DreINT0131485 @ danRer10
Intron Retention
Gene
ENSDARG00000098738 | scn4aa
Description
sodium channel, voltage-gated, type IV, alpha, a [Source:ZFIN;Acc:ZDB-GENE-051201-2]
Coordinates
chr12:4850099-4851835:+
Coord C1 exon
chr12:4850099-4850464
Coord A exon
chr12:4850465-4851702
Coord C2 exon
chr12:4851703-4851835
Length
1238 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TTGTGCTGTGTGCTACACAGGCC
3' ss Score
8.46
Exon sequences
Seq C1 exon
GTGCTGAATCTGTTTCTGGCCCTGCTGCTTAGCTCCTTCAGTGGAGATAACCTGTCTGGAGGTGATGATGATGGAGAGATGAACAACCTTCAGATTGCCATTGGCCGCATCACCAGGGGTATCGATTGGGTTAAAGCCTTAGTTGCCAGTATGGTGCAACGGATTCTGGGAAAGAAACCTGATAATACCAAAGAGGAAGGGGAGGGAGACATAGAACTGTACGCTTTAAATCACCTTGATGAAGGAAAAATGGCAGATGGTTTGACCAACTGTTTGTCTCCAACATTGACTGTACCTATTGCTCGTTGTGAGTCTGATGTGGAGGAAGATGAGGACTCTGAATCTTCTGATGAGGAAGACGCAAAG
Seq A exon
GTAAGGCAGTCCAGTTTAACTTTATCAGTATCTAGAATTAGTGGCGTCAGAAGTTTCTAAAGTATTTTCTTCTTCAAGCATGAGACGATGAGACTATAAGATGTATACTTCACATAACATTAGATACTTTGTAGTAATGTTATAAAGTTCATTCGTGCCTGATACCTTTTCCTGTAATGTTAGTTCTTGAGAACTTTAATGAGGAAAATAACTACAATCCCTTGAAGCATTGACTGAATTGGTGAAGAAAAACTGAATAGACGAAGAAAAGCAAAACAATTATAGTTGTGTCCATAGATTGAATACAGTACAAATACAATACACAATTTAATTTACTGCCTCAGAGCTAAAAATTGGTTTCCATATGAAGAAAATTAAGGATTTTTTACTTCCAGAACCCAACAGTTGCACTCAATACTGTGCTGTGTACCACTATTTTGAAAAATATTATGAAAGCTAAAAACCGTTAAGTATGCTAGATAAACATAGAAATGATTTTGTGCATCATATGCGCTGTTGACCATTTTAACAGCAGAAAGAAAAACATAAAGTTTGGAGACTCTGAAGAAATATATCCTTTAAACGGTGTATAAACAATTCTAAAACATACAGGAGGGTTAAAATGGTGATCTAATTTTAATGACAAGGCATTTTCAAAGTTGTGGCATCCAAGAATAATCCTGTAATGCAAGAAGTAGGTCATTTTTAATTTTGTATACATGAATATGCTGGGCGAAGCAGTGTTGCAGTAGGTAGTGCTGTCGCCTCACAGCAAGAAGGTCGCTGAGTCGCTGGTTCGAGCCTCGGCTCAGTTGGCGTTTCTGTGTGGAGTTTGCATGTTCTCCCTGCATTCGCGTGGGTTTCCTCCAGGTGCTCCGGTGTCCCCCACAGTCCAAAGACATGCGGTACAGGTGAATTGGGTAGACTAAATTGTACGTAGTGTATGAATGTGTGTGTGAATGTTTCATAAAGATGGGTTGCAGCTAGAAGGGCATCCGCTGTGTAAAAACTTGCTGGATAAGTTGGCGGTTCATTCCGCTGTGGTGACCCCGGATTAATAAAGGGACTAAGCCGACAAGAAAATGAATGAGTGAATGACTATGCTGCCTTCATTAAGTTTAATCATTAATCTCTCAAGATGATTAACAAGATTAATCAAACGTTTTTTTTATTAAATATGTACATTTTGTCTTTCACCTTTTTGTTCTCTCCTCTTTTTTGTGCTGTGTGCTACACAG
Seq C2 exon
GCCACTCTTAATGATGGTGACTCTTCGGTTTGTAGCACAGTGGACTACCAGCCTCCAGAACCTGAGCCTGAACCTGAAGAGGTAGAAGAAGAGGAACCAGAACCTGAAGAACCAGAGGCCTGTTTCACAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098738:ENSDART00000170961:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.303 A=NA C2=0.778
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=6.6),PF065128=Na_trans_assoc=PU(52.1=80.3)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(23.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGTATGGTGCAACGGATT
R:
AGGCCTCTGGTTCTTCAGGTT
Band lengths:
343-1581
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]