BtaINT0129400 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:31053332-31054286:-
Coord C1 exon
chr2:31054197-31054286
Coord A exon
chr2:31053461-31054196
Coord C2 exon
chr2:31053332-31053460
Length
736 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
GCTTGGCTATTTTCTCTCAGGTA
3' ss Score
7.75
Exon sequences
Seq C1 exon
TTTATTCAATGTGCTCATTATGTGCACTATTCTTACCAACTGTGTATTTATGACCATGAGTAACCCTCCAGACTGGACAAAGAATGTGGA
Seq A exon
GTAAGTAGAAGATTTTTTAAAAATCTTGCAATATTGTTGTCCCTTTATGTTTTGAGTTGTGCTTCTATCATTTTGACACCTCATCAGTTTCTTCAGCAAGTTGTACTGGCTACTCCAAACCAGTTACACAGTGACTCAAGTTCATTTCAACCACTGATTTTCTGTAGTACAAAGCTTGCCCTGGCTCATTCAGTTGCTGCACTGATTTGACTGCCAATATGTATAGCCCTTTATCTTCCTCGTGAGTCTCACACTCTTTTCAAGATCATCAGTGATTACTAGTATCTGATGATAAATTTATACATAGTTTGTATGTTCTTTTCCTCATAGCTATCACTTTTATATGATTTATTAGTTTATATTTCATGGCTCGTAATGATGCCCACTTTATTAAACAAAAAAGTCTTCATTTATTTTTGTATTAATAACTACTTGCTTAAATTGGACCAAAACCAGTGTATTTCATTTAATATGTATAGAATCATGTTATTTGAACCTTCAAATTAATTAATATAAGCAAGTACAATACTCATATTTAGTCAATGAGAATGTCTTTCAGTATGTAATGTTTCTTTTTTTTTTTTCCTTAAGCCCTACCTATGGTCTAAATCATGGGAAGACCAATATAGACCTATATAGAACCCTCTAATTTTTATTTGTTGCTTTTCTCCTTTAGTATATTTACATGTAAATTACCTTCAGGATCTTTAATGTGGGCTTGGCTATTTTCTCTCAG
Seq C2 exon
GTACACCTTTACAGGAATTTATACTTTTGAATCACTTATAAAAATACTTGCAAGGGGCTTTTGTTTAGAAGATTTCACATTTCTACGGGACCCATGGAATTGGTTGGATTTCACAGTCATTACTTTTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:4
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=PU(0.7=6.5)
A:
NA
C2:
PF0052026=Ion_trans=FE(16.0=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:
ATTCAATGTGCTCATTATGTGCA
R:
GCAAAAGTAATGACTGTGAAATCCA
Band lengths:
216-952
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]