BtaINT0130841 @ 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
chr8:90261126-90262973:+
Coord C1 exon
chr8:90261126-90261223
Coord A exon
chr8:90261224-90261597
Coord C2 exon
chr8:90261598-90262973
Length
374 bp
Sequences
Splice sites
5' ss Seq
TGGGTACGT
5' ss Score
7.7
3' ss Seq
AGTCCATGGTGTTCTTTCAGGAA
3' ss Score
8.49
Exon sequences
Seq C1 exon
AGGCGACCCAGCAGGAGAGGTGGACCAGAGAGCTCGCCAGCTGGAGGGCCGTGGTTGGGGAGCACGACCGCATGATGCAGAGCTGGAGGAAGGCGTGG
Seq A exon
GTACGTGGCTGGGCATGAGGCAGGGCAGGGGTCTGGGATGACAGCTGTCCCTCTTGGGGGCCTATCCTGCCAGAGGGCCCCATGTGCTTCCTCCTGGCCCACAAAGCAGTTGTGCTTTCTGAAACCCACACCCCTTCTACCTGTCCCCTTCCAGCCTGGGGGTAGGGAGAGGCGGCTCTTACAGGAAACCAAAGTTAGGTGGGGCCAGCTGCTTCCAGCAAGAAGCCTCCCACGGTCACCCTGACCCCTAGCCCAGAGCTTAGTAGGCCCAGGCTTCCCTCCTGCAGGTCCCTGGACCCCCCAGGAAGCACATGGGAAGCAGGTTCCAGGCTTTTCTGTTATACCAAGAACTGAAGTCCATGGTGTTCTTTCAG
Seq C2 exon
GAAAGCTGTAACCAAGACGCATTCTAGCCACAGGAAGCCGTGCTGACCAGGCTGACCGTGCTGCCACCCGACACACAGCCCCGGAGGCCTCAGGGCAGTGAGCTCCCTGTCTGCGGGACACAGCTCTTCGGGTTGCACAGCCGAGAACACGGAGCCCTGAGGGGGCCTGCGGCAGTAGCCAGAACGTGTTTTAATTAGGTACTTAGATGGGACAGAATGGCCTGTCTGGCAGGAGCAGGAAACCGGGGTTAACAGGCTACAGACAGGAACTCTGGTTAAGACAGCAGTGTGCGTGATGGGTCCTTTTCCAGAAGCACTGTTGTTACACTCCACAGGTCTGAGTTACTTTCATGTCATGCAATGGGTTGTCCTTCACACAGCCGAGTGTTAGCTCAGCTCTCGTGACTGCTGGTTTTACTGCTCTGGAGCCCCCTTCACACTCAGCTGCTCATCTCTAGGAGACAAGGCAGGAAGGACAAGGCTCCAGATGACCAGAATTTGCCTTAAACCTTGAGTGCTGAGGTCCACACTCAGGCGCTAACTTGGATGGGAGACTTTGTGTTATTACTCACTCATGTCAGAGCCTGCTTCCTAAAGCTCCAAGTGGGCACCCGTCCACTCGCAGCCACGGCCCAGGTGTTGAGCCTGTCTGATGGAAAAGCCAGCAGGTCTGCGTCTCCTGGTCCCGGTCACCCTGCTCACAGCAGTACGGGTCTAATTAGGCTACTCTGTCCACGTGGTATGGGGTCCCCAAGTTACTCACACTGCACCTGGAGACTGCCGTGTGTAAATGTGGCGGCCGAGGCTGCTCAGTCTGGAACCTTATAGGCACTGTTTGCAGAATGACTGCTTTTAGTGGAATGCTCACCTATCACAAAACTAAAATCTCTGTTAAATTAAGTGGTACTTCTCATGACCCTAGCAAATGGACATCTCCTCAGCCTCATGACCACAGCCTGTTTCCAGACCCCTTGTTCTGAAGCTGGGTGCCTTTGTTCAAGAGCAGCACATGTTTCCAGCCAGTCACCTCCAGGATCCGTCGTGAACAAGGCTTCTGAGGACGGCTGGTTTGGGGGTCAGAGTCATCCTAGTTGCCACCGAGCTGCCAGTCCGCCTTGTCAGCAGAGGCTGAGCTGGATCACAGATCACCCACGATGCACTGTGACAAGACTTTTGGCACAACATCCATCCGCTCTCGCTGTGGGTCTCACGTGGGGTGGTTGCTCTGCTCTATGGGCAGGGCCTTCTCCTTGGTGCTAGGATCAGAACAGACGCTTGCAGTTATTGTAGTATCAGCATGCAGGGTTCTGGTGGGAAAGGTAGTTATGAGTTCTGATTCTCTGAACCGTGGGGAAAAAAATAAAAGAGTTCCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001941:ENSBTAT00000002525:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGAGAGGTGGACCAGAGAG
R:
CCTGTTAACCCCGGTTTCCTG
Band lengths:
343-717
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]