BtaINT0130808 @ 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
chr21:22038146-22040306:+
Coord C1 exon
chr21:22038146-22038312
Coord A exon
chr21:22038313-22040226
Coord C2 exon
chr21:22040227-22040306
Length
1914 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
AGACTCTCTTTGGTCCCCAGGCC
3' ss Score
8.28
Exon sequences
Seq C1 exon
GGATTGCTGTACGCTGCCTCACACTCGAGCGTAGTCAAGGTGCCTGTGGCCAACTGCAGCCTGTACCAGAGCTGCAGGGACTGCCTCCTGGCCCGGGACCCCTACTGCGCTTGGAGCGGCTGGAGGTGTGCGTCCGTCAGCCTCTACCAACCAGAGGTGGCCGTCAG
Seq A exon
GTAAGAGCTAGTTTGGGCCCCTTCCCCTTGTCCCTCCTGGCGCACCTGCCTCCAAGTGTCTCTGCTTTAGACCCTCTGTGGAATCACCACACAGCCTCATTTGTGTCCGCTGTCTGGGCATCATTTTTTTTTTAATCATTGTATTTATTTATTTTTGACTATGCTGGGTCTTTGTTGCTATGCAGGCTTTGCCCTAGTTGTGGCGAGTGGGGGCTACTCTAATTGCAGTGCACAGGCTTCTCCTTGCAGTGGCTTCTCTTGCTGGGGAGCATGGGCTCTAGAGTGTGGGCTTCAGTACAGCTCTCAGGCTCTAGAGCACAGGCTCAGGAGTTGTGGTGCACAGGTTGCTTCGCAGTAGGTGAGACGTTCCTGGATCAGGGATTGAAGCCGATATCTCCTGCATCGGCAGGTGGATTCTTCACCACTGAGCCAGCCACCAGGGAAGCCCTGGGGATAATTATTAATCAGCTCCCTTCCTGACTCTCAAAAGAGTTGTAACTCAGACAGTAAATTATGTTTGTCTTACCCATCTGTAAAGCAGGGACAGGATTGGGTAGTTAGTATAAAATGTCATAGCTGTGAAAAGATTTGCTGGAGAATGTGAATTGGCACATGAATGTAGTTAAATAACAGAAAATAAGGGCTCCATAACAATCCATTAACAGACCCATTAAGGGACTTCCTGGTGGTCCAGTGGTTAGAACTCTGCTCTTCCACTGAAGGGGACGAGGGTTTATTCCCTGACCAGGAAACTAAGATCCCGAAAGTGGCGTGGCTAAAAACAAACCAATTAAAAATTGTTTTCAGAATAACTTATTTTGTCTAAGAAAACTTAGACAATAGAGATAAGCAGAAACAAAATAAAAACTATCCAAATTTTACAACCTAGAGAGACTTAGATTTAATATATATCCTCCCAGATTTTTCCAAATATGTGTAATATGAACAAAAATACTTTTTTTTTTTAAAAACTAAAAAAAAAAAGTTTGGCTGCAGTTGGTCTTTGATCTTTGTTGTGACATGTGGGATCTAGTTTCCAGACCAGGGATCAAGCCCAGGCCCCCTGCATTGGAAGCTCAGGGTCTTAACCACTGGAGTATGAGGGAAGTCCCAAATACATACATTTTAAGTAAAAATTGGATCTGTCCTATTTGTAGTGTCTATACTTCACTCAAGGGCATACCTGTTTCCAGTTTTATATTTTAAAACATCACGTGTGTGTGTGTACACATATGTATACCTGAAGGGACACTCCAAAAAATACCACCTTTATTGTTGAATAGGTAATTGCGTTTTTTTTTAATTATATTTTAGCTCCATAAAGTTTTGTTTTGTTTTTAATACTTATGTATTTATTTGGTTATTCTGAGTCTTAGTTGCAGCATGTGGGATCTAATACCCTGACCGGGGATGGAACCTGGGCTCCCTGCATTGGAAGCTCGGACTCTTAGCCATTGGACTACCAGGGAAGCCTCTGATTGTGACTTTTGTAATATTCGGTTGAGTTTGTGCTTGATTGAGTTCTGTGTTTTCCAAAATTAAGTCAGTGCCTGTGCTTTGCTTTAAAAGAGACAGATATATGTTAATACGTACAGATTTGGCTGCCCTTCCAGACGTTCTCTAGGGACTCACTCTGCTTTTGTGATTAAGGAATTATCACAGCAACTTTAATATGAAGTAAATACTGTGTAGACAGAGGAGATGCCAGCTCTGTCTACAGAGCCTGTGGGCTGGGGAGTTGCGAAGGGAGGCCGCCTGCCTTTCACCCCTGCCTTGGTCCTGGTTGTCCCTGAGCCCTTCCCCAGGCCTACATCTGCAGGGCTGTGTGACAGTGCGTACTGCACGGAGGAGGATGGGGGCAGATGCAGGCTGTTGGGGTTTCCTGGCCCATCCCAGACTCTCTTTGGTCCCCAG
Seq C2 exon
GCCATGGATCCAGGACATCGAGGGGGTCAGTGCCAAGAACGCCTGCAGCCCTTCCAAGATCCGGGCGTTTGTACCAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021273:ENSBTAT00000028346:12
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:
PF0143720=PSI=PU(64.4=67.9)
A:
NA
C2:
PF0143720=PSI=PD(33.9=71.4)
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:
GATTGCTGTACGCTGCCTCAC
R:
GTACAAACGCCCGGATCTTGG
Band lengths:
240-2154
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]