BtaINT0130835 @ 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
chr8:90239005-90240388:+
Coord C1 exon
chr8:90239005-90239227
Coord A exon
chr8:90239228-90240272
Coord C2 exon
chr8:90240273-90240388
Length
1045 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
ATGCAGCTTTCACCTTGCAGACC
3' ss Score
7.71
Exon sequences
Seq C1 exon
TGTATCAACCGGGAGGCACGGGCGGCCAACTTTTCTAGCTCGCTCAACCTGCCGGACAAGACCCTGCAGTTCGTCAAAGACCACCCCCTGATGGACGACTCCGTGACCCCGATAGACAGTAGGCCCCGGCTGATCAAAGGCGACGTGAACTACACGCAGATTGTGGTGGACAGGGCCCGGGCCCTGGATGGAACCATCCACGACGTCATGTTTGTCAGCACAG
Seq A exon
GTGGGTCCCTGGGTAAGAACACGGGTACGTCCAGTGGTGGCTCAGTGGTAAAGAATCCACCTGCCAACGCAAGAGACACAGGTTCAATGCCTGGGTTGGGAAGATCCCTTGGAGAAGGCAAGGGCAACCCACTCCAGTGTTCTTGTCAGGAGAATCCCACGGACAGAGGAGCCTGGTGGGCTACAGTTTATAGGACTACAAAAAGTCAGACATGACTTGAGCAACCAAACAATGAAGACCAGCTAATCTCTGCCACACGGAGCCAGCATCTCGCCCGGGTGCCCGAGTAGTGGGAGGATTTGTTAGTGTGTGGGAAGATTTCTGAGAAGTCCCCACACCTTGGTGGCTTCAGATCTCTGTGACCATCAGAACACCTGGAGCGCCAGTTAAAAATGCAGGTCCTGACCCAGATCTAGAAATTCAGGTCTGATGGGTCTGGGCTGGTGTAGAGGGAGGCCAGGTGGTGCCATGGAGGTGAGGTGAGAGCTGCAGACAGGCATGTCCTGCCTCCCTGAGTGACAACTGGGCTCGAGACCTGTCCTGACCTGCCGTGGGAGACACACCTCTCCTGGTGGCCCGTAGATGCCAACACAAGTTTCCTGGAATGGAAATGGTGACCAGGCAAAGGAGCAGCAGCAGTGGGCAGGCTCTGTGGTCAGCCCTGGGTGCTGCCCAGCCCCTGGCTGCCCCTGCCTGGGGCTCCTGGTGGGCTGGCACCCCCAGAGGCCTGTGGTGCCCAAGAACCACGTCACATTTATTTGGATGACACAGTGTCGACCATTCTGATGGGGAGTATTGGACTTAACAAAGAGCTGTTTATTTTTTCTGAAAAAGATGGGGATGACCCATGCCAGCTGGGTGTCCAGTTGTTTATTTTGCATATGACTCTTCCCTTTGTGAGTCTAACGCAAAAACATCATCTGTTTCTAAGCCTCCTGTTGGGGGAAGGTGCGGGAGGCAGAAGGGTGACTGTTTGCTGCTGTGGCCAACAGCGCCAGCACCGTCCCCTTCTCCTGGGGACTGACATGCAGCTTTCACCTTGCAG
Seq C2 exon
ACCGGGGAGCCCTGCACAAAGCCATCAGCCTTGAGAATGACATCCACATCATTGAGGAGACTCAGCTCTTCCAGGACTTCGAGCCCATCCAGAGCCTGCTGCTGTCTTCCAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001941:ENSBTAT00000002525:12
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:
PF0140314=Sema=FE(17.1=100)
A:
NA
C2:
PF0140314=Sema=FE(8.8=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:
GGCGGCCAACTTTTCTAGCTC
R:
TTCTTGGAAGACAGCAGCAGG
Band lengths:
318-1363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]