BtaINT0132412 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015375 | SH2D3C
Description
Bos taurus SH2 domain containing 3C (SH2D3C), mRNA. [Source:RefSeq mRNA;Acc:NM_001098039]
Coordinates
chr11:98444974-98447009:-
Coord C1 exon
chr11:98446881-98447009
Coord A exon
chr11:98445429-98446880
Coord C2 exon
chr11:98444974-98445428
Length
1452 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
CTGACCCTTGCCTCTTCCAGGTC
3' ss Score
11.48
Exon sequences
Seq C1 exon
TTCTCCAAGGAGAAGTACATCTTAGACTCATCGCCTGAGAAACTGCACAAGGAGTTGGAGGAAGAGCTCAAACTCAGCAGCACAGATCTCCGCAGCCATGCCTGGTACCACGGCCGCATCCCACGTGAG
Seq A exon
GTGAGTGGGCCCTGAGCTGGGACCCCAGCCCTAGACCCTTCCCCCCACCGCCTTGGCCAGTCCCAGACCAGAAAAGCTCCAACTATCATTCGGTGGGTTCAATCAGAGTAGACTGGGATGAGGTCTAGCTCTGCCATTTAACTGACTGTGTGACCTTGAACAAGTCTCTTTACCTCTCTGAGCCCCAGTTTCCTCACCTATAACATTGAGGATATGGGGCTTCTCTGGTGGTCCAGTGGTTTAGACTCTGTGCTTCCACTGCAGGGGCCACAGGTTTGATCCCTGGTCAGGGAACTAAAATCCCACATGCTGCAAGGTGTGGGCTAAATTAATTAATTAATTAAGTGAGGGCTAATAATAGTACCTATTGTAAAGGTTGGTTGTGAGAATTCCCAGGTGGCTCTATTGGTAAAGAACTCTCCTGCCAATGCAGGAGGCATAAGAGATGCAGGTTTGATTCCTGAGTCGGGAAGATCCCCTGGAGGAGGGCATGGTAACCCACTCTAGTTTTCTTGCCTGGAGAATCCCAAACGCAGAGGAGCCTAGTGGGCTATGGTCCCTAGGGTCACAAAGAGTCAGACACAACTAAAGTAACTCAGCACGTGAGAATTAAATGAGTTAATTCATGTGAGGTGCTTAACATGATGTCTGATATGCAGTGAGCTCAATGAACATTGTCCTTTATGGTGGTGGTGGTGGTGATTACTATTAACACTAATATTTTTAGTTACTGTTATAGGTCTATACATCAGCCTCTTATGTGTTTGGTTAGTGAATATCAGCACTTCAGTGATTCAGTTTTGATAAGGTTGACTTTCTGGGCTGAGGCATAGGCTTGGGCTAACGGTCACCTGTTCTTCTACTTTTCATGCTTGCTATAAATCTTTGTCAATTATCAACTCTGCCAGCTCCTGTGCTGGGCACCAAGGATGCAGAGATAAAATAGGTGGTGACTTCCCTCGACAGCTGGTAGTCCAGGGTAGGGGTCGACAGGCAGGCAGTCAGAACCCAGTGGGAGAAGCTCAAGAATGGATTGCCAGGCAGGGGGTGTGGGCTGCCCCAAGGAAGGGGTGCTGAGGAGACAGGCCATTGTGGAAGGGATAGTTCACCAGGTGAGCAGGAATGGGAGGATATTCAGCCCAGAGACATGCCAGAGCCCTGGCTGTTTGGAGGAAGAAGGATGGGGAATTCACTGTGCCCAGTGAGATCCCTGAGAAGGAGTAGGTCTGAGACCTGAGTTTCAGATCTTGGGGACTCCCTTTCCAGAGTGCGATGTCCCTCCATGTCTGAGCCTCTGTGCTCAGACCCATGGCTTCTGGCTGAGATGCACCCTCTGAATCTGGGTCGTTGGGTCCCCCTCCCAAGCTTCAGCTGTCTCTGTTGACTGTGTGCCCCAGACCCAGGGTCTGGCCCTCTCCTGCCCCGCTCCAGCCTGACCCTTGCCTCTTCCAG
Seq C2 exon
GTCTCGGAGACCCTGGTGCAGCGCAATGGTGACTTCCTCATCCGGGACTCGCTCACCAGCCTGGGTGACTATGTGCTTACGTGCCGCTGGCGCAACCAGGCCTTGCACTTCAAGATCAACAAGGTGGTGGTGAAGGCGGGTGAGAGCTACACCCACATCCAATACCTGTTCGAGCAGGAGAGCTTCGACCACGTGCCGGCCCTGGTGCGGTACCATGTGGGCAGCCGCAAGGCTGTGTCGGAGCAGAGCGGTGCCATCATCTACTGCCCGGTCAACCGCACCTTCCCACTGCGCTACCTGGAGGCCTGCTATGGCCTGGGCCAGGGCGGGGGCAAGGCCGCCAGCCCTGCCAGCCCCTCGGGCCCCAAGGGCAGCCACATGAAGCGGCGGAGCGTCACCATGACCGATGGGCTTACTGCTGACAAGGTCACCCGCAGTGATGGCTGCCCCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015375:ENSBTAT00000020433:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.163 A=NA C2=0.270
Domain overlap (PFAM):
C1:
PF0001719=SH2=PU(9.9=18.6)
A:
NA
C2:
PF0001719=SH2=PD(87.7=46.7)
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:
ACTGCACAAGGAGTTGGAGGA
R:
AGTAGATGATGGCACCGCTCT
Band lengths:
353-1805
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development