BtaINT0129425 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019385 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:31280313-31282041:+
Coord C1 exon
chr2:31280313-31280417
Coord A exon
chr2:31280418-31281770
Coord C2 exon
chr2:31281771-31282041
Length
1353 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGA
5' ss Score
4.95
3' ss Seq
TATTTTCTCTCTCTTTCTAGAAC
3' ss Score
12.23
Exon sequences
Seq C1 exon
TTTGGAGGGCAAGACATCTTTATGACAGAGGAACAGAAAAAATACTACAATGCAATGAAGAAACTTGGGTCTAAGAAACCTCAGAAACCCATACCTCGGCCTGCA
Seq A exon
GTAAGAATTACTCATCTCCTTGAACATTCCAAAGCCCTATTTCCATATGATGAAACTGGGCAGTGCTGGTTCAGAACATATTAGGTGATATCACCAATATATATACCATGATCTAGTCGTAAAGTACATATTGTATAACACAATTTGCAATTACTACACTCTAAGAATTACTAAGCTCTTAAAAATGAAGCAATGTTCTTTACTTGTCAGTTGAAAAGTTCCAAGTCAGAGTTCCCGGTAACTGCTCCCAAAGCGAGCTCATGCTCCCGCTGCCACCTACTGCTGCCAACGGCGCACCCGGTTTCTCCTTCTCTGATCTGTGATATGGCCCCCCTCTTGTCCTTTTAAGTAGATGAACTTAAAACCTCCCCTTCAACACCCATGACCTCCCTCTGTGCCATTTGTTCTCTCCATTGTTATAACAGAAAACGATTTTTCACCTACTTAGAAAGGAAAGGGTGTCATCAAAATAGTTGGTTTCAGCACACACACACACACACACACACACACAAATGATTTATCTAGAACGCATACCCTGTAGAGCTTCATTATAGTGAAAAGACATAAAGATGGTGTATTATGTCCACAGAGTTGTATTCTAAATTATCTATGCTCTTAGATGGGTAAGGAACAAGGAAACTAAGACCCAAGGAAGGTATATATTGTACCCAAAGTCACAAAGCCTATAGTTGCTGAACTAGGACTTGACAAAATCTCATGAATCTTATAAATGACTTCACTTTGCATAATTTTTAAGAGGGTACAGTCTGGGCAGGGGTGGCGGGGCAGGGGCAGGAGGGAAGGGAGGGGAGGCAGAAAGTAGGACAGGATACACAAAAGGACATAAACCTACTTTACTGAATGTCATTTAAGTATTATTGTTAAAGAAGCAGAATTAAATAAAAAATGACTGATATTTTGAGTCATGGACAGACAGAAATAAGACATAATTCAAAATTCCTAAAGTGTTGATAAATCAACTGGCATATTCATCCATCTAAAAGTCTGTCTACATTAACCTACTTTGTAAATCTTCATTGTTAGTTGTTACATTTTTTGTAAAAATTACCAGTTATTAAAATCAAGCAAAGCCCATGCACATTATCAGCCAGTTGCCACCAATTTATGTCATTCAGCTTTGTCTTCCCATAGAATTTAAATAAAACAATTATGCTTTGCTTTTGTCATATGACATTTTTCATTTCCTTCTCTTTTTTAAACAGATTTGTTTCAGGTAGTGTGAGAAAGGTACACATCCCATGGGCCATATACAGAAGGACTTCATCTTCAATTTTGTGGCTCATTATTTATGAAATATGCCTATTAACCTTCTTATTTTCTCTCTCTTTCTAG
Seq C2 exon
AACAAATTCCAAGGAATGGTCTTTGATTTTGTAACCAGACAAGTTTTTGATATCAGTATCATGATCCTCATCTGTCTCAATATGGTCACTATGATGGTAGAAACTGATGACCAGAGCAAATACATGACTCTAGTTTTGTCCCGAATCAACCTTGTGTTCATTATCCTGTTCACTGGAGAATTTGTGCTGAAATTGATCTCCCTCAGATACTACTACTTCACCATAGGTTGGAACATCTTTGATTTTGTGGTAGTGATTCTTTCCATCGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019385:ENSBTAT00000025829:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGGAGGGCAAGACATCTTT
R:
ACCACAAAATCAAAGATGTTCCAACC
Band lengths:
356-1709
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]