BtaINT0132416 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015375 | SH2D3C
Description
Bos taurus SH2 domain containing 3C (SH2D3C), mRNA. [Source:RefSeq mRNA;Acc:NM_001098039]
Coordinates
chr11:98439066-98440333:-
Coord C1 exon
chr11:98440218-98440333
Coord A exon
chr11:98439238-98440217
Coord C2 exon
chr11:98439066-98439237
Length
980 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TGACCCGGCCGCTCCAACAGGTT
3' ss Score
7.81
Exon sequences
Seq C1 exon
GTTGCTAGGATACTGGGCGTTACCAAGGAGATGCAGACCCTAATGGGAGTCCGCTGGGGCATGGAGCTGCTCACTCTCCCCCATGGCCGGCAGCTACGACTAGACCTGCTGGAAAG
Seq A exon
GTAAGGCGCGCGCACACACGGGAGTCACCGGGAACCAACCCCCTGGACTACCTCGCTGCTCTTCACTGTGGCCGGTTGGCCAATCGCAGTCTCTCACCCCGGCTCCCAGATCATAGCCACGCCCTCTATCCCATTGACCAATTGTTCCTGATATCCAGTTCATTCAATCAGTTCAGTCGCTCAGTCGTATCCGACACTTTGCAACCCCAAGGACTGCAGCCCGCCAGGCCTCCCCATCCATCATCAACTCCTGGAGTTTACTCAAAGTCATGCCCGTTGAGTCGGTGATGCCATCCAACTATCTCATCCTCTGTCGTCGCCTTCTCCTCCCGCCTTCAATCTTTCCCAGCATCAGGGTCTTTTCGAATGAGTCAGTTCTTCGCATCAGGGGGTCAAAGTATTGGAGTTTCAGCTTCAGCATCAGTTCTTCCAATGAAAATTCAGGACTGATCTCCTTTAGGATGGACTGGTTGGATCTCCTTGTAGTCCAAGGGACTCTCAAGAGTCTTCTCCAACACCACAGTTCAAAAGCATCAATTCTTGGGTGCTCAGCTTTCTTTATCCAGTTCCAAGTAATCCTGGTTTTTCAAAGACTGAGTCCTTTATCTCCGAATTCACTTTCTGTATTCTCTTGACTGACCACAATCTGTGAGCCTTGGCCCGCCCATCAGCTCCGGCTTCTCTTCTTTCTTTTCTTAGAACAGCTCTGTCGGATGATTTCTGATGATTTCCTCTGATCGGTCCCACGGTCCTCAGCCTGGCGCTCACGGGTGTCTGGCCCCGCCCCCTGACTTATACTGACCAATCAGAACCCCTTAACTTTGCTTTATCCCCGCCCACACTTTGGCCGCACCCCCTAATCTCATTGCCTCTTTACAACCTCTCACTTTTGGCTCTATCCTCCACCCCTCGGCGCCCAACCACAGGGACCCCAACCCTAGATCCCTGGCCCCGCCCCTCTGACCCGGCCGCTCCAACAG
Seq C2 exon
GTTCCACACCATGTCCATCATGCTGGCCATGGACATCCTGGGCTGCACGGGCTCCGCTGAGGAGCGGGCAGCGCTCCTGCACAAGACCATCCAGCTGGCAGCCGAGCTTCGAGGGACCATGGGCAACATGTTCAGCTTCGCTGCGGTCATGGGTGCCCTGGATATGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015375:ENSBTAT00000020433:8
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=FE(25.5=100)
A:
NA
C2:
PF0061714=RasGEF=FE(38.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATACTGGGCGTTACCAAGG
R:
CCCATGACCGCAGCGAAG
Band lengths:
262-1242
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development