DreINT0124490 @ danRer10
Intron Retention
Gene
ENSDARG00000043593 | rapgef1a
Description
Rap guanine nucleotide exchange factor (GEF) 1a [Source:ZFIN;Acc:ZDB-GENE-081105-26]
Coordinates
chr8:11794162-11794544:-
Coord C1 exon
chr8:11794388-11794544
Coord A exon
chr8:11794251-11794387
Coord C2 exon
chr8:11794162-11794250
Length
137 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTG
5' ss Score
7.76
3' ss Seq
GCTTCTGTGGTTTCCTGCAGGAG
3' ss Score
10.27
Exon sequences
Seq C1 exon
TTCAAGGGTGTCCTCCTGTCTCAACCGACTCTATCAAAGCCTTGCAAACCTCATTCGCTGGTCGGACCAAGTAATGCTGGAGGGTGTGAATTTGGAAGATAAAGACACAATAACAACAGTCACAAATGTGATCAAAGCAGTGCTGGATGGTGTAAAG
Seq A exon
GTATTGATGTTCTGTAGAACTCTGTCAGGGCTTGTTTTTGACATGCTGCTGATGTGTCGATTTATTCTCCACCCATAATCCAGCTGGATTTAGCCACAGGCTTTGTTTTTAGTTGATGCTTCTGTGGTTTCCTGCAG
Seq C2 exon
GAGCTGGTTAAAGTTGCCATTGAGAAGCAGGAGCACCCTTCACCTACGACACCTGTCAAAACCATTCCTCCAGTTGCCAGCCCACAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000043593:ENSDART00000139947:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.820
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGGGTGTCCTCCTGTCTCA
R:
CTGTGGGCTGGCAACTGG
Band lengths:
242-379
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]