BtaINT0132415 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015375 | SH2D3C
Description
Bos taurus SH2 domain containing 3C (SH2D3C), mRNA. [Source:RefSeq mRNA;Acc:NM_001098039]
Coordinates
chr11:98440218-98441819:-
Coord C1 exon
chr11:98441284-98441819
Coord A exon
chr11:98440334-98441283
Coord C2 exon
chr11:98440218-98440333
Length
950 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
CCCTCTGGGCGTCCTTGTAGGTT
3' ss Score
9.55
Exon sequences
Seq C1 exon
TGACCCGTGTCCATGCCGCCCCTGCCGCCCCCTCAGCCACAGCACTGCCCGCCTCCCCTGTCACGCGCCGCTCCAGCGAACCCCAGCTGTGTCCCGGAAGTGTTCCAAAGCCCCACGGGGAGTCGGACAAGGGCCCTTACTCCAGCCCCTCCCACACCCTCTGCAAGGCCTCCCCATCACCGTCGCTCAGCAGCTACAGTGACCCGGACTCTGGCCATTACTGCCAGCTCCAGCCTCCTGTCCGTGGCAGCCGAGAGTGGGCAGCAGCTGAAGCCTCCGGCCGCCAGGCCAGGAGCTATGGGGAGAAGCTTAAGGAACTGTCAGAAAACGGGGCCTCCGAAGGGGACTGGGGCAGAACCTTCACAGTCCCTGTTGTGGAAGCCACCTCTTCCTTTAACCCGGCTACCTTCCAGTCACTGTTGATCCCCAAGGATAACCGGCCACTGGAGGTGGGCCTCCTGCGTAAGGTCAAGGAGCTGCTGGCAGAGGTCGACGCCCGGACACTGGCCCGGCACGTTACCAAGGTTGACTGCCTG
Seq A exon
GTAGGTGCTGGGTGCACACTGGGGCAGGGGTATACCTTTATCCTCTAGCTTTGGGACAGGGGTTAGGGTGGTGAGGAACTGGCCCCCACATCCCCAAGTAGAGTGAGTGGTCCTGGATTCTGATTTCATGGCTGCCCTTTACTTGCTGTGTGACTCTGACTAATCACTTTACCTCTCTGGGCTCCCATTTTCTCCTTGAAAAAAAAAAAGCAAAAGCTGAGATACTCTTGCTTCCTCCAGATGTCAGTTTGGCACTGGAACCGAGGAGTCCTGAAAACTAGTGGTGTCTGGCTCCCTGGGACATTTTTTGAGCCCGGTGAGAGTTGGTCTGGCCGGTCCAGGGACTATAAGAGGCCAGACTCCCTACCCCCACCCCCCTAGTGGACAAAACTCATTGTCTAGGTCCATAAATTGTTAATGCCTGGGCCTTTGCTTTGAATGAATCCTGCCCATCTAAGGACCCTAACTTGATCTATGCCTCAGTTTCTCCCTCTGAAGTTTGGGGTGTGTGTGTGTGTGTGTGTTGGGGAGGGGAACACTGATTATTTGGTCACACTTGTCTCTGAGCTCAAAAAGAAAGAAAAGAAACAGCGCTGAGATGCGGCGCTGTGAAAAGTACTAGGCATGAAGGAAGAAGCCCTGGGTTCTAGGTCCAGTGTGTGACCTAGGACAAGCCCTTTCCCTCCCTGGACCTTATTTCTTCTGAAATAAGAGTGTCCTGGGCACCTCTGGCACATGTCAGACCCCATTGGGCATTTTTCCATTTATCCTGCGTTTCATAGATGGGGAGAGTGAAACTCATTTGCTCCATGTCAGAGGGTTAGTCATAAACCTGGAATTCAGAGCCGGCTTCCCAGCCAGGCTGCCCTGCTAGATAAAGCTCTCTGACTCCCAGATGGCTTGGGCTAGCCCTGACAGGAAATTAATCAGCCCTCTGGGCGTCCTTGTAG
Seq C2 exon
GTTGCTAGGATACTGGGCGTTACCAAGGAGATGCAGACCCTAATGGGAGTCCGCTGGGGCATGGAGCTGCTCACTCTCCCCCATGGCCGGCAGCTACGACTAGACCTGCTGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015375:ENSBTAT00000020433:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.603 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0061714=RasGEF=PU(11.4=9.5)
A:
NA
C2:
PF0061714=RasGEF=FE(25.5=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:
CAGGAGCTATGGGGAGAAGCT
R:
AGCAGGTCTAGTCGTAGCTGC
Band lengths:
357-1307
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development