BtaINT0132414 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015375 | SH2D3C
Description
Bos taurus SH2 domain containing 3C (SH2D3C), mRNA. [Source:RefSeq mRNA;Acc:NM_001098039]
Coordinates
chr11:98441284-98443455:-
Coord C1 exon
chr11:98443331-98443455
Coord A exon
chr11:98441820-98443330
Coord C2 exon
chr11:98441284-98441819
Length
1511 bp
Sequences
Splice sites
5' ss Seq
CCGGTATGG
5' ss Score
8.44
3' ss Seq
CTCTCTTTATTTCCCTGCAGTGA
3' ss Score
10.15
Exon sequences
Seq C1 exon
CACATCACTGCCCCACCCCCGGGAATCCATCCGCAACTGTGCACTCAGCATGGACCAGATCCAAGACCTGCACTCGCCCATGTCCCCTATCTCCGAGAGCCCCAGCTCCCCTGCCTATAGTACCG
Seq A exon
GTATGGCCAGTGGAGGGGGGCGCGTGGGGGTCTGGTGGGGGTGGCCTCGTGTGCCCATGTGTGCACTGTCTGACGATTTCTGTTACAGTGTTTGATCATGTGTGCCTCTTCCTCTTATCTGAGAGACATGCCCTGCATCAGTGGATACTAAAACTATCCATGTTGACATGCAAAACATAGCCGTGGCTGGTTCATTCTGCAACAATTCACTGAGTCCCTATTGGATACCAGGCACTGTGGATGTGGTTTCCATGCATTCTCTTGAATGCTACTGAATCTGGGCTTCAATGCTATGAAGTTTGTGCAGTCAGCAACACTCAGTCCCCATTGGTCAAGAGCCTCCGCATGTGAGGAGCCACTTGACCAGGCCCTGTTATTGGCTGGGATTTAATGTATCCCTGATTCCAAATGGTGGGATCCAACTGGACTGGTCAAGCTTGCTTTATTCATTTATTTTTTCTTTTAAATAGATCTTTTCAGAGAAGTTCTACATTCCCAGCAAAATTGAGCAGAAAGCACAGAGCACTGTGCATTTTTTTTTAATATAAAGAAGATTTCTACTGTAGAAACATGCCACTAGCTCATTTCTGGAAGAAAAAAAAATAATGTTTTCAGCAGGCCATACCACATATTGTCCACATGGCAGGCAAAGCGTGCAGAGGGGCAGCCCAGGGGAACCTTTGCTGGGAAATGCCCTGTTGCCATGTAGTTGTCTATATGGGTTGTCACAAATTCTTCTCTAACCACGGGCCTGCCAGCTTGTCATAACTGCCAACTTGCCTTCCAAACAACACCCCTGAGTGTAAATGTTAAGACGCTTTGCCACAAATTATTTATTGGACAACTTCTAAGCAACATGGCACAGGGAAGTACCCAGGAGTGAGGACTCGACACCTGGTTTTGAATCCCAGCTCTACCCTTTGCTGGTTGGGTGACCTTAGGCAGGTCAGCTGGCTTCTCTGAGTCTCACTTTTCTCATCTGAAGAATGAGGATCATAAAAGTACTCATGCTCAGGATGTTGAGAGGGTTAAACAGATTAAGGGGCAGCGAAGGATCTCGCAGGCAGTTAGAACTCAATAAACATCACCTCTAATTTTGGATGATGGTTTTACTGTTTTGACCGGTGTAGCTACAGCATGTCACCAGCTCCCAGAACACATGTCCTCAATAAATCCTTATTATTAATTCATTGAGAAATGATTCCACATAGTGAACTCCAGCAAGTGCTTAGCTTCTCTGAATCACAGAAAGCTCCTTCAAGTAGCTCAGTGGTTCCCCAAGGCTGCAGCAGCCTTAGGATAAGAAAGTCTGACCCCTGGGGTCCAGGGAATTTGAGAATATCACTGAGGGCTGGTCAATGTGCCAGTGTCAGCTGGGCCTGGCCTGGGTACAGGGAGGTGGGATATCACCCCTGTAGGGTGGGTGGAGCTTGTCCTCTGGGAAAGCAGTGGGGGAACCACACTGGCTAGGGAGTCATGGTAACTAGTTGTCTCTCTTTATTTCCCTGCAG
Seq C2 exon
TGACCCGTGTCCATGCCGCCCCTGCCGCCCCCTCAGCCACAGCACTGCCCGCCTCCCCTGTCACGCGCCGCTCCAGCGAACCCCAGCTGTGTCCCGGAAGTGTTCCAAAGCCCCACGGGGAGTCGGACAAGGGCCCTTACTCCAGCCCCTCCCACACCCTCTGCAAGGCCTCCCCATCACCGTCGCTCAGCAGCTACAGTGACCCGGACTCTGGCCATTACTGCCAGCTCCAGCCTCCTGTCCGTGGCAGCCGAGAGTGGGCAGCAGCTGAAGCCTCCGGCCGCCAGGCCAGGAGCTATGGGGAGAAGCTTAAGGAACTGTCAGAAAACGGGGCCTCCGAAGGGGACTGGGGCAGAACCTTCACAGTCCCTGTTGTGGAAGCCACCTCTTCCTTTAACCCGGCTACCTTCCAGTCACTGTTGATCCCCAAGGATAACCGGCCACTGGAGGTGGGCCTCCTGCGTAAGGTCAAGGAGCTGCTGGCAGAGGTCGACGCCCGGACACTGGCCCGGCACGTTACCAAGGTTGACTGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015375:ENSBTAT00000020433:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.977 A=NA C2=0.603
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0061714=RasGEF=PU(11.4=9.5)
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:
ATGTCCCCTATCTCCGAGAGC
R:
AGCTTCTCCCCATAGCTCCTG
Band lengths:
356-1867
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development