BtaINT0129411 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019385 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:31233050-31234551:+
Coord C1 exon
chr2:31233050-31233394
Coord A exon
chr2:31233395-31234418
Coord C2 exon
chr2:31234419-31234551
Length
1024 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
CATCAGTATTTGGTTTGCAGGGT
3' ss Score
5.3
Exon sequences
Seq C1 exon
TCTCTGTTAAGTATCCGTGGTTCCCTGTTTTCCCCACGACGCAATAGCAAAACAAGTATTTTCAGCTTCAGAGGTCGGGCAAAGGATATCGGTTCTGAAAATGACTTTGCTGATGACGAACACAGTACATTTGAAGACAGCGAGAGCAGGAGAGACTCACTGTTTGTGCCGCACAGACACGGAGAGCGACGCAACAGTAACGTTAGTCAGGCCAGTATGTCATCCAGGATGGTGCCAGGGCTTCCAGCCAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTGGGTGGACCATCAGCTCTAACCTCACCTACTGGACATCGGCCAGAG
Seq A exon
GTGATAATAGATAATAAATTAGCTACTACTGACATTATACACCGATTTGAAATAATCAAGGCCTGGGCGGTTTAGCCTGTTATACTATCCTACTTCCCCAAAATGAAAGTCCTTAAAAATAACATATGATTTTACTGAATGAAAAAACCAATAGACTCTTGAGAACCAATTGAATTGTATGGGACCATTAACTTTCAAATGCTTTAGGTTAAAAGAGCCTGGTTTTTAGAGTTTGGGGTGAAAACTCCTATCTGCAAATTCAACACAAAATAATGGGCACTATGACAACCTATTACAGATGTCTGTTCACCCAGAATTGTATAATAGTCTATTCATATTCTGGAAATTTCATATACTTAAAATTAAATAATTTAATGGTCAACATATTGATAACAGGCAGTTTCGGTACAACTGCCAATATTTTACAGTGACTCTAAAATGTTCTGATGTCTATTAAATGACTCTAAAATGTTTTGATTTCTTATAGGATGGCACATGGAAATAATTAAAAAAATCTCAGGAAAGCACACACATTTCATTGTACATCTGTGTTCGTGCATAGAAAAAAATCGGCCCATATATGTCAATATTTTCAATATAGCCTCAAGAAAATAATTCAGCCTTAATATTAATATTACATAATACTATTATTTGTTTTGGGGGAAGAGTAATCTGATTTTAATTATTGAGAAAGCTAAAATACTTTTCATTTGAATTAAATGAAATAATAAATGATTTATGAAAAATTTCTCTGGAAATTCCAACAGGTAAATTAAAATATTTCTGCAACATAATTGCCTTATACAATTGCACCCAACTGGTAAATTCTTGTTTTAACCCTGTAGGGTATCACCTGTGATTTTTTTAAGTATTTATAATTTAATAATAAATTAGTATTTTATTATTATTTGAAAATTGTTACTTGGGAAAACTGCACGTGGCATGACTTTCCAAAGAAATGCTAATGTTGTGTTGTATTACTCACTGAAAAGGGTGGTTTGAGCCATCAGTATTTGGTTTGCAG
Seq C2 exon
GGTACCACCACTGAAACGGAAGTCAGAAAGAGAAGGCTAAGTTCTTACCAGATTTCAATGGAGATGCTAGAAGATTCCTCCGGAAGGCAAAGAGCCATGAGCATAGCCAGCATCTTGACTAACACGATGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019385:ENSBTAT00000025829:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.665 A=NA C2=0.244
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(50.2=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.3=82.2)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTTCCCTGTTTTCCCCAC
R:
GACTTCCGTTTCAGTGGTGGT
Band lengths:
353-1377
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]