DreINT0132552 @ danRer10
Intron Retention
Gene
ENSDARG00000007560 | sema3bl
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3bl [Source:ZFIN;Acc:ZDB-GENE-030131-2956]
Coordinates
chr8:26539015-26539951:+
Coord C1 exon
chr8:26539015-26539105
Coord A exon
chr8:26539106-26539834
Coord C2 exon
chr8:26539835-26539951
Length
729 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTT
5' ss Score
6.3
3' ss Seq
ATTCTCTCTCGCTTTCTCAGGTG
3' ss Score
11.25
Exon sequences
Seq C1 exon
CATGTGTTTAGCTTGGATCAAACCACAGTGCAGAACGGGAGGGGGAGATGCCCTCATGACCCCAAACTACCCTTCGCAAGCACCTTCACAG
Seq A exon
GTAGTTTCAAAGTTCATGCCACTTAATGTTTATGTTATGTGTTTATTAGTATGCCAGAGCCTGTGTGTGTATGTTGGCTCTTGTGTATCTGTGGGGTGGAGGTTTCAGCTTGTCAGCTGTCAGTGAGTTTATGGGCCGTTAAAGATTGAGTGCTCTGATGGGGGAAATCTGACATGCTGTAAAGCCAGGTTTAGTGTTGCGGGGGTCTCATGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGAGTGTGTGATGGTGGGTGTGTTACAGTAATCTGGGGCAGAGACATGTCTCCCACTGTGTATAGTGTAACACTGCTCAATCTTGGCTCTCATTGTGTGCCGTTTTGCCAGATCCAACATGTTTTGGACAGATTTTTAACACTGCATATTAGTGAACTTGAAGATTCACATACTGGCACACATTTCTATCAGGTTCTTGGCAACAGCTATTTTGAAGAAGTATTTTTTTAAGTCGTTTAAAAACTGAAATTGTATGATCTCATGCACTGTATGTAGATGATCAACTAGCCTGTGTGTGAGACTTTGAAAGGCTGTTGACTCTGCTATATATCAGCTTTCAGCTCATTCAAACGTGTGTTAGTGTGATTTCAAGCTGCTAACAATTTAATGGCCATTTTAGGGGCAGTCTGGCTTCCTGCACGTACAGTAAGACACGAAATTCAGCACTTCCAGCACTGACTGCTAATTCTCTCTCGCTTTCTCAG
Seq C2 exon
GTGGAGAGCTGTACACTGGTCTGACTGCTGATTTTTTGGGGAGAGACTCTGTGATTTCAAGAGGTTTCGGGACCCGCTCACCCATGAGAACAGAAACAGATCAGAGAATACTCCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000007560:ENSDART00000046863:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.226 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(6.4=100)
A:
NA
C2:
PF0140314=Sema=FE(8.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGTGTTTAGCTTGGATCAAACCA
R:
TGGAGTATTCTCTGATCTGTTTCTGT
Band lengths:
206-935
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]