GgaINT1024517 @ galGal4
Intron Retention
Gene
ENSGALG00000027702 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr2:5335534-5338309:+
Coord C1 exon
chr2:5335534-5335798
Coord A exon
chr2:5335799-5337167
Coord C2 exon
chr2:5337168-5338309
Length
1369 bp
Sequences
Splice sites
5' ss Seq
TTAGTAAGT
5' ss Score
7.79
3' ss Seq
TTTTCTTTTTCATTTCAAAGGTA
3' ss Score
10.29
Exon sequences
Seq C1 exon
AATGCATTTCAAGGATTTTTCTTTGACATAGTGTCACACAAAGCATTTGACATTAGTGTGGTGACTCTCATCTGTCTAAATATGGTTGTGATGATGGCAGAAAGTGACAATGGAGAAGTCAGGGATGTTCTTAAAAAAATCAACTACTTCTTTGTGACAGTATTTACTGGGGAATGCATCATAAAAATAATAGCCTTGAGACATTACTTCTTCACCACTGGCTGGAACATATTTGATTTAGTTGTTGTGGTCCTTTCACTAGTTA
Seq A exon
GTAAGTATCAATTGCTGCTAGATCAGATGGTGTGTCTTAACATTCAGCCAAATTTCAAAATGAAGTGACAACTTACATATATCTGATAACTTCCAGATCCATTTTACAAACCATATCCAAATTGATTCCTTCTAAAATGTTATGTACTGTTTTCTGTTGTATTTTTTGCGGAGTATTAAGAGAAAAATGGATTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTCCTTCTTTCTTTTGAAAGTATGAGTTTTATTGAGTAATTATCAGAATAGCATTTTAATGAAGCAGCATCTTTTCTAAGCTGTTGTACTTAAGTTATGGTAGTCTTAATGTTTTTCTACTTTTGATTTGTAAGTAATCCAAGTAGCCATCATTTTCACAGTAAAAGTAATTTTGGGTTAAAAATTCATTTGTATGAAAAATGAGAGACTTTTATTTCCAGGACATTCTTTGAGAATCCAGATCATGAGAGTTGGTGAGAAAAGCTTAGAAAAATTGAATAGTTTAACACCATTCTGTGTCTGCATGACTGTCTGTGGCTTTGGAAACTCCTGTCATAATCTTAGTGCAAAGAGGGCGATAGGAAAGAAAAACTGGTCTGAAAAACTGTTCTCTGTTTCATCCCTAATCTCTGCTATTCCATGAAATCCAAAAGACAGCTGATTCTTAGGTCGTCTGTTTGTAATCATGCTTTACTACCGCTGAAGGTAATGTTAAGATCACTGGAATGAATTGTGATGGAGGATTAATAGTGATAGCAGTTTTCTTTTATGTTCTTTTTATCTGATCTCTCATCCAAATACCAAGCATTATAGTCAATTTCAGCTTTTAACATCTGGCTCATGCCAGCAGAAGCAGGAGCAGGAACAATTGGTCAGCAGCTAGGAGATGAGCCCCATAGCTTCCAGCACAGAAGCCAAATGATTTGTGAAGGGTTTTTTAAAAGTGCTAGAGCAGTGCATGCTTCATTACAGAAATTTGCAAGAATGTGTTTTTCACACTAAACAGAAACTTGATAATTCTGCAGTATTTCAAGGTATTACAATTTGTTTTGCTTTTCCTGAGCTCTTTCATAAGCCATTGTGGTATTGGTGATAATGTTTTTCTTGAAAGTGATATAATATAAAGTGATAAAGTTGATTACTTTCCTCACCCGAAATGTAGAATGTAACAAAATGACCATAAATGCAGAATGTCATTGATATGTCCTGAAAATACTTTCTTTTCTTTTTCATTTCAAAG
Seq C2 exon
GTATTGCACTTGCTGAAGTCTTTTCAAAGTTCTTCTCTCCTACGCTTCTGAGAATTATTCGTTTGGCACGAATTGGCCGCATTCTGAGATTAGTTAAAAGAGCTAAAGGAATTCGAACTCTTCTTTTTGCCTTATTGATGTCTCTTCCGTCTCTGTTCAACATTGGCCTCTTGCTATTTCTGGTTATGTTCATTTATGCTATTGTGGGCATGACAAATTTTGCCTGTCTTGGCTGGGAAGGTGGGATCGATAACCTTTTCAACTTTCAAACTTTTGATAGTAGCATACTCTGTCTCTTCCAAATTACGACATCAGCTGGCTGGGATAGCCTTCTGAGTCCAGTGTTGAAAGAATCCGAAACGTGTGCTCCCAATGTACCACAGAATAACTCTAGTTGCAGAAATAAAGTGGTTGGTATTACATTTTTCGTAAGCTATGTCATTATATCCTTTCTTATTGTTGTAAATATGTACATAGCTGTCATTTTAGAGAACTTCAGCGTTGCCACTGAAGAAAGTGCAGATCCTCTTTCTGAGGATGACTTTGATATGTTTTATGAAACCTGGGGAAATTTCGATCCTCAGGCAACGCAATTTATTGAATACTCTGCACTTTCAGACTTTGCAGACGCTCTGGCAGAGCCCTTACGCATTCCAAAGCCAAATACGATTCAGCTCATATCCATGGACCTCCCCATAGTGAGTGGAGATAAGATCCACTGCTTGGATATCTTGCTCGCCTTCACTAAAAGGGTTTTAGGAGAAGCTGGGAATTTTGAGGGTCTTGAATTACACATGGAAGAAAAATTTATGGCTGCCAATCCATCTAAAGTTTCCTACAAGCCAATTACTACCACACTTAAAAGAAAGCAAGAGGAGGTGTCAGCACTTGTTATTCAGAGGGCCTTCAGGAGGCATTTGTTGCAGCGTTCTCTGGAACATAAGCCTTTCTTACACTGTCGTAGACGTTTTAACAGTGCAGTCTATGCAGAAGAGATGCGTGAGAAAGATGGCCTCATTGCATCAATGCGTGGTGAAAATTATGGGAGGAAGCTAGATAAATCACAAACTACATCTTCCATATCTCTCCCTTTATTTTATGATGGTATTGCTGGAACAGATACCAATAAGGTGGACACATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027702:ENSGALT00000042757:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.024
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(21.0=48.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(78.5=42.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCAGAAAGTGACAATGGAGA
R:
AGCAAGAGGCCAATGTTGAACA
Band lengths:
346-1715
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]