BtaINT0132403 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013857 | SH2D3A
Description
Bos taurus SH2 domain containing 3A (SH2D3A), mRNA. [Source:RefSeq mRNA;Acc:NM_001205669]
Coordinates
chr7:18957451-18958180:+
Coord C1 exon
chr7:18957451-18957932
Coord A exon
chr7:18957933-18958064
Coord C2 exon
chr7:18958065-18958180
Length
132 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
CCCCCACCCCCCATCACCAGGCC
3' ss Score
8.38
Exon sequences
Seq C1 exon
GAGCCTCCACTGTACCTGCATCTGGCCTGCCTCGGACAGGTAGTGACCCCGTGATACTAAAGACCCCAGTTCCCTTGGGGTCCGTTGCTGACAGTCTCAGGGCCTCTGATGGGCAGCTTCATGCCAAGGCCCCAACCAAGCCACCTCGAACACCCTCATTGCTACTGCCTGATGCCTCTGGACGCCCCCCGACGTACTGTGAGCTGGTGCCCCGAGTGCTCAGGTTCCAAGGACCACCCCCTGGCCACAGCTGCCCAGAGTCAGAGGTGCCCTGGTGGGAAGCCGAGGAGGAGAAAGAGGAGGACAGATGTTTTGCAAGACCACAGGCTGAGGTCTCTTTCTGTCTCCCTGACACCCCCTCCTGCCTGCTGGGCTCCCAGAATCGGCCTCTGGAACCCGAAGTCCTGCATACTCTCCGTGGCCTGTTCCTGGAACACCATCCTGGGAGCACAGCTCTCCACCTGCTATTGGTAGACTGCCAG
Seq A exon
GTGGGTCCCCCTACCAGGTTTCCCTCCCCAGGTAGGGCCTGAAGCCAGGGCATGACCAAACCCCACCTCACACCCATAGACTCACTCTGCTCCTTTAACGTCCCTACTCTTACCCCCACCCCCCATCACCAG
Seq C2 exon
GCCACAGGTGTCCTGGGAGTGACCAAGGCTCAGCGGGGCGCCATGGGGGTCGCCTCCGGTCTGGAGCTGCTCACACTTCCCCACGGGCATCGCTTGAGATTGGAATTGCTGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013857:ENSBTAT00000018405:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.547 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061714=RasGEF=PU(6.7=20.5)
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:
TGTTTTGCAAGACCACAGGCT
R:
GAAGTGTGAGCAGCTCCAGAC
Band lengths:
253-385
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]