BtaINT0129366 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018520 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:30410283-30412264:+
Coord C1 exon
chr2:30410283-30410387
Coord A exon
chr2:30410388-30411993
Coord C2 exon
chr2:30411994-30412264
Length
1606 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGA
5' ss Score
4.36
3' ss Seq
GCTTTTCTGTTTCTCTACAGAAC
3' ss Score
11.78
Exon sequences
Seq C1 exon
TTTGGAGGTCAAGACATCTTTATGACAGAAGAACAGAAGAAATACTATAATGCAATGAAAAAATTAGGATCAAAAAAGCCACAAAAGCCTATACCTCGACCAGGA
Seq A exon
GTAAGAAATACCAAATGATATGGGGGAAAATGTACAAAAACAAAAATTTGCCTAGTTTTTCTCACAGAAGAGATAGCAGCTAACATTTCTAGCAGCAAAGATTTCTCCCAATTTTAGAGCATCATTAATTCATACATTTTATGGTAATGGTAAAATAATTTTTTACAGAAAGAGGCCAAAAGGAAAAAGAGGAAACAGAAAATGTACCTTTATTGTCAAGTCAATTAGAATTATACAACTAGAATCGAAATGAAAAGCCAAAAGACACATAGGCAGTGTTATGTGCACAAGAAATTTGATCATGTAACTCAAGAGTAGTTGCTGAGTCATGCATATATAGAAGTAAATCTTTGATAGGGTTCCTGATAAACAAGTTTAACAGTTTCCTGATAAGCAAGTTGATGAACTGTTAAGTGAAATAATACCTTACTTCCATTTTATTTTTCATTAGAGGTACCAAGTATTTTGGAGATGAAAAGACTTCTAGTATCTAATATTCATATATATGGCTATAAAGTTAGAAATTACTAATGTCTACAGAAGTCAGAGCCAATAAGTACAATTCATGATGATAAGAAACAGGTGTCATGTTTCCATGACAACCAATGAAACAACTGCTATGAAATAGAGAGCCTTATCCCACATTGTGTTGATTTTTATGATGATGACATGTGAGGTTAAAGCAACCCCTGGGGTGTACTGGGGAATAAAATGTTAATGAACATTCATATTCATATTGTGCTAGCCCACACTTGCTTTCTTGAGAATGATAAAAAACATATGCTGTCCTCTGTGAAGGCTTAACACTGAAAGTAGAAATGAGTCAATTACGTGTAGGAAAAATGTAAGACAGAAGATATCCTCAAAGTTCCTCAGTGGCCTAGGAAAGTGGGTCAGACAGTGAAAGTGAAGTGAAATTGAAAGTCCCTCCATCATGTCTGATTCTTTGCAACCCTGTGGACTATACAGTCCATGGAATTCTCTAAGCAAGAAGCCTGGAGTGGGTAGCCTTTCCCTTCTTCAGGGGATCTTCCCAACCCAGGATCGAACCCAGGTATCCCACATTGCAGGTGGATTCTTTACCAGCTGAGCCACAAGGGAAGCCCAGTGGGTCAGACAATGGCCTGCAATGAATGACAGTGGCAAAATCACAGATCAGTGAAAAGCGCCATGGGTTTTTGACATCAAAGCATAAGGAATGTCTTCCGGTTTGATTATCCCTGTGTAGGCTCAGCATTCTGTGTGTGACAATATCAGCAAAGACTGCTTGGTGGAAGAACATCAATATTGCCACACAGGGACTTTAAAGGCATAATGTTATAGCTGTGTGTGGCCTCTCAGAGTAGTGTGTAATAGTATGCAGTGTTTCTTATCAGAAGTCCCTTTTTGACAAGGGATTGTTATTCTGTGGAATATATTTTGGTAAATAGTAATTTGGATAACTAAATTTAAAAACTTAAATGTGATACACACCATCTTTCACGAAATTCAGAGCCAGTGGTTCTTCGGTACAATCCTAGACAGTCAGTACAGAAACTACTTATATAGAAGTTCATGTGTAGAGGGAAACTCCTCTGTCCCTAAAAGCTTTTCTGTTTCTCTACAG
Seq C2 exon
AACAAATTCCAAGGAATGGTCTTTGACTTCGTCACCAGACAAGTTTTTGACATCAGCATCATGATTCTTATCTGTCTCAACATGGTCACCATGATGGTGGAAACCGACGACCAGAGCGACTGTGTGACTAGCATTTTGTCCCGCATCAACTTGGTGTTCATTGTGCTGTTCACTGGGGAGTGTGTGCTGAAGCTCATCTCCCTCCGCCATTACTATTTTACTATAGGCTGGAATATCTTTGATTTTGTGGTGGTCATTCTCTCCATAGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018520:ENSBTAT00000021951:24
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
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACATCTTTATGACAGAAGAACAGAA
R:
TGGAGAGAATGACCACCACAA
Band lengths:
358-1964
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]