DreINT0132539 @ 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
chr8:26575108-26576077:-
Coord C1 exon
chr8:26575958-26576077
Coord A exon
chr8:26575251-26575957
Coord C2 exon
chr8:26575108-26575250
Length
707 bp
Sequences
Splice sites
5' ss Seq
ATGGTGCGT
5' ss Score
8.27
3' ss Seq
AATGATGCTGTGTGTTTCAGAGC
3' ss Score
9.07
Exon sequences
Seq C1 exon
GTGATGAGCTTTATGCAGGTGTGGCCACTGATTTGATGGGACGCGACTTTACAATCTTTCGCAGTATGGGACAAAAACCCTCCATACGGACTGAACAGCACGATTCTCGGTGGCTCAATG
Seq A exon
GTGCGTTTGTTCACCAAAGGGTGTCTTTTTCAGTTTGTTTATGTCTGTTAAAATGACTTGATTCTATAATGCAGAATTTTATTATGTTATTATTTATTAATAATTAACTATTATTATATTTTTTAATCATTTGTGAAAATATATATAAGTGTTTATAACAATACTGTATCCACATTGGAATGATAGGAATAATAAAAGGAAAGTGGTAATGATAAATTGAGCATGCATCTGACATTAATTTTAAATTAGGGTAATACTTGATATATGAGTACATTATTATGCGTGTATTCATGCACACATTTATAATACAACATCATTGCATAATGATTTCTTTGCAAAACATTCACTACATAAATTTCTATCAATAAGCTAAAATACATGGTATTGCCTATGGTATTCATTGTATACAGTTAAAATTATGTTGCAACATCAATACATTCATGACACATTTAATTAATAGCAGTTCATAAATGTATTTGTTGCTAGTGCAGTAGTCGTTAATTAATGCTTGATTAATATATTAACTCATGAGTTCAGCATGATCTAGTGCTCCTACAGTCTTACCTAAATAAATAAATAAATATATAACTTTTATTTTTATTTTCCTTATCTTGCAAACACTTATTTGTCTCTGAATCATTTATTTGGATATTTATCTGTTGTTGTATAATGCCAATAAGACCTGTAAATGATGCTGTGTGTTTCAG
Seq C2 exon
AGCCCAAGTTTATTGCAGCATTTGGTGTTCCTGAGAGTGATAACCCTGACGACGATAAAGTCTTCTTCTTCTTCAGGGAAACTGCTGTAGAAGCTCAGGGATTTGGGAAGGTTACTTATTCCCGGATTGGTCAGCTCTGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011672:ENSDART00000027301:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.098 A=NA C2=0.021
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(9.0=100)
A:
NA
C2:
PF0140314=Sema=FE(10.6=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:
TGATGAGCTTTATGCAGGTGTGG
R:
CCTGCAGAGCTGACCAATCC
Band lengths:
262-969
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]