DreINT0131459 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10015907-10016539:-
Coord C1 exon
chr6:10016402-10016539
Coord A exon
chr6:10016012-10016401
Coord C2 exon
chr6:10015907-10016011
Length
390 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
CTTCTCCATTTGCTCTTTACCTT
3' ss Score
0.08
Exon sequences
Seq C1 exon
TTGGAGCAACAGCCTGTCTATGAAACAAACCTTTACATGTACCTGTACTTCGTCATATTCATCATCTTCGGCTCCTTCTTTACCCTCAACCTCTTCATTGGTGTCATCATCGATAACTTCAATCAGCAGAAGAAAAAG
Seq A exon
ATAAGTATTAAAACTGAGGACGATGAATCCAAGCACCTAAACACCACCGTACAGCCAATAAGGAATGTTTATCATTCACTCGAAACCTCAAATCTGCCTCTGCCATTTTCGGTTTACTTTCAAAGAGGTGTAATGTGATACTGTATGTACACAGTCTCTGGTTTTGTTTAGTGAGCACAATGGTACCTTATTGAACTGGTTTTGTTTGTAAAGCACACACAATGCTAGTCTTTTGAGAGATAAATGCGACCTGGTACAGGCTGAACTGCCTGTTTGACATTTCCCTGAGGTTCACAGGTGAAAACTAACAGAAGCCTGGTTGCATTAGGTTTGTGTTGTGACATATAATTAAACCATGGTTGTAACCAGTCTTCTCCATTTGCTCTTTAC
Seq C2 exon
CTTGGAGGTCAGGATATCTTCATGACAGAAGAGCAAAAGAAATATTACAATGCTATGAAGAAGTTGGGATCTAAGAAACCTCAGAAGCCAATTCCCAGACCTGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:24
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
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAGCAACAGCCTGTCTATG
R:
GCAGGTCTGGGAATTGGCTTC
Band lengths:
241-631
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]