DreINT0071479 @ danRer10
Intron Retention
Gene
ENSDARG00000060631 | garnl3
Description
GTPase activating Rap/RanGAP domain-like 3 (garnl3), mRNA [Source:RefSeq mRNA;Acc:NM_001128527]
Coordinates
chr5:32794025-32794421:-
Coord C1 exon
chr5:32794346-32794421
Coord A exon
chr5:32794124-32794345
Coord C2 exon
chr5:32794025-32794123
Length
222 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGC
5' ss Score
8.27
3' ss Seq
TTGCTTTGTACTATTTTCAGAAA
3' ss Score
7.42
Exon sequences
Seq C1 exon
GGAAGCGTTAACTTTAAATTTGGTGTTCTTTATGCCAAGGACGGACAGTTGACAGATGATGAAATGTTCAGCAATG
Seq A exon
GTGAGCACAGCACCACTCGCAATGTACTCAGAATACTAATTAAATATTTCTTTCTTTTCTGCACAGATGAATAACCTGTACATTTGTAAAATTACATGCATTGGTGTATATCTATGTCTGTGTGTGTGTCTGTGTGTGTGTGTGAGAGAGAAAGAATCTTATTATTTTATTTCATTTATTTTCTTTAATATTAATTTTGATTTTGCTTTGTACTATTTTCAG
Seq C2 exon
AAATGGGAAGTGAGACCTTTGAGAAATTTCTGAATCTCCTTGGTGATACGATCTGTCTACAGGGCTGGGCAGGGTACCGAGGAGGACTCGACACTAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060631:ENSDART00000085636:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.077 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0214510=Rap_GAP=PU(2.1=15.4)
A:
NA
C2:
PF0214510=Rap_GAP=FE(17.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAGCGTTAACTTTAAATTTGGTGT
R:
TCTTAGTGTCGAGTCCTCCTC
Band lengths:
175-397
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]