DreINT0132616 @ danRer10
Intron Retention
Gene
ENSDARG00000011163 | sema3fa
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3Fa [Source:ZFIN;Acc:ZDB-GENE-050513-1]
Coordinates
chr6:42884856-42885210:+
Coord C1 exon
chr6:42884856-42885016
Coord A exon
chr6:42885017-42885147
Coord C2 exon
chr6:42885148-42885210
Length
131 bp
Sequences
Splice sites
5' ss Seq
ATAGTAAGA
5' ss Score
4.74
3' ss Seq
ATCTTTGTGTTTTTCCTCAGATT
3' ss Score
11.57
Exon sequences
Seq C1 exon
AGCTGAAGTCTACTGGAACAGCCCATCACTTTGCCTTCCTGCTGAACTCGACGGACTACAGAATCCTCCGCATGGACGAGGATCATGATCGCATGTATGTGGGCAGCAAGGATTACATTCTGTCTCTAGACCTGAATGACATCAACAAAGAGCCCCTTATA
Seq A exon
GTAAGATTTATCAGTTACTCAACTGTAACAAACACAACTATAAACAAGGCTTGGCCATAGTAAAATTGGTAGTAAATGCAGTCACTGGATGAGTATGACCCACATTTGTTTATCTTTGTGTTTTTCCTCAG
Seq C2 exon
ATTCACTGGCCTGTAGCTCCACAGAAAAGGACTGAATGTGTACTCTCAGGGAAAGACATCAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011163:ENSDART00000046498:3
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(7.2=63.0)
A:
NA
C2:
PF0140314=Sema=FE(4.2=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:
TGGAACAGCCCATCACTTTGC
R:
TTGATGTCTTTCCCTGAGAGTACAC
Band lengths:
210-341
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]