DreINT0132534 @ 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
chr8:26567345-26568635:-
Coord C1 exon
chr8:26568496-26568635
Coord A exon
chr8:26568313-26568495
Coord C2 exon
chr8:26567345-26568312
Length
183 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TGTGTGTTTGTGTGTAACAGGTG
3' ss Score
10.7
Exon sequences
Seq C1 exon
ACCATCAGAAGCAGCGTGTCCTGGAGAAGAGGTTGTACGCTGTGGATGGAAGCAGCTCCTTCCTGGAATGCGTCCCGAAATCACTGCAGGCCCAGATTACATGGACCTATCAGAAGCTTCCGGAAAACCCACGGGAGGAG
Seq A exon
GTGAGAGGCAGGCTGGGGCAGATATGTGGGCTTATTATGAGAAAGACGGATATAGACAGCACTGATAACAGATGATAAATGTGTGTCTTTGTTTCAATTAATGACTTTCATTTTCTCTCTGCTATCAGTGCCATCGCTACTGATGCTTGATGCATTCATTGGGTGTGTGTTTGTGTGTAACAG
Seq C2 exon
GTGCGTCTGGATGAGCGTGTTCTGCAAACTGAGCGAGGGTTATTGCTGAGGCGAGCTGTGCGTAGAGACGCCGGTGTATATCAATGCCACTCTATGGAGCACGGATTCACCCAGACTATCCTGGCCATCACACTGGAGATTTTGCCTTCGGCTGGCTCCGCCCCTTCTGCTGTTAACCCCCGCAGCCCCGCCCACTCACATGTCAGTCATGGCCAGTCCACCAATCAAAAACTGTGGTACAGGGACTTTATGCAGTTGGTCGATCATCCAAACTTAAACACAGTCGACCAGATCTGTGAACAAGTGTGGTCGCGGAAGCACAGCCTATCAGGGAAGAGCCCACCAGATCCAGCCATCGAGGTGCCAGCTCATGATCCGCTGAACTCCAAAAAGTGGAAGCACCTAAAGGAAATGAGGAAGGGCCGAAATCGCCGAACACACGATGGCAAACCTGCATCCAGAGCACCGCGGAGCGCAGGAGAGTAGCGAAGGATAAAACTAAGAGACAGAAAGAACACAAAATAACCACTGGAGGTGGACAGATTCTCACACGACATCTCATTCGGTGACTGTTTATCACCCGTTCTGCTTCTTATGACCCCTGTGACGACACTCTACTGCCTGCTATTAGTCTCTATATACTCTATTGCCCTCATCTCCAGTCTGAAGACTCAATCTAGTGCCCTCACGACCCCAATCCCCATCCCGCCAGCATCTATTACCCCACACTCCATCCAGTTCATCTAAATACTAATACAAACTCGAGAGGTCCTGAACTCTAAAGTAAGTCCTTTTGAATTGTAGCTGGAAGATTGCTTTGATTGGATATTGAAGACATGAGACATGCATGCGCTGCATCGATCGGTAAACACAAGCTCACACTCACATCCAAGCATAGTCACCTGTTTTCTTCTGGGTGTTTGTGTAAGGTGTGTTCAGTAGATTAGATTCTTCTTTCACTTTGGCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011672:ENSDART00000027301:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.522
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(6.8=8.5),PF0248011=Herpes_gE=PU(22.7=53.2)
A:
NA
C2:
PF0248011=Herpes_gE=PD(75.5=51.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGTTGTACGCTGTGGATGG
R:
TCCAGTGTGATGGCCAGGATA
Band lengths:
249-432
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]