAGTAATTAACCCCATTTGTCATTAGCTTGTTCCCACTGTCAGCTGCTCCATAGTGCTAAGAAGGCCAGCATAAGCCGTCTGTCCAAATGCCACCGTGCTTTCCCTTTGCAG
Seq C2 exon
GAACCACCATCTGGGAAGGACGGACATCCCAGAGATCCTTCGGTCAGCAGTGCATCTGGGAAGGACAGCAGAGAAAATGGGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039844-Rapgef1:NM_001039086:13
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGAAAAGGCCAGCAGTGAG
R:
CTTTCCCCATTTTCTCTGCTGT
Band lengths:
182-1667
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: