DreINT0131458 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10016402-10018441:-
Coord C1 exon
chr6:10018388-10018441
Coord A exon
chr6:10016540-10018387
Coord C2 exon
chr6:10016402-10016539
Length
1848 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
AGCATTTCTCTTACTCACAGTTG
3' ss Score
6.82
Exon sequences
Seq C1 exon
GCCACATTTAAAGGATGGATGGACATCATGTACGCAGCTGTAGATTCTCGTGAT
Seq A exon
GTAAGTGTTTTTTACTATCCCTGTTACTCTTTAAAATATCCTAATAATATAGTATGTAAATAAATGATGGATTTTTTTCATAACTACGCAAAATACATTTGTAGTAAAGTCTTAAATTCATAAAGATATGTAATTAAAGGGGCTCTATGAACGTTTTTGACTCTTCCTAAAGCATAAAATCACCATAATATGTTAAAAAAAAACATGCCAAGTGAACATTGTTCTTTATCTAAAAAATATTAAAGTCAGACATTCTGCTTTGAAAATGTTTGTTACGTGCCAGAATGTCTGTCTTTGTGTTGGTTCTTTTAACTTTCCCAATGCCACTTTAGCCAATTATAATTTAGCACTCAAGTTTCCCTTTAAGGAAAACAGTGTATTTCATTCATTTAGTCAGAAAGACTCTCAAAGTGTGCATCCGTGATCAAAATGCGATCATAAATATTACAAATGTAAACATTATGTGAGCAGGTTACATGTAATCCCGTGTCCTAACAACACGCTGCGTGATGAGATTTGCAGTTAGAAGCAATTTGGCTTTTTTCACCAGATAAAAACATGATAGAAATTTAAATACAGCCACTCAGAAGCACAGAACAGTGCACTTACTGCACTCCAACAAAATGGTAAGATTTACAATCAAATTAATACATATTGAACCTCTTTAACATTATTATATGTGCATGCTGAATCACTGATATTTGTTAACTTGGCTTGCACTGAGTCACAGTTCTAAAGTTCAGCTTCAAATGGTTTATTTTATTTTCAGGATCTGAGATTAACTATCTGCTGCTGCTTTCAGTAGTATGGCAATAAATGTCACCTAAAATGACATTCAAACTCACATTATTAGCATTTAACACTGAATAAAGCACATGAGATGTACCTTTGGTGATCGTTTTTCACTTTTGAGAAATAGAAGCCGTTTCTAAAATAGAAATTTTAGGTGTTTGGACAAAAACTCCTTTTAGTATGGAAAATATTTCTTCTATTGTGTACCGTTGCTTTTAGTTAGAAAACAGTTAAAATCAGCCTTAAATCAGCCTTAAGGTTCGATAGTCAGGCACACTCATGTCAATCTGTTAACTTTGCGCTTTGTTTCAGGAGTGCAATATCTAGTTCAATTACTGAGTGTCAAACTTGCATACCGCACCTTTAATTGTCACATAACTTCCAACATATTCCTCCGTTTTTTTTTTCTTTCCAGTATAAATATCACAGTATCATTTACTCCAAATACATTTCCGTTTGACTTGTTTACATGTGTACTGACTTAAGAATCTTTAGATATCTAGACAATTTACAACAACAGTAAATTTCCCTAATGTTTGGGAGCAAAAATATTCAAACCTTTAGACGTAAAACAAAGACCTACAGTAACTAAAACTAAAACCTTAATTGTGTTAAATAATTGTGCGTTTACAATCAATTTACCTTAAGGGCGTCACACCCCGGATGCGCCGCGACACTGTGCGCACATGACAGTAGAAAGTATCACACACCAGACGCACCAGACTCACATTCGCATGGTATTTTAAAGGAAACTAATCAGATGGCGCTCTATAAACTTTGTCCTGAATCGTGGCTGGGCGCGCCGACACCCACCGACTTGCAGTACCGGTGTGTGTACCCTGATAGAAAGCTATGTTTAGAATTCTAAAATGCATGCGAGCGGCACTTCTGGTGTGCGACCTGCTTTAGAAATCAATTTACATTTGTGTTTCCTTCAAATCATTTAGAATTCACTTAGCTTCCTAAAATAAAAGCTTTTTTCTGTGTTTGTGAATGTGCTAATGAAGATTAATAATGCAAATGTGTAATAACATACAGCATTTCTCTTACTCACAG
Seq C2 exon
TTGGAGCAACAGCCTGTCTATGAAACAAACCTTTACATGTACCTGTACTTCGTCATATTCATCATCTTCGGCTCCTTCTTTACCCTCAACCTCTTCATTGGTGTCATCATCGATAACTTCAATCAGCAGAAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:23
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=FE(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCACATTTAAAGGATGGATGGAC
R:
TTTTCTTCTGCTGATTGAAGTTATCG
Band lengths:
190-2038
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]