GgaINT1024515 @ galGal4
Intron Retention
Gene
ENSGALG00000027702 | SCN11A
Description
sodium channel, voltage gated, type XI alpha subunit [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr2:5331940-5335106:+
Coord C1 exon
chr2:5331940-5332077
Coord A exon
chr2:5332078-5335004
Coord C2 exon
chr2:5335005-5335106
Length
2927 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
GTATTCTTTCCCTCTACTTAGGT
3' ss Score
-7.49
Exon sequences
Seq C1 exon
ATAGATGAACAGCCACAATTTGAGGCATGCTCAGCTATGTATTTTTACTTTGTGATTTTCATTATTTTTGGATCTTTCTTCATGCTGAATCTTTTCATTGGAGTGGTTATCAGCAACTTTAACCAACAAAGGAAAAAG
Seq A exon
ATAAGTACTGTATGAAATGATTCATGGTCTCTTGTAATCCCAATTTGATTGAGTCTGTGCCAGTTTGGCGTGTAGATGTATACAATTTTCAGGTAACTATTTATAGATATCTCAGGCTTGGAGAATAAAAAGCTCGGTAGCCTCTTATGATGGATTTACAGCATCAGTGGATAAAGGAAGAGCAACTGATGTTATCTACTTGGACTTGTGCAAAGCCTTTGACACTGTCCCGCATGACATTCTGGTCACCAAATTGTGGAAAAATGGATCTGATGGATGGACCACTCACTGGATAAGGAATTGGGTGGATGGTCACACTGGGAGAGTTGTGGTCAACAGCTCAGTGTCCAAGTGTAGAGTGGTGACAAGTGGTGTCCTCAGAGATCAGTGTTGGGACCAGTGTTATTTTACATTTTTGTAGGCGACATGGACAGTGGGATTGAGTGCATCCTCAGCAAATTTGCAGATGACACCAAGATGAGTGGTACAGTTGACACGCTAGAGGGAAGAGGTGCTATCCAGAGGGACCTGGACAGCCTTGAGAGGTGGGCCCATTCCAACCTCATGAGTTCAACAAGGCCAAGTGCAAGGTCCTGCACTAGGGTAGGGGCAATCTCAAGCACAGATACAGGTTGGGAGGAGTCTGGCTTGAGAGAAGCCCTGAGGAGAAAGATTTGGGTGTTTTGGTTGATGAAAGATTCAATGTGAGCCAGCAGTGTGCATGTGCAGCCCAGAAGGCCAACCATATCCTGGGTTGCATCAGTTGACGAGAAGTGTGACCAGCAGGTCAAGTCTGCTCTCATGAGACCCAATCTGGAGTATTGTGCCCAGTTCTGGAGCCCCCAACACAAGAAGGTCATGGAGCTGTTGGAGCAGGTCCAGTGGACAGCCATGAAGATAAGGGCTGGAGCACCTCCCCTATGGGACTGAGAGAGCTGGGGCTTTTCACTGGAGAAGAAGAGGCTCCAAGGAGATCTTGTAGAGGCCTTCAAGTACCTGGAGGGGGCCTACAGGAAAGCTGGGGAGGGTGTTGTTATAAGGGCATTCAGTGACAGGATGAGGGAAAATGGTTTTAAAATGGAAGAAGGTAGGTTTAGACTAGACACAGGGAAGAAATTCATTACTGTGGTGGTGGTGAGACACTGAACAGGTTGCCTAGTGAGGTTATATCCCTTCCTTGGAAATATTCAAGGCGGGGCTGTGAGCAACCTGGTCTAGAGGGAGGTGTCCCTGCCTATAGCAGGGGCGTTGAAACTAGATGATCTTAAAGGCCCCTTCCAACCCAAATCATTCTATGACAATGCTTTAAAGATTTTCTGTGAAGAACAGAACAACCCTTTTTGCTGGGTGGAAACACCTAACAAACATGGTAAGGATGATTAAACTGCTGATGGGAGAAGTAGCAACTGTTTTCCTGGTGAAGGAACTTGAAAAGGCCTCGTTAATAAGAACTTTTTCAAAAACTAGCTTAATTTAAAAAAAAAAGTCTAATCTTTTGTGAATTACTCTACAAGTTAATTTATTAAGTTTAAAAAAGAATTCTGTAGTCAAATCCAAACCATCAACCCAGAAAAAAAGACAGATAACCATTTAAAGGCTTCTTAAAGCCCATGAGGACTGTGTCCTCTCCTCATTGTTGCTAGATTATCTAAAATTTTTATTAAGTCAGAAGCTGAAGGAAAAATCTTAAAAGGAAAAATACAGCAAGAGAAAAGCAACAGTTAGCCTTCCCTGGTAAGCTTCAGCATCTGGAACAGTATTTATTGTCAAGCTTATTTATTGATTGAGTTCTCTCCATGATTCATTTAGGAACTTAATATATCCATAATATTAAGGGTAATTGAGTCCATGAATCCACTTGGGAGTCTTATAATAAAACAAGTAAGCATGTTTGTTGGCAGACTGACAGGAGGTTTGCAATTTCAAGGTACACATTTGGAAGACACTCTCCACAGGAGCAATTTCATTATTTCCATAGGCTGAATTTTTCATTGTTTCCACAGGCTGACTTTTACTCCAAGTACCAAAGCACTACTGCCTTAGGTAGAAGATAAAAAGGCACACAAGAAATTGTTTCTTTCTGCATCTGGTCAGAGAAAAGATATGTATGAGGAGCAAATGTCCAATTTCACGGTCATAATTTCCTTTTACAACAAAGTACCAGTTGGCATGATCCCAACTGACATTAATAATGTTGGTTAAGCAACCGATGAGCCCAAACACTTTCTAGAATTTGATGGGGATGTAACACTTTTTTCCAAGTACGTGATATAACTGTGTATTTTTTTCATTTCTTTTCTCCTTTTGGGGGATTTTCATTGTGATAGATTGTAATGAATTTAAATTGAATTTTCAGAGGTCTTGCTAGAGTGATTAGAAGCTTAGATGCCCTAGGAGACATTGTTAAATGTTTTGTTTTACAAAATGTCAATCATTCAGTGATTCTGTGATGGCTTCTCCTAGATAATTGCTAAGTAATACAGATGGCATAGGTGGTAAATAGAAAAGTACCAAAAATGTGTGGTAAAGAGAATCCCCCAGAATTCAGTCCCAAAGTGCTTTATCTTCCATTTACTTGGTAACAGCCACACACTTCTGCTCTGGCCTTTCCCAGAAATGTAAATGAAGAACATTTTATTGATGAGTCTTCTATTGTGTTTAAAATAAGAAATAGATTTATCAAAACTTCAGAAAGGCTCTCCCAGTTGAGGAATCTAACTCAGGAATACTGTCTGGAATAGATTTTCACAATTAAGCTCTGATCATATTTTTCAGTCCCCCTTTTTAAAGAAAAGAAGAAATACTGAAGGAATGCTGTTTTTGTGTGTTATTTTTGTTGTTGTTTGTTTTTAACATAAACTTGCTGGTGTTTATTTAGTTGAGTCCTTAAGCTTCAACTGAATAACAGTATTCTTTCCCTCTACTTA
Seq C2 exon
GGTGGAAAAGATCTCTTTTTGACTGAGGAACAGAAAAAGTACTATAATGCCCTAAAAAAACTCGGATCCAAGAAACCTCAAAAACCCATCCCAAGACCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000027702:ENSGALT00000042757:23
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=PD(15.9=76.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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]