BtaINT0129419 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019385 | SCN3A
Description
sodium channel, voltage gated, type III alpha subunit [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:31202204-31203901:+
Coord C1 exon
chr2:31202204-31202335
Coord A exon
chr2:31202336-31203806
Coord C2 exon
chr2:31203807-31203901
Length
1471 bp
Sequences
Splice sites
5' ss Seq
TATGTGAAT
5' ss Score
-3.61
3' ss Seq
CATTTGTTCCTTAACTATAATCT
3' ss Score
-2.99
Exon sequences
Seq C1 exon
ACTTTTATAGTATTGAATAAAGGGAAGGCAATTTTCCGATTCAGTGCCACCTCTGCCTTGTATATTTTAACTCCACTAAACCCTATTAGGAAAATTGCTATTAAGATTTTGGTACATTCATATCCTTTTTAT
Seq A exon
GTGAATTGTCTAAATGTTGTTTCTAGTAGCTGATTTTATAAAGAATGTCATTCTTTTTATAATATATATATATAATTCTCTCAGATTAATTGGTAACCTTGTTATTTAATCTATTGTACTCACTGATTTTCTGCTCTTTATAACAAGATTATTGTAGAATGACAATTATGATTCTAGTAGTAAAAAGAAAACTATGATAGTAAATGAAACACACTGTGTAGCAGGAACAACAGCAAATCTCCTTCAAACTGTTATTAACCTCAATTAGACCATATATAGCCATCATTAAAGAAGCATAGCCTCCTGTGCTTAGTATTATTATCTATATTCCAAACGTTCAAATTTTTTTGCCTTAATTGGTTCTGTATCTTCATCACCTGGACTTTCCTTCCTTCCTTCCTTCCTTCCTTCTTTTCTTCCTTCAGTAAATATTTATTAAACTACTATGCATCTGATTGATAGCATCTATTTAAAAATCATTGAACTTAAAACTACCTACAATGATAGTCAAAAACTTTATGTAAAATGACATAATAGGTGTGGATTTCAAGAAAACTCTCAAGAAGTGATAATAAACTAGATGATCTTCAGAGGCAGTGATCCAAAATAGGCATCTTATACAAACAGATTCAAAACAGGTCAACATAAAAACTAAAAGAGACAAAAGACACAGGGTTAACCTAGAGACAGGGAAAAGAGGACGGATAGCCTTTGAAGTGCTTTTGAATTCTCCCAGTCCATAGTTTGCTATTGGAAAGTATTTACATTTTAAAACAGAAAGATTTACTTCAAAAAATGTAATCCTTAGTTTTCTTAGAGTGAAGTCTGGGTTGAAATTCTAAGAGAAATCATTACAGCTAATTCTTAGAAAGGTTTAAAAACAGTGTGTGTTTAGGTATGGTAAGGACAAGATACAGAAAGATAATTAAATGTCCTGATAAGTTCCTATACTCGCAAGTGAAAATAAAAAGCTAGAAAATAAAACTAGCTCATTAGCAAAATTTGTCTCTCCCTTTATTCTTATGTGGTAAATGCTAAAGGGACAAGTTCCATCACTGTACGGCTACTAGAGTTCCTAATTACAGTAGAATCAATCAATGTAATCCTTGAATACACAGGGATATACATTCTCAGGTTTATTATATTCCATTCATTAACCTTTTGTCCATCAGTGGAAATTTTAAAGGGTAGCTGAAGTATAACTTTTAGACTTACACTAGAAAATTCCCATTTGCTTCAAACAGAGATCTCTTTCTATTGAATTCAGTTTTGTGAGGGAATGATGCAAAACAAAAAAACAACGAACCAAGAATACAAAGAATATATGATAGACTTCGGAGTTTCGTTTTTTTCTTTGTCATTGTTTTAAAACAAATAAGTAAAATTAATTTTACAGGTAACTTGGTTTCTTTGCATTGGATTATTTGTAAATTGCCACAAAATTGTACTAGCATTTGTTCCTTAACTATAA
Seq C2 exon
TCTACTTTATTCAGCATGCTTATCATGTGCACTATCTTGACCAACTGTGTATTTATGACCTTGAGTAATCCTCCAGACTGGACAAAGAATGTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019385:ENSBTAT00000025829:2
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(0.7=6.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAATAAAGGGAAGGCAATTTTCCG
R:
TCTACATTCTTTGTCCAGTCTGGA
Band lengths:
214-1685
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]