BtaINT0129402 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:31051515-31052762:-
Coord C1 exon
chr2:31052671-31052762
Coord A exon
chr2:31051788-31052670
Coord C2 exon
chr2:31051515-31051787
Length
883 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCCTTTGATTTTATTTGTAGGCC
3' ss Score
9.2
Exon sequences
Seq C1 exon
ATATGTGACAGAATTTGTGGACCTGGGCAATGTCTCAGCGTTGAGAACCTTCAGAGTTCTCCGAGCTTTGAAAACAATTTCAGTCATTCCAG
Seq A exon
GTGAGAGCTAGGTTAAACACCGAGGCTGACTTCAGCAGCATTAGTGGTACAATCACAGCTTTTGTGCGTAAGCCTTGCTGCTTTTCACTTATTGCAAATGTTTTTTAAAAAAAGCAAGAATCAATACACCGTGTTTTGGATGGATTTGATTCTTTGCTTTTACTAGTTGTTTTCTTTAAAATGATCAGTTCTAAATCAGCCTTTGAGTTTAACAAGTTTTTGCATGAGGCATTTGCAGTAACAGGCTACATGGTTTGCGTCCTGTAACATCAAGCTTTCCGCATAGAAGCTAAACTATGAGGCATTCGAACTGATGCAAATTTGACCAGTTAGGTCTAAAATTGGTAATTATGTTAACTTCAAATAAATAAAAGAGCGAGAGATAGCATGAGTGCTGCATGGGACTCAGTTTTCAGATGTCTTCCTTTTTTAACCCATTCTCAAGCTGATAGAATTTACCAATATATAACCTCATAATTCAGTGACTTCAAATTTTCTTACTATATTATTCATACAGATTTTTCTAAAACCAGTGAGAGGTTAGGGAGTAAGACATCTGCAAATAAAAGCAAAGTCTTTATACAAGGTTGATGTTTAAGCATGAATATCAAAACCATTTCTTTTGCTCTGAGGAGTATTTGGAAATACACTTTTGGTTTGTTTCCATTCACAGTTCTCTAATGAAAATACAAATTCTGCTTTCATTCATTTTCACCAGCTAGCGGGCTTTCCATGAAAGTGTTATTCAGTCACAAACATTAAACTAATATTGTTGGCATTCTGCATGACATCTTTATTTTCCAGGACAAGCTCCTGATGTTTTTCTCTCTAACATAGCTGTTGAATAGTATACTTAAATTCCTCCCTTTGATTTTATTTGTAG
Seq C2 exon
GCCTGAAGACCATCGTGGGGGCCCTAATCCAGTCGGTGAAGAAGCTCTCAGATGTAATGATCCTGACTGTGTTCTGCCTGAGCGTGTTTGCACTAATAGGATTACAGCTGTTTATGGGCAACCTGCGAAACAAATGTTTGCAATGGCCCCCAGATAATTCTTCCTTTGAACTAAACATCACTTCCTTCTTTAATAACTCATTGGATGGGAACGGTACCACTTTCAATAGGACAGTGAGCATGTTTAATTGGGATGAATATATTGAAGATAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:6
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:
PF0052026=Ion_trans=FE(11.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(34.0=100)
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:
ACAGAATTTGTGGACCTGGGC
R:
TTCATCCCAATTAAACATGCTCACTG
Band lengths:
342-1225
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]