DreINT0131427 @ danRer10
Intron Retention
Gene
ENSDARG00000086819 | scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:ZFIN;Acc:ZDB-GENE-040426-751]
Coordinates
chr9:50215661-50217966:-
Coord C1 exon
chr9:50217829-50217966
Coord A exon
chr9:50215766-50217828
Coord C2 exon
chr9:50215661-50215765
Length
2063 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
TTTCTGTTGTCTTCTTTTACTTT
3' ss Score
2.84
Exon sequences
Seq C1 exon
CCAGAAGAACAGCCGGAGTATGAGGTGAATCTGTACATGTACCTCTATTTTGTCATCTTCATCATCCTTGGAGCCTTCTTCACATTAAACCTCTTCATTGGCGTCATCATTGACAACTTCAATCAGCAGAAGAAAAAG
Seq A exon
ATAAGTATTTACACCGAGTCATATAAGCTTGATTATACTATTTGTAATATGTATAATATTTTCAGACTAAGGTTGACTTTAGATGGTTTTCTAATTTTAGTTTGTTGTCTGCCTCTTCAAATACATGCAAAGTACAGTTGAATTAAAATCATTTTAATCTAATTTTTCCAATTAAACTCATTATCTTTCCTGTGAAATTTGTATTCTTTTCATTTGAATTTATTTCCAATGTGTTGCTTAACAGAGCAAAGAAAAGGTGTTTACAGTATTTCATATTTAGCTTTTCTAAGTCTTATTTCTTTTATTTTGGCTGGAATAATGCAAAAAAATATATACACTATCTGACAAAAGTCTTGTCGTCGATTGCAGTTGTAAGAGCAACAAATAATAACTTGACTTCTAGTTGATCAACTGGAAAAGTGGCAGATGGTCGATTTTTGTGATAAATCATCTGTTGAGCTGCATCCCAATCATCACAAATACTGCAGAAGACCTACTGGAACCCGCATGGACCCAAGATTCTCACAGAAATCAGTCAAGTGTGGTGAAGGACAAATCATGGTTTGGGGTTACATTCAGTATGGGGGCGTGTGAGAGATCTGCAGAGTGGATGGCAACATCAACAGCCTGAGGTATCAAGACATTTGTGCTGCCTATTACATTACAAACCACAGCAGAGGGCAAATTCTTCAGCAGGATAGCGCTCCTTCTCATACTGCAGCCTCCACATCAAAGCTCCTGAAAGCAAAGAAGGCTCCAGGATTGGCCAGCTCAGTCACCAGAGTTGAACATTATTGAGCATGTCTGGGGGAAGATGATGGATTAGGCATTGAAGATGAACCCAAAGAATCTTGATGAACTCTGGGAGTCCTGCAAGAACGCTTTCTTTGCCATTTCAGATGACTTTATTAATAGGTGATTTGAGTCAGTGCAGAGATGTATGGATGCAGTCCTCCAAGCTCATGATGGAGTCAGTCACAATAGTCATTCTGTTTCCACTGCAGCATGACTTTATATTCTATACTGGACATTACTTTTGTTCAGTGACAAGACTTTTGTCTAATCAAAGTCAGACCCTACTGTCTTAATTAAATCATTAAAAATCAAGGTGTGATCATATTTTATTGTGGAGGTCATGGAGGAGTGGAGAGCATGAGATTGATTCCTGTGACGCTCCAGGGACTGACGAGTCTTGGCTGAGGTCCAGATTCCAGCCTTTGGCACCTAAACTGCAGCTCTGCACAAGACCTTTGGCCATAGGAGAAATGGTCGTGCCCGTCTGTGCCTGGTTCTCGAGGTTTTTTTTCTTCAGTTCCACCAATTGGTGAAGTTTTTTCCTTACTGCTGTCGCCACTGGCTCGCATGGTTCTGGATCTGTAGAGCTACGCATCGATGGATTTGCTCTTCAGTGTTTGGACTCTCACTAGTGATTATTACACCACACTGAACTGAGCTAAACTTAATTGAACTTAAACTTTAAAATCTGAACTACACTGTTTCAATTTACTATGATATTTTATGTGAAGTTGCTTTGACACAATCTACATTGTAAAAGTGCTATACTAATAAAGAAGAATTGAATTGAATTGAATTGGTAAAATAAGCATAATCTAGAGGCCTTTGCCTTTCTTTGAGACACTTCTGATACCAAATGATCAGAAGTTATTGTTTGCTGTTCCTAAAACTTGGATAGGCGACAGACTTTTGTCAGGTAGTGTATATATCAGGGGTGGCCAACCCTGTTCCTGGAGAGCCACCTTCCTGCAGATTTCAGTTGCTACCCAAGTCAAACACACCTGAACCAATTAATTAGGACCTGAACACCACGTGATAATTACAGGCAGGTGTGTTTGATATGGGTTGCAACTGAAATCTGCAGGAAGGTGGCTCTCCAGGAACAGGGTTGGCCACCCCTGGTATATATATATATATATATATATATATAAAACAATAATAAAAAATCATTAATAAATCTGTCTCCAACTGTACTACTTTTTTATCAGACAAAAATCTATGCTTGTTTTTTATACCCAAAAATGATCTTTTCTGTTGTCTTCTTTTAC
Seq C2 exon
TTTGGGGGTCAGGATATTTTCATGACAGAAGAACAGAAGAAATATTACAACGCCATGAAGAAACTAGGCTCAAAGAAACCCCAAAAACCCATTCCAAGACCAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000086819:ENSDART00000161648:17
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(15.9=76.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
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]