BtaINT0132404 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013857 | SH2D3A
Description
Bos taurus SH2 domain containing 3A (SH2D3A), mRNA. [Source:RefSeq mRNA;Acc:NM_001205669]
Coordinates
chr7:18958065-18958513:+
Coord C1 exon
chr7:18958065-18958180
Coord A exon
chr7:18958181-18958338
Coord C2 exon
chr7:18958339-18958513
Length
158 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CTTGCCCTCCGCCTCTACAGGCT
3' ss Score
9.67
Exon sequences
Seq C1 exon
GCCACAGGTGTCCTGGGAGTGACCAAGGCTCAGCGGGGCGCCATGGGGGTCGCCTCCGGTCTGGAGCTGCTCACACTTCCCCACGGGCATCGCTTGAGATTGGAATTGCTGGAGAG
Seq A exon
GTGAGACAGCCACCTGAAATCCCCAGGGTCTTCAAACCTCCTCCCATTCCCGGTTCCCCAGGAAGGAGGGGAATGGGCAATGCCGCTGACTGTCCCTCCTCACCCCCACATCGCAAACCTCCCCACTGCCCCCAGACCCTTGCCCTCCGCCTCTACAG
Seq C2 exon
GCTCGAGACGCTGGCGTTGGCGGGGGCGCTGGCAGTGCTGGGCTGCGCAGGGCCGCTGGAAGAACGCGCGGCCGCCCTGAGGGGCCTGGTGGAGCTGGCCGTGGCGCTGCGGCCAGGGGCGGTGGGGGACCTGCCCGGACTGGCCGCGGTGATGGGCGCCTTGCTCATGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013857:ENSBTAT00000018405:6
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:
PF0061714=RasGEF=PU(6.7=20.5)
A:
NA
C2:
PF0061714=RasGEF=FE(48.3=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:
GGTCTGGAGCTGCTCACACTT
R:
CTGGGGCATGAGCAAGGC
Band lengths:
234-392
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]