BtaINT0130810 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021273 | SEMA4B
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4B [Source:HGNC Symbol;Acc:HGNC:10730]
Coordinates
chr21:22030474-22030910:+
Coord C1 exon
chr21:22030474-22030637
Coord A exon
chr21:22030638-22030847
Coord C2 exon
chr21:22030848-22030910
Length
210 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGA
5' ss Score
5.24
3' ss Seq
TCCCCTTTCTGGTTCCCCAGCTG
3' ss Score
8.96
Exon sequences
Seq C1 exon
GCTCTGAAAAGCGACCATTCCTCAGATTTGAAGCTGAAAACGTCTTCAACTACACATCCTTCCTGCTGAGCAAGGATGGCAGGACTGTGTACGTGGGCGCTCGAGAGGCCCTCTTGGCACTCAACAGCAGCGTCAGCTTCCTGCCAGGCGGGGAGTACCAGGAG
Seq A exon
GTCAGATGATGCTCAGGGCTAGGCTGGGTGGACGGTGCCGGTGGGTGGCTGGGTGGGGGGTGGAACTTCTGGGCCCCAGGATGATGCAAATGGGGGAGGGGTGAAGAAACGGGAGGCGGAGCCTCTGCTCCCAGGGGGAGGGGCGAAGACACGGGAGGCGGAGCCTCTGCTCCTAGGTGCACACTGACCTTCCCCTTTCTGGTTCCCCAG
Seq C2 exon
CTGCTGTGGCGCGCAGATGCAGAGAGAAAAAAGCAGTGCAGTTTCAAGGGCAAAAACCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021273:ENSBTAT00000028346:2
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=0.048
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(16.8=67.3)
A:
NA
C2:
PF0140314=Sema=FE(4.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCTGAAAAGCGACCATTCC
R:
GGGTTTTTGCCCTTGAAACTGC
Band lengths:
223-433
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]