BtaINT0129396 @ bosTau6
Intron Retention
Gene
ENSBTAG00000038180 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:30991647-30992259:-
Coord C1 exon
chr2:30992122-30992259
Coord A exon
chr2:30991752-30992121
Coord C2 exon
chr2:30991647-30991751
Length
370 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
TTTTCCTTTCATTTCTTTACTTT
3' ss Score
1.72
Exon sequences
Seq C1 exon
GTAGAATTACAACCCAAGTATGAAGACAATCTGTACATGTATCTGTATTTTGTCATCTTTATTATTTTTGGTTCATTCTTTACTCTAAATCTTTTCATTGGTGTCATCATAGATAACTTCAACCAGCAGAAAAAAAAG
Seq A exon
ATAAGTATACTAAAACTTCATCTTTGCTCTAAAGTGCTAACTAAATATACCCCAATGTTTCTTTTGGCTCCAAGTGCAGTCATTAAGAAGAAAGAATATAAAATTCAGAAATTATTTTGACTTAATCATCTATTAGTTTTTAAGTGATTGATAATTCAGATAGCTGAATTACTATCAGCTGTCTGAAAGTACTGATATTTCCAGTACAGAAATATGACTAATTTACACGTTGAATATATGCATATCTAAAATACATGTTTGTTAGTAACTTTAGAATAGAATGTGGAGACATTTTTGACACAATTACTAATATGGATTTTATAGCTAGCAAAGAACATGATTTTTACAAGTTTTCCTTTCATTTCTTTAC
Seq C2 exon
TTTGGAGGTCAAGACATTTTTATGACAGAAGAACAGAAGAAATACTACAATGCGATGAAAAAATTGGGTTCAAAGAAACCACAAAAACCCATACCTCGACCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000038180:ENSBTAT00000061380:24
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:
PF0052026=Ion_trans=PD(15.3=76.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAATTACAACCCAAGTATGAAGACA
R:
AGCAGGTCGAGGTATGGGTTT
Band lengths:
241-611
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]