BtaINT0132406 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013857 | SH2D3A
Description
Bos taurus SH2 domain containing 3A (SH2D3A), mRNA. [Source:RefSeq mRNA;Acc:NM_001205669]
Coordinates
chr7:18958597-18959402:+
Coord C1 exon
chr7:18958597-18958708
Coord A exon
chr7:18958709-18959214
Coord C2 exon
chr7:18959215-18959402
Length
506 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
CCAGACCCTTCCCCCAACAGGAC
3' ss Score
9.22
Exon sequences
Seq C1 exon
GTGTCGCGTTTGGAACGCACGTGGCGCCACCTGCGAAGGAGCCACACGGAGGCTGCGCTGGCCTTTGAGCAGGAGCTGAAGCCGCTGATGCGATCGCTGAATGAGGGCGCCG
Seq A exon
GTGAGTGGTGGCTTTCGAGGAGTGATAACCCTAACCAGAATCTGGATTCAGCCCTAAGCCCCGCCCGCCCGTGTCTTAGTCCCCGCCCCTGGGTCTCTCCTAGGCCACGCCCCCTGCCTAGGCCCGGCCCCTGACTCACATCCAGCAATGCGCTAGGCTCTGGCCTCCCGGCCTCGCGCCGAACCCTTGTTTCTGTCTCGGGCTCCACCTTGGCGGTACGAGCCGCCAGCTCGTTAGGTCCTAGGCCCCGCCCTCCGCGCTCTTGCCCCCGCCCTCTACGCGAGACTCTGCCCTGGACCCAACCCCTGGGCGGGCCTGTTCTAGGCTCCGCCCCAGCTTTAGGCCACACCCTTGTCCTCCCCTGGTCTGGCTCGAGCCTCAGTGTCTGACCCAAACCCCACCCTCTGCCCTGCCCTAGGATGCCCTGGCCCCAGTATATGTTGAGTCCTCTTCACCCTAGGACCCGCACCCCGTCCCTAGCCCAGCCCAGACCCTTCCCCCAACAG
Seq C2 exon
GACCCAGCGATCCCGGCGAGGTGGCGCTGCCACACGTGGCACCCGCGGCGCGCCTGCTGGAGGGTGAGGAACTCCCGGGGCCCTTGGACGAGAGCTGCGAGCGGCTGCTGCGCACCCTGCACCGGGCGCGTCAGACGGCCCGGGACGCGCCCAGATTCCGCGAGGCGGTGGCGCGGCGCCTGCGAGGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013857:ENSBTAT00000018405:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.263 A=NA C2=0.524
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=FE(30.8=100)
A:
NA
C2:
PF0061714=RasGEF=PD(12.5=23.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTGGAACGCACGTGGC
R:
CTCGCAGCTCTCGTCCAAG
Band lengths:
206-712
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]