DreINT0071455 @ danRer10
Intron Retention
Gene
ENSDARG00000060631 | garnl3
Description
GTPase activating Rap/RanGAP domain-like 3 (garnl3), mRNA [Source:RefSeq mRNA;Acc:NM_001128527]
Coordinates
chr5:32787225-32787548:-
Coord C1 exon
chr5:32787440-32787548
Coord A exon
chr5:32787271-32787439
Coord C2 exon
chr5:32787225-32787270
Length
169 bp
Sequences
Splice sites
5' ss Seq
CACGTATCC
5' ss Score
0.74
3' ss Seq
TTCCTTGACAAACCACTTAGATA
3' ss Score
2.1
Exon sequences
Seq C1 exon
GTAGAGAGGAAGAGACACATTGGGAACGACATCGTGACCATCGTGTTTCAGGAGGGAGATGACGCCTCGCCGTCCTTTAAACCCTCCATGATTCGCTCCCATTTCACAC
Seq A exon
GTATCCTTCATACTAGAGTGGAAAGGATGGAATGAGTCACTCAGTGTGACAGTGTTTAGGCTGTGTTTGTGGGGGATGTTTTTTAATACAACAAAATGATTTTAAAAATGACATCCAAATTTGCTTGTGTAAGTAGTTTTCAAAATGTTTTCCTTGACAAACCACTTAG
Seq C2 exon
ATATTTTTGCCTTAGTTCGATATAATAGCCAGAATGATAGTTATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000060631:ENSDART00000085636:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0214510=Rap_GAP=FE(19.1=100)
A:
NA
C2:
PF0214510=Rap_GAP=FE(8.0=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:
AGAGAGGAAGAGACACATTGGGA
R:
TCTGGCTATTATATCGAACTAAGGCA
Band lengths:
140-309
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]