DreINT0132535 @ danRer10
Intron Retention
Gene
ENSDARG00000011672 | sema3b
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:ZFIN;Acc:ZDB-GENE-081105-78]
Coordinates
chr8:26586009-26588046:-
Coord C1 exon
chr8:26587889-26588046
Coord A exon
chr8:26586072-26587888
Coord C2 exon
chr8:26586009-26586071
Length
1817 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
AACTCCTCTTTCTTTCTCAGATC
3' ss Score
10.81
Exon sequences
Seq C1 exon
ATCTTCAGCAGTTTAATGGCATTAAGCGGTTTGACTTGGAGCGTTCGTGTTCTTTCGGAGCTCTGCTATTGGACGAAGAGAGGGGGCGACTGTTTGTTGGAGCTCGAAACTTTCTGCTATCTCTGAGTCTCGACAACATCAGCAAACAGGAACAGAAG
Seq A exon
GTACAGTACACTTCTTACTCTCTCCCTCTTCGTTTCCTTCATCCATAATGTAAGAGTGAAAGGAAGCATCTTCTCTTCAGTTTGTCTGTCATCGTCTAATTAAGTTTTAAACAAAGGTGTAACCCTGTCAGTCATAACTCATTCGTATACAGGATAAGCACCTGGGGACGATCCACCAAGAAGTTCTGTCTCTTTTTTTATTTTTTTTTTTAGGATTGGCTGACTATAGCTACTAGTCATTATTAACGTCCTACAATATAACTGTATACTTACTGTATGTGGCATAAACTTTTTAATATATATAAATGTATATACTATTAAGATTGGTACAGTATAACATGATACATGTTCATATGTAAATTATATATTTTATATATTAAAATATTCTACAAATATAATGAAATATTTTATACCACAAAAAAATATTGTATATTCCTTCATTTTCTTGTTGGCTTAGTCCCTTTATTAATTCGGGGACGCCACAGCGGAATGAATCGGCAACTTATCCAGAGGATTGCGAGTTCACAAACGCATTAAAATCCATAAACAAAGCAGCACACATCAGGTTTTCAACATGGTTTTAGACGCGTTATGAGATTACAAAGAGTTAACCAGATACAGTACAAGCGGTTACGGCCAGGGGTTTCAAATTTACCGGGTCTGCGCGTGCAAAAAAATGGGCGGGGCTTGAGTTTTATATCGCAGTCACGCCGGCACGGCTAAAGACTTGTTACTGCGGCGATTTATTCGAACCACTATGAGTCGACTCTTTTATAGATGAACCAATAGTTTTAAACATGGTGCACTTTCAGATTTACGCCTTAGCTGGATATTTCACTTCACTCAGTGCTGTGTTACACTCTGTATGGAAGGTCATTTTCAAATACCCATAATAGGGGCTCTTTAAACATCATAATAATCGTTTTTTATTTATTCATCTTATTAAAATTATTGCAAAAAATGTATTTTAATTAAAAAAATACTGCACATAATATCTGTTGTTGCAGTGCGTATCATTTGAAAATGTTGTACAGTACATTATATTGTACATGTGTATATTATACATTGACTTTTTTGTACTTTACTGCTACTGTATCATCAAATATAATCTTGAAAAATACATTCATTAAACATTTTACTTAAAATTGTATATAATTTATCCTAAAATTATTTCAAAAATACTAATAAATGTAGGGTGCAAACTACTAATAAATACGAAATATTAACATCAGTGAAACAGAAATCTGTAGTTAAAAGTGTTATTCTTTATTTGTGTGTGACTGCAAAGCCTGTTTATGTCCCTCCTTGAATCCCTCTAATATTATTATATGCATAATACATTTACTGTATTTTAATGAAATAACCCAGAGCCAAAACTTACCCTGGTTTAAACTATTAACAAGTAAAAGGATCAAACAATTAGATGTTTTATAACCCATTTATGTTTGTATTTTAAGCTAATAGCATGGGACTAGATTGCATTTGATTTTGCGAGAGAAACAAAAAGGAAGCTTCAGCATTTATCATGTGTAAAGTTAATCAGCCTTTAAAGTCACGCCAGATGATTAACAGTGGTTCAGGCCAACATGCCGATGACAGATTGATGGATTTTTATTTCTTCAGGAAGGAAAGAGAAGGAATGACGAGTTAGAGTTGTCGGTCACTGTGTTCTGGCTTTAGACACACACAGGTGTGGTTTAAGGCTGGATGTGTCCGGATGTGTGTGCATGAGAGAATGTCCCTCAAGCTAGTGAACACGTCTAACCCTGCAGTGTCCAAAACTTCTGCTCACCTCTGAACTCCTCTTTCTTTCTCAG
Seq C2 exon
ATCTACTGGCCAGCGCCTGTCGACTGGAGAGAAGAGTGCAACTGGGCCGGGAAAGACATCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011672:ENSDART00000027301:2
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:
PF0140314=Sema=PU(7.7=64.2)
A:
NA
C2:
PF0140314=Sema=FE(4.5=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:
TCAGCAGTTTAATGGCATTAAGC
R:
ATTGATGTCTTTCCCGGCCCA
Band lengths:
217-2034
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]