BtaINT0130812 @ 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
chr21:22032882-22033753:+
Coord C1 exon
chr21:22032882-22032980
Coord A exon
chr21:22032981-22033641
Coord C2 exon
chr21:22033642-22033753
Length
661 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
CCTGCTCTGCTCCCCTGCAGGAC
3' ss Score
12.12
Exon sequences
Seq C1 exon
CGGGACTGTCAAAACTACATCAAGATTCTCCTGCCACTCAACAGCAGCCACTTGATCGCCTGTGGCACGGAGGCCTTCAGCCCTGCGTGCACCTACATT
Seq A exon
GTGAGTGCCCTTCTGCACCCCGGGCTGGCCCCCGGCTGGCCCAGGAAGTACCCTCTTTCTGCCCCCAGGGAACTGGTCTGTAGCACTGACCCCTGGTGAAGGGCAGGGCCCTGGTGGGAGGCTTCTGGGAGGTCAAGGGCCCTGAGAGCCTGGGGACCCTGCCCAGCCCTGATGGGTGGGTTTCCCTGCAGGGTGCGGGTAGAAGACAGACCTATAGGATTCCCTGAGCACAAGATCCTGGCTGACCCACGATCACACCCTCTCACTTCCTCCAGCTCTCGCTTAGTCCTGGCCAGCCCATCTCATCCACCCTCCTCATCACACACACGCCCTTGTGTTTCTGCCCTTTGCACAACTTTGTAGAGGGTGGCATTTTCAGGGCGTGAGTCGGAGCAGCCAGGTTCCGAGTCAGACGTTCCTGGGTTTGAACCACATCACTGTCCTTTCCTGGCTCACGTCGCCTGTCTGAGCCTCTTCTCTGCCCCGTGGGCCAGCCACTGTGAGGGGTCATGGCAAGGCGCTGCAGGGACTGTGCCCCAGAGGCCAGGATCGGGAGGAGGCCCTTGGACCACTGCCCTCGCTCTGGACACCTCCCTGCTCTTCCGCCAAGCTCGCTCACTCCCCGGTGTGGCCCTGACCTCCCTGCTCTGCTCCCCTGCAG
Seq C2 exon
GACGTGGAGAACTTCACGCTCGCACAGGACAAGCAGGGCAACATCCTCCTGGAAGATGGCAAGGGCCGTTGTCCTTTTGACCCTAATTTCAAGTCCACGGCCCTAGTGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021273:ENSBTAT00000028346:4
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=FE(14.5=100)
A:
NA
C2:
PF0140314=Sema=FE(16.8=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:
CGGGACTGTCAAAACTACATCA
R:
AATCACTAGGGCCGTGGACTT
Band lengths:
210-871
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]