BtaINT0129415 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019385 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:31243879-31246827:+
Coord C1 exon
chr2:31243879-31244235
Coord A exon
chr2:31244236-31246356
Coord C2 exon
chr2:31246357-31246827
Length
2121 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
ATTTTCTTTTTTTCTTTTAGGTT
3' ss Score
13.58
Exon sequences
Seq C1 exon
CTTCGAGTTTTCAAGTTGGCAAAATCCTGGCCCACCCTGAATATGCTAATCAAGATCATCGGTAATTCAGTGGGAGCTCTGGGTAACCTCACCTTGGTGTTGGCCATCATCGTCTTCATTTTCGCCGTGGTCGGCATGCAGCTCTTTGGGAAGAGCTATAAAGAATGTGTCTGCAAGATTTCTAGTGATTGTGAACTCCCACGCTGGCACATGAATGACTTCTTCCACTCCTTCCTGATTGTGTTCCGGGTGCTGTGTGGAGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTCGCCGGTCAAACCATGTGCCTTATTGTTTTCATGCTGGTCATGGTCATTGGAAACCTGGTG
Seq A exon
GTACGTATGTATTACAAACACTCATAATTAAGAACAAGATCAGATAGTAGGTGGGAAGGAGGCCTGATGCAACAGACATATTTGGTTTTACCATCAACAATGTAGACTCAAATCCCAGTACTGGGACTCTGAGCAGGGGCAAGTCACTTAACTTCCCTCAGGCTCAAATTCCAAACTATGAAACTGGAATAACAAAACTGAAATCTTGTAGTTTATGTGAGGATTACATGAGGTATATATATCTGTGAAAGTCTTGGGACAAAAATATTAGTTTTCCTTCTTCAAAGAAATGTTTTCAGCATCAAAACTGATTTGTCTTAATTTTATTTTTATGGCTTGAATTATTTTTTATTCTATTATTATTTTGACAAGATAATGATCTCCAGTAATTACACATACATAGTTTATATTGTTTGTTTACTCAGAGGCATATGTTGCATATCACCAAATTTTAAAGACAAATTTCAATGAAATCTTAGCTCTGTATTGTAATTATCCAAAAAAATTGGAAGGGGACTAAATATATTTTTCCCAGAATTTGTTTTATCAAAGGAAAATAAATTATTGTAGTTTCAGTTATACACATGTATAAACATTGACCGGATTTAAAAGGCTTACTTTTAGTTCTGACTTAAAAGCACTAATATAGAACCACAATTTGCATGTTTGTGTGTTTTAATGCTTACATTTTTCAATTATGCAGTGTCAGAGTATTTCTTTATTTCATCATTCTGAAACTTTCCTTTGAGAAGTACATATCAAATGAGATTTCTTAAAAAATGGTTTGTGGGATATCTGTGGACATGCAACTTTTTTGAGAATTGTAAATAAGGAAGTTCTAGATTCTGAACAAATCTGATATAAAAATAAGGAAATAAACTGGGATTCTGGCTAAGTGTGTGTCTTCCTACCATGTAACATTTTTTGAAATTCAGTAACTACATTTCAAGCTAAAAATATTCTCATAAATTTTCTTTTGCATCAGTTATAATGAACTATTCCTGTATTAATCATATTTTGCCAATTAATTGAATAATATTTTCCCTCACGTATCCCAATGATATGCTGAGATTTCACCACATTTTCTGCAAAAAAAAAAAAGGAAAAAGAAAAGTAATTTACATTATATGGGTCTAGCCTAAACCCTGGAATAATTTTAGACTTTTCTCCATCTGTTGAACTATTTGGACAGATATACTTCAAAGTATATTGATGGGAAATGTGTTAAACCTTATATAATCTGCCTTTGCTGCTGCTGCTGCTGCTAAGTCGCTTCAGTTGTATCTGACTCTGTGCGACCCCATAGACAGCAGCCCATCAGGCTCCTCTGTCCCTGGGATTCTCCAGGCAAGAATACTGGAGTGGGTTGCCTTTGCTGCTGCTGCTAAGTCGCTTCAGTCGTATCCGACTCTGTGCGACCCCATAGACGGCAGCCCACCAGGCTCCCTGTCCCTGGGATTCTCCAGGCAAGACCTCTGGAGTGGGTTGCCATTTCCTTCTCCAATGCATGAAAGTGAAAAGTGAAAGTGAAGTCACTCAGTCGTGTCGGACTCCTAGCAACCCCATGGACTACAGCCTACAAGGCCCTCCGTCCAAGGGATTTTCCAGGCAAGAGTACTGGAGTGAGTTGCCATTGCCTTCAGGCTACTCTAAAAGCTTTTGGCCATTGGAATTTACATTTCAAGTATATTGTTTTAATACAATCCATCGGCTATTAAATAAATAAATTCATTATTTACACACACAAAGCTAGACATTCCCTAGACAAACTGGTAAAATGACTGAAGTGAAAATATCCCATTTTTCCTCTTTGGCCAAAACCACAAAAATGGGATTTTTGTTTTTCACTAGCAACTCTGAGTAGACACAATTTAAATCTCAGAAGCTCCAGTTTCCTGGTTGTCCTCCGTTTGAAAGGAAAATCATTTGTTTTACCATTTTGCCCTTAGAGCAGATTCTTTAAATAGCGTGTGACTAAGACAAGGTGTCTGAAATATAGCAAACAGTCAAGAAGCATTTGTTGAATTAATTTCAGCAAAGAGCTGTGAGTGCTCTGCTTAAACTATTATGTTTACACATATTTCAATATTAATACAGCAAAATTTTCTTTTTTTCTTTTAG
Seq C2 exon
GTTCTGAACCTCTTTCTGGCCTTACTGTTGAGTTCATTTAGCTCAGACAATCTTGCTGCTACTGATGATGATAATGAAATGAACAATCTCCAGATTGCAGTAGGAAGGATGCAAAAGGGAATTGATTATGTGAAAAATAAGATACGGGAGTGTTTCCAAAAAACCTTTTTCAGAAAGCCAAAAGTTATAGAAATCCATGAAGGCAACAAAATAGACAGCTGTGTGTCTAATAATACTGGAATTGAAATAAGCAAAGAGCTTAATTATCTTAAAGATGGGAATGGAACCACCAGTGGTGTAGGTACTGGAAGCAGTGCTGAAAAATATGTAATTGATGAAAACGATTATATGTCATTCATAAACAATCCCAGCCTCACTGTAACGGTGCCAATTGCTGTTGGAGAGTCTGACTTTGAAAATTTAAATACTGAGGAGTTCAGCAGTGAGTCAGAACTAGAAGAAAGCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019385:ENSBTAT00000025829:16
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=0.166
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(60.7=84.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]