DreINT0131575 @ danRer10
Intron Retention
Gene
ENSDARG00000018032 | scn8ab
Description
sodium channel, voltage gated, type VIII, alpha subunit b [Source:ZFIN;Acc:ZDB-GENE-060906-2]
Coordinates
chr6:39394906-39397703:-
Coord C1 exon
chr6:39397433-39397703
Coord A exon
chr6:39396063-39397432
Coord C2 exon
chr6:39394906-39396062
Length
1370 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
GTTTTCGCTTGGTTTTTCAGGTA
3' ss Score
10.87
Exon sequences
Seq C1 exon
AACAAAATCCAGGGGATGGTATTTGACTTTGTCACTCAGCAGGCCTTTGATATTTCCATCATGATGCTCATCTGTCTTAACATGGTAACCATGATGGTGGAAACAGATGATCAGTCAGACGAGACAGAGAACATCTTGTATTGGATAAACTTCGTATTCATCGTGGCCTTCACTGGCGAGTTCGTCCTGAAACTCTTTGCGCTGCGACACTATTATTTCACCAATGGCTGGAATGTCTTTGACTGCGTCGTTGTCATTCTGTCCATTGTGG
Seq A exon
GTAAGTGCTGTGTCTAAATGTTTTTTTCTGTTTTCTAAAGTACCCAGCATGAACTAGTACATCCTGACAGATTTTTCCTTTAAATTACCTTTCTATGGGATCTTATACAAAAAGATATTTGTGCAGATCTGTTTTTAAGTTCTGTTTTAAGTCAATTAGTTAGTCTTACTATTCTATCAAATTAAGTTAAGATCGTGGTGCAAAAAAATGAGTACACCCCAATTAGGAGAACTCAGAACATAACATTTGAATTCACCAGCAGATGAGTCAGATCAACTCCCACTTACTGCAATGCTGACACAATGACATCAAATGGAAAAATGCCACAATACAAGTGTCACTTTGATAAGGAAGGACAAAGCTATAGGAAAGCTTTGCTAGTAAGTATGAAAAATGTTGCTGTATGATAAAAAATAGAATTTTGGGACGATTGCTGGGAAATATAGGTGTCTAACTGAAGTTGGTACAGATGGCTGAATCATTATAAAGTCAAACTGGGGTGATTGTTTCCTTTGACTTGATATGACATACAGGTACAGCATTTACAGGACTGACATCCATGGCTGTGGTTTATGATGGAAGCCACTCCTGATGCCCCTAGGCAAAAAGCCCATCTAGTATTTGCGAGGGCTCATGTTTGACAAAAGCAAAGACTACAGGGACTTTGTATTTTGAAGGGATCTGAAAGAGAATAATCTATTTGGCTCTGATGGGTTCCAAACTGTTTGGAATCTCAAGACAAAATGCAACTGTAAAGCATGATGGTACCAGTGCTCTTGTGAAGGGTTGAATGAGTTCTGCAGGGGTCGAGGAGCTGTATTTCATAGATTGCAGAGGAGATGAAAGAGAAGATGATGTCATCACTTCATGTTCTACGCTACCAAAAACCCATTCAAAAGGATTATGATCCAAAACTAACACCCAAGGTCACTGGTTCATTTCCGTGGAAGAACAGGGTAAAAGAGATTCAGTAAAAGCATGTCCTCAGACCTCAATCTAACAGAACACTTTTAAGGAGTTTGAAAAGACAAGATGAATGTCGTTCTCCATCCAGGATCTGAAATAGAGACTAGAGGAATGGAGAAAAAAGGTGTTGCTTTAGGTCATCAGTTAGTTCATTGAAAGTCTAGCAGAATTAGTTCAATTATGAAAAATCAATGAAGCCATATAAAATATTAGATTTAGCTGAGATTTGTTATCAGTTGTAAACATTTTTGTAACAACTTGTTTGAACTCCATGTATAATTTTCACAAGATCATATTCTTGTGTTAATAAAAATAAACCAAAATTTTAAAGGGGGTGTACTCATTTATGCTGGGCACTGTACATTTTGTAAGGTTTTGTAATGTGTTTTCGCTTGGTTTTTCAG
Seq C2 exon
GTATGTTCCTGGCAGACCTCATCGAGAAATACTTTGTCTCACCAACTTTATTCAGAGTAATCCGTCTGGCTCGAATCGGCCGAATCCTGCGTCTGATTAAAGGAGCCAAGGGCATCCGGACATTACTGTTTGCTTTGATGATGTCACTTCCTGCTCTGTTCAACATTGGCTTATTGCTTTTCCTAGTCATGTTCATCTTCTCTATCTTTGGCATGTCCAACTTTGCCTACGTGAAGAGAGAAATAGGAATTGACGACATGTATAACTTTGAAACCTTTGGCAACAGCATGATCTGTCTATTCATGATCACCACATCAGCTGGCTGGGATGGCCTGTTGGCTCCTATCTTGAACTATCCGCCTGACTGCGACCCTAATAAAGAGAACCCAGGAACCACAGTTAAGGGCAACTGTGGCAATCCTTCAGTGGGAATCTTCTTCTTTGTAATGTACATTATCGTGTCTTTCCTGATTGTGGTGAACATGTACATCGCTATCATCTTGGAGAACTTCAGCGTTGCCACCGAAGAGAGTGCGGATCCACTGTGCGAAGACGACTTTGAGTCCTTCTATGAAATCTGGGAAAAGTTTGACCCCGACGCTTCCCAGTTCATCACCTTCGCCAAGCTGCCAGACTTTGCGGATACATTAGAGCATCCCCTCCGTGTGCCAAAGCCAAACATCATCGAGCTGATCGCCATGGACCTGCCCATGGTGAGCGGCGACCGCATTCATTGCTTGGACATTCTGTTTGCCTTTACCAAGCGCGTGCTGGGTGACAGCGGTGACCTGGACATGATGCGACAGCAAATGGAGGAGCGCTTTGTGGCAGCCAACCCGTCCAAGGTGTCATATGAGCCCATCACCACCACACTACGGCGTAAGCAGGAAGAGGTGTCAGCCATCGTGATCCAGAGATCTTACCGGTCCCACCTCGCGAGCAGGGGCTTCATCTGCAAACGCAGGCCTGCCAACAACAAACTGGAGAACGGTGGGGGCAATCAGGAGAAGAAAGAGGGCACACCTTCCACTGCATCCCTGCCATCCTATGACAGTGTAACCAAGCCCGAGAAGGAAAAGCAGGACGACAACAACGAAGGCAAGGGCCGCAAGGAGAAAGGCCGAAACCAAAAAGATGTCAGGGAATCTAAGTGTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018032:ENSDART00000151299:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.226
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.5=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.0=43.0),PF0061222=IQ=WD(100=5.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGTCGTTGTCATTCTGTCCA
R:
GCCAGCTGATGTGGTGATCAT
Band lengths:
350-1720
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]