BtaINT0130845 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001941 | SEMA4D
Description
Bos taurus sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D (SEMA4D), mRNA. [Source:RefSeq mRNA;Acc:NM_001098160]
Coordinates
chr8:90229335-90231343:+
Coord C1 exon
chr8:90229335-90229397
Coord A exon
chr8:90229398-90231244
Coord C2 exon
chr8:90231245-90231343
Length
1847 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
TGCGTGTCTCTTCCCTGTAGACA
3' ss Score
10.97
Exon sequences
Seq C1 exon
GCTTATTGGAAGGTTTCAGAAGATAAAAAAGCAAGATGTGCAGAAAAGGGGAAGTCAAAACAG
Seq A exon
GTAATTTCTTTTGCAAGCTTCAGAGACCACCTGGGGAACGGCTTACTTGTTTTACTCTCCCCAGTGCCCCGACTTGTGCGGAGTAGCCCCAGAGTGTTCATTGCTGCTGATCCTGCAGGTCATTTCTCTTTTCCCAAATGGTGAGCTTGGGGCTCTCAATGCCAGTGCCAAACATACCAGGCTTTTGAAAATTACTTTAAAGTCAATCTGAGTTTAATTGGTCCAAATGGCCTGAAACTTTGACTATAGAAAATGATGTCTGATGTTTGCCGGCTAAAGGTGTAAAACGCAGGGAGGGCTTGTGCTTCCCTTGAACAGCAGTGGCCTGGAGGGGTTGCTGTAGGATTTTTGGCAACATCTATCCATTCCTGGAGATTCTGCTCCTTCTCTAGGTACCTCATGCTGGGCACCTCAGCATGGGGCTTCCCCGATGGCTCAGTGGGTAAAGAATCTGCCTGCAGTGCAGGAGACTCTGCAGATGCGAGTTCAATCCCTTGGTTGGGAAGATTCCCCTGGAGGAGGGCATGGCAACCCACTCCAGTATTCTTGCCTGAAGAATCACATGGACAGAGGAGCTTGGTGGGCTATAGTCCATGGCGTCACAGCGAGTTGGACACAGTTGAGCAACTAAGCACAGCCTGGTCCATCTGGGGAACACTGGGCTGAATGTCCATCTCCCTCCAGAATTCTGGGTTACCACCACCTGCTGGGCCCACGTCAGAGTCTCAAAGTACAAGAGCCCCATCTTCCCTGGTCATTGGTTAAGACAGCTCAGTTATGGTCAGTTTCAGTAGTTGGTGGCTAATTTCAAAACAATTAAAATTTAAACAAAAACAGAAATTTGGGCTAAACTTTTTTTTTAGCAAAATACTAAGCACTGTCACGAAAGTCACTAAATTGGAAACGAGGGAAAATGCAGGCATTGTAATGTAATAACAGGTGTCTCAGGGAGTTATCTTAGACCTAAGTTACAACAGGCACTTGGGCTGGGCCCACGTGGAGGTCGTACAGCGGACAAGGGTCCCTCCCAGTTCTTTCATGGAGTATGAATTACTTCCCAACCAGTTTAAAAACAATCATGGCAAAAGAAGCCTTTCCTGAATGGAGATAATTTCAGATGCTACCACATATAATCCCAGTGCATTTCAGTCTAAAATAGCCAAGTGGGTTCCTCAGTGGCATCTGGTTTTCCTGATGGGCCTCTCTGATGTACAGCCAGGCTGGGAGCCCCTCCTTAGTCCTGCCTCTCCCCTGAGCTGGGCGGGCTGGGCACACCCCTCTCCTGAGCAGCACTGTTTCCAGTTGCATGCATTAGGTTGTCAAGGGTAGGGCCCCCCAGAGAAAAGGAAGGCAGAGGGAACTCTGCACAGCACACCCCCGCATGGGTCTGCCATCATAGTGAATGGTTTGTGTGTTCTCTAAGAGCAAATGCATTTTTCCTGTGCTGGGTATCCACTGAGATCCAGGGTCAGCTCGCCTTGCTTTCTGGCCAGCACGTCTTTGCTGCGTGTAAATCAGTGACTGGGGTAAAGTCCATTTGGCACCTGACAGCAGCCCATGAACCCTGCAGAAATTGAAGCACACGGGCCAGCTGCACAAATAGGATTGCCCAAATCTGGGGTCAGATCTCATGGAGCCTGCCTGCACTGTGCCAGGCAGAGCAGGGCTGGCCTGTGGAAATGGAAGGCATCTGAGGCCTGAGGTGGTCAGCGAGCTGTGAGGAGCTGCTGTCGGGCATGTGCTCAGGACTGGTCCCTGCTCTAGAGCGAGCAGGGTGAGCCGTTGGGATCGTTGGCATCCGGTGGAACCTGCACAGTGCTTGACCCGTGCGTGTCTCTTCCCTGTAG
Seq C2 exon
ACAGAATGCCTCAACTACATCCGTGTGTTGCAGCCACTCAGCACCAACGCCCTTTACGTGTGCGGGACCAATGCGTTCCAGCCAGCCTGTGACCACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001941:ENSBTAT00000002525:5
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(4.6=100)
A:
NA
C2:
PF0140314=Sema=FE(7.4=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]