BtaINT0129426 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019385 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:31281771-31283753:+
Coord C1 exon
chr2:31281771-31282041
Coord A exon
chr2:31282042-31282557
Coord C2 exon
chr2:31282558-31283753
Length
516 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
TTTTCTGTATTTTTCCATAGGTA
3' ss Score
12.58
Exon sequences
Seq C1 exon
AACAAATTCCAAGGAATGGTCTTTGATTTTGTAACCAGACAAGTTTTTGATATCAGTATCATGATCCTCATCTGTCTCAATATGGTCACTATGATGGTAGAAACTGATGACCAGAGCAAATACATGACTCTAGTTTTGTCCCGAATCAACCTTGTGTTCATTATCCTGTTCACTGGAGAATTTGTGCTGAAATTGATCTCCCTCAGATACTACTACTTCACCATAGGTTGGAACATCTTTGATTTTGTGGTAGTGATTCTTTCCATCGTAG
Seq A exon
GTAAGAATGGTTTATTTACAGAGAAGTATAGTTGTTGAAAAAATCGCCCACAGCCTACCACCTGTGTGACACGGAAATTAGATCTGAGAATCATCATGTGTACAGATCTAAAGTTCAACACTCTTGGTCATTTTCCACTAATTGAAAAATGACAGTATTCAAAAAGAAAGCAATATATTTGAAGATTTCAGAAACAGTCTTTGTTTGCTGTTGAAACATTTCATATATGAGGATAACTATTCATAGTAATTGGGAGTATGTAATCTTAAAATGCCATACGAGTATGTGAGATTATTTAATTTATAGGATTTTGCAAGAGTCCACATTGGTTTATGACATTATAGAATTATTAAATAAAACTCTATAATCTTTCATTGGTAACATTAGAAAGTGGATCCAAATAGTAAAGATTTATACTTATGACAAATTTGTTGTTTTCAATAACCTCACAAAGAAAAAGCATCCATATGAGCCTAAAATACTCACTGTTTAGCGGTTTTCTGTATTTTTCCATAG
Seq C2 exon
GTATGTTTCTGGCTGAGCTGATAGAGAAATATTTTGTGTCCCCTACCTTGTTCCGAGTGATCCGTCTTGCCAGGATTGGCCGAATCCTGCGTCTGATCAAAGGGGCTAAGGGGATCCGCACGCTGCTCTTTGCTTTGATGATGTCCCTTCCTGCGCTGTTTAACATCGGCCTCCTGCTCTTCCTGGTCATGTTCATCTATGCCATCTTTGGAATGTCCAATTTTGCCTATGTTAAAAAAGAAGCTGGAATTGACGACATGTTCAACTTTGAGACCTTTGGCAACAGCATGATCTGCCTGTTCCAGATTACCACCTCTGCTGGCTGGGACGGATTGCTAGCACCTATTCTCAACAGTGCACCACCAGACTGTGACCCTGACACAATTCACCCTGGCAGCTCAGTTAAGGGAGACTGTGGAAACCCGTCTGTTGGGATTTTCTTTTTCGTCAGTTACATCATCATATCATTTCTGGTTGTGGTGAACATGTACATTGCTGTCATCCTGGAGAACTTCAGTGTTGCTACTGAAGAAAGTGCAGAGCCCCTGAGTGAGGACGACTTTGAGATGTTCTACGAGGTTTGGGAGAAGTTTGATCCTGATGCCACCCAGTTCATAGAGTTCTCCAAGCTCTCTGATTTTGCAGCTGCCCTGGATCCTCCTCTTCTCATAGCAAAACCGAACAAAGTCCAGCTCATTGCCATGGACCTGCCCATGGTCAGTGGGGACAGGATCCACTGCCTTGACATTTTATTTGCCTTTACAAAGCGTGTTTTGGGTGAGAGTGGAGAGATGGATGCCCTTCGAATTCAGATGGAAGATCGGTTCATGGCGTCAAATCCCTCCAAAGTCTCCTATGAGCCCATTACAACCACTCTGAAACGCAAACAAGAGGAGGTGTCTGCTGCTATCATTCAGCGTAATTTCAGGTGTTATCTTTTAAAGCAAAGGTTAAAGAAGGTAGTAAATGAGTATAACAAAGAGGCGATCAAAGGGAGGATTGACTTACCTATAAAAGATGACATGATTATTGACAAATTAAATGGGAACTCCACCCCAGAAAAAACAGATGGAAGTTCCTCTACCACCTCTCCTCCTTCCTATGATAGTGTAACAAAGCCAGACAAAGAAAAATTTGAGAAGGACAAACCAGAAAAAGAAAGCAAAGGGAAAGAGGTCAGGGAAAATCAAAAGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019385:ENSBTAT00000025829:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.153
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=41.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTAGAAACTGATGACCAGAGCA
R:
GCAGGAGGCCGATGTTAAACA
Band lengths:
353-869
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]