DreINT0131453 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10022185-10025444:-
Coord C1 exon
chr6:10025290-10025444
Coord A exon
chr6:10022359-10025289
Coord C2 exon
chr6:10022185-10022358
Length
2931 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
CTGTATATGTTTGTGTTCAGGCT
3' ss Score
7.78
Exon sequences
Seq C1 exon
GCTGTGTGATGAGGTTTCAGTGCTGTCAGGTCGATGTGGAGAAGGGAAAATGGAAGAGTTGGTGGATTCTCAGGAAAACCTGCTTTATCATAGTAGAGCACAACTGGTTTGAGTCCTTCATCATCTTCATGATTTTACTCAGCAGCGGAGCACTG
Seq A exon
GTGAGCACCCACACAACCATAACAAACACAATACAACCACCCACTCACAACCGGCCCGATCTCTGTTACTAGCTGTTGAAATGTGTTGATGTGTACAGTTGATGTCAGAATTATTATTGTTCCCCCCAATTTCTGTCTAACAGAGAGATTTTTTTTCCAACACATTTCTAATCATAACAGTTTTAAGACCTAATTTCTAATTGATTTCTTTTATCTCTGCCATTATGACAGTACATCATATTTTACTTTTACTCAAGATACTCGTGTTCAGCTTAAAGTGACATTTTAAGTCTAACAGGGTTAATTAGGCAAGATAGGGTAATTAGGCAAGTCACTAGCTATGTTTCCATCTACCTATGTTTATACGCATTTTGGATATTTTGAAAATGCCCATGAAAACTTATGCGATTTTATTATAAGAGATCATGTGATGATGAAAACCAGCAGGCTGACCACATTGTAAAACATCAAAAATCTTGTTTCTCGATTCTAAAACGCCTTAATCATTTTTCTATTAGGTTTGTTATATGTTACGATAACCAGCGATCATTCACTGGAGATCGCTGGTTTCCTCTTTCTTCATGAACCTCACTTCCGCATTCCCCAGGACTACATTTCCATACATGCACTTCTTCCAATCACGCACGCCTGGTCACTCATCTTCCTGATTACATCACCAGCTGAAACCTGTTACAGAGACTGATTACACACAGTATTTAAGCAGCACACACACTCATTCACATGGCCGAGTCTTGTCTACTGTTTGGTGACATTTCTACGCGTTTCTCCCGATCTTGTTTCTCCGTGTCTGTACCTAGCTTCGTTTCCTAGTTATCCTGTTTAGCCGCCAGCCTTTCGATCTTTTGCCTGTTTACCGACTTCGACTCTGGATTTGCCCGTATATGCCTGTTCATACCTGTTTTGACCATTGCTTGCCTGACCAACGAATAAACCTGCATTTGGATCTTACCTTCTGTTGTTGGTGTCACTCCCCGGCGTAACATATATTAATAATGATCTCCAGAATAGTCAAGTGTGTCTGTACTCCATGTCTCAGGCCTTCAAGCGCCATCACGCATTCATTGCATGTCGGCATTTGTCTTCTGATGTGCACGTCATTTATTAAATACGGAAAAGACTCGCGCAGCTTCTCCTACCGCATCAAGGTCTATTTTTACTTTTAATATTTGGTTCCAGTTAATCAGAAACTGACTATTTGGTTCTCGTTGTACTCGTTGGATGGAAACTTTGCTTTATTTGCACTTCTTTTTTGCCATATTTCTGTTTAATAATAAATTGAATTTGCATCTATTGATGGAAGCATAGCTATTATATAATAATGGTTTGTTCTTTAAACCAGGGGTTCTCAAACTTTTCAGTCCACGATCACCAAAATAACAATGCTAGTGATGCGTGACCCCCTATATCCTCTGAGGTGGTTATAAATATATAAACCTTACACATCCGCACACACATACCAACAGGCCCAAGTCTATTCATCATATAATTTTGAAGAACACCACTCGGAGACTATCCTGCATGTTTGGTTGTGGCTTGTATTTATGTTTAATGTACATGAGTGCCGTAAAGATGTCAGAAAGTTTAACCTGGTGCATTAAAATCAATGTGCTGTCTCTTTAATATTACATAATCACCCCAGGGGTCGCAAAAAATGGAAAGGCTGATGGCTTTTTATTTGCATGTTTTTTTAATGTAACTAGTGACTACTATTATTTACTTCTGTTGGTTATGGATAAAATATGATATTCTAGTAGTTTAATAAAATTAATTAGATTTTTGTAAATCCCCAAGCGACCCCCCGTCATTGTCTCATGATCCCTCAGGGGGTCCCGACCCCCACTTTGAGAGCCACTGCTTTAGACAATCAAAAAAATACTGCTTAAGGGCGCTTGTAATTTTGACCTGCTTTTATTCTATTATTTTATTCTATAATAAAACAAATAAGACTTTCTCCAGAAAAAAAAGGAAATACTGTGAAGAATTCCTTGCTCTGTTAAACTTTGGGAAATATTAGAAAAAGTAAAAACCCAGTAGGCACAGGACATTAACATGACGTCAGATTGACGTCGTACCCCAACATTGTAGTGACGTACTGTAGTAATTGTTTGGAAATGAAAATCGGGTTGACGTCAGAACCCAACATCTGATCGACATCCATGTCCAACGTCCAACTTAAAATCAACCAAATATCAACATCTAATTATGTTACAGCTTGACGTTGTGTGGACGGTACCACTATGATGTCCATCAGATGTTGAATTTTGCTCACCATACCTGACAAATAAATGTAATTTGACATCAATATGATGTTGGTTTAAGATGTTGGCTCGAAGTTGGATTTTCGGTCACTTTCCAACAAAACCTAAAATAAACAAAATATTAGACGAAAACATTTGACGATGTTATTGGACATCAAAGTAATGTTGCCTTTTGGTGCTGGCTAGACAATGAATTTTTGTCACCTGACGTCACAACTTACAATTGAAGTCAGAATTATTAGCCACCTGAATTATTAGCCCCAGTTTATTTTTTCCCCAATATCAGTTTAACGAAGAGAAACTCCATTAAACTCCGTTTTTTTCAACACATTTCTAGGTCTGTAGACTAGCTACAGTATATAGCTTAAAGGGGCTAATAATTTTGACCTTGAAATGATGTTTAAAAAATTATTTTATTCCAGTGGAAATAAAACAAATAAAACTTTCTCCAGAAGAAGAAATATTATCAGACATACTGTGGAAATGTCTTTGCTCTGTTAAACATCATTTGGGAAATATTTTAAAAAGAAAAAGAAATTCAAAGGGGGGCTAATAATTCTGACTTATAATATTAACATCTTATGACATTGTGTGCCTGCTGGGAAAAATCGTAGGAGGGCTAATAATTTTGACTGTATATGTTTGTGTTCAG
Seq C2 exon
GCTTTCGAGGATATTTACATCGAGCAGCGCAAGACCATAAAGACGGTGTTGGAATATGCAGATAAAGTCTTCACATATATATTCATCCTGGAGATGCTTCTGAAGTGGGTTGCATACGGCTTCGCCAAATACTTCACTAACGCCTGGTGCTGGCTTGACTTCCTGATTGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:19
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:
PF065128=Na_trans_assoc=PD(19.1=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]