BtaINT0130815 @ 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
chr21:22034230-22035978:+
Coord C1 exon
chr21:22034230-22034381
Coord A exon
chr21:22034382-22035796
Coord C2 exon
chr21:22035797-22035978
Length
1415 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
AGCCCCTCTCCCTGGTGCAGGGC
3' ss Score
7.95
Exon sequences
Seq C1 exon
ACCCAGCGTTTATGGCCTCAGCCTACATTCCCGAGAGCCTGGGCAGCTCGGAAGGGGACGATGACAAGATCTACTTCTTCTTCAGAGAGATTGGCCAGGAGTTGGAATTCTTTGAGAACACCATGGTGTCCCGCATCGCCCGTATCTGCAAG
Seq A exon
GTGAGGGGGCTGGGCCACCCTAGAGGCCCCACGTCTGTGGCCTTCTCCTGTCCTCCAGAAGGAACGGCTTGGCTACTGGCATTTCTCTTTTTTTCTTGAATTTTTGGCTGAGCTACATCTTCAGTGCTTCCCGGGCTCTTCTCTAGCTGTGCTGAGCGGCAGCTTTTTCTCTAGTTGAGGTGCACGGGCTTCTCACTGCAGTGGCTTCTCTTGTTGCAGAGCCCAGGCTGAACGTGCAGCTCAGTAGTTGTGGTGCACGGGCTTAGTTGCCCTGCGACCTGTGGGACCTTCCTGGACCAGGGATCAAATCCGTGTCCCTTACATTGGCTGGCAGATTCATAACCACTGGACCACCAGAGAAGTCTTCTCTTCTTTTAAGTTAAAATGTCTGTTTTTTTCTTATTTAAAAGAAACGTGAAAACATAGCAAAGTATACACAAAAATCACAAGATAAAGAGGCAGCTTGGTATGGTGATTAAGAGTGTCGACGCTGGAGCCCAGCTGCCTGGGTTCAAACCCTGCGGGTCGTGTGATCTTGGGCAATTTCCTTGCTGAGAAATCTGTTTCAGTTCCCGCCTCTGTTCAGCATGTACGGTGCTTGGAAATGTGCTGAGCAACCACTAGATGGTGACTGTCGGTGTTAAAATCTCATCCTTCCACAAGAAGTGACCACTGTTAACAATTTAGAATGTTCCTTGCTAATCTTTATACTTTTGCCCATATGTAAAGACTTACATATTTGTCTTGTGTAAAACCATGTGCAAACAAAGAGACACTGTAATGCAACTCTTTAGCCTCCCTTTCTGCTCAGCAGTAAATCGTGACGTCTTTTCATGTTTGTAGACAGATTCCCTTCGTCCTTTTTCTGGCTCCTTGCAGTTAGGGAAGCACTGTCATTTACCTAGCCAGCCTTCTGGCAAGGGGGGGACTGAAGGCTGCCACTTCAAGTCTTTTTTTTTTAATTTATTGTTTATGTGAAATTTAGATCTAGCCGGAGGCGTGCTCTCTCTCTCTCTCTCTCTATGTATATATACACATAAACACACACATATATTGGCCATGGGATGCAACATGTGGGATCTTAGTTCCCTCATCAGGGATTGAACCAGCGTCCCCTGCACTGGAAGCATAGGGTCTTAACCACTGGACCACCAGGGAAGTCCCCTGTCTTCTTGATTTGAGATGAGCTCAGGCCTGGTGTTGTGTCCGTCGGGCCCTTCCTGGTGTCCCGGGAGGGGAAGCGAGGAGCCGTCCCTGAGCCCAGCCCCTCTCCCCCTGGTGCAGGGCGACGAAGCCCTGTCTTCTTGATTTGAGATGAGCTCAGGCCTGGTGTTGTGTCCGTCGGGCCCTTCTTGGTGTCTGGGGAGGGGAAGCGAGGCGCTGTCCCCTGAGCCCAGCCCCTCTCCCTGGTGCAG
Seq C2 exon
GGCGACGAAGGGGGCGGGCGCGTCCTGCAGCAGCGCTGGACGTCCTTCCTGAAGGCACAGCTGCTGTGCCTGCGGCCCGACGACGGCTTCCCGTTCAACGTGCTACAGGACATGTTCACGCTGACGCCCCGCCCCGAGGACTGGCCCGACACCCTCTTCTACGGGGTCTTCACATCCCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021273:ENSBTAT00000028346:7
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(11.4=100)
A:
NA
C2:
PF0140314=Sema=FE(13.7=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:
ACCCAGCGTTTATGGCCTCAG
R:
CACTGGGATGTGAAGACCCCG
Band lengths:
334-1749
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]