DreINT0152429 @ danRer10
Intron Retention
Gene
ENSDARG00000004246 | slit2
Description
slit homolog 2 (Drosophila) [Source:ZFIN;Acc:ZDB-GENE-010306-3]
Coordinates
chr1:23188376-23189059:+
Coord C1 exon
chr1:23188376-23188539
Coord A exon
chr1:23188540-23188934
Coord C2 exon
chr1:23188935-23189059
Length
395 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAA
5' ss Score
7.46
3' ss Seq
TCTCTCTGCATTTCTCTTAGGTC
3' ss Score
10.27
Exon sequences
Seq C1 exon
GGCTCTGGGCGCAAACCCCCTGTACTGTGACTGTCACATGCAGTGGCTCTCTGACTGGGTAAAGAGTGGATACAAGGAGCCTGGCATCGCCCGCTGTACCGGTCCTGGAGACATGACTGACAAACTGCTGCTCACTACACCCTCTAAGAAATTCACATGCACAG
Seq A exon
GTATAAAAAACCCACTTAAGACACATTTATCCTGTCACAGAGAGGGCATTAACATTAACTCTAACACTAGCTTATATATGCAGATGGTAATATCGTAAGTAATATGATATGATTGGTGCATTTGTAGAGGTGCCGGGGACTTGTGGTTTTCCTGTGCCAGGTAAGGAAGCCAATCAGAGCCCAGAGAGCTCCTATAGCCCCACACCCGTATCTGCCTTCTAAACTTTTCCCGGTTTTAAAGTGACCTTTTGACCTGTGTTTAATTGTGAATAATTTGTGTGATGCCTTACCTGATCAATCCTATGTGTGTTTGTGAGCCTGTGAACATTTGTTAAATTTCTGTTTGCGTGCATAACATGCTGTGTAATTTCCTTTTCTCTCTGCATTTCTCTTAG
Seq C2 exon
GTCCAGTGGATGTAAGCATTTTGGCTAAATGTAACCCTTGCTTGTCCAATCCCTGCAAGAATGATGGGACCTGCAGTAACCATCCTGTAGATTTTTACAGATGCACCTGCCCGTATGGTTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004246:ENSDART00000007531:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138551=LRR_8=PD(11.5=12.5)
A:
NA
C2:
PF0000822=EGF=PU(87.5=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCAAACCCCCTGTACTGTG
R:
TAAAACCATACGGGCAGGTGC
Band lengths:
278-673
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]