MmuINT0139627 @ mm9
Intron Retention
Gene
ENSMUSG00000064329 | Scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:MGI Symbol;Acc:MGI:98246]
Coordinates
chr2:66108839-66115889:-
Coord C1 exon
chr2:66115619-66115889
Coord A exon
chr2:66112120-66115618
Coord C2 exon
chr2:66108839-66112119
Length
3499 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
GTTTAATTATCTTCCCACAGGGA
3' ss Score
9.35
Exon sequences
Seq C1 exon
AACAAATTTCAAGGAATGGTTTTTGACTTTGTAACCAGACAAGTGTTTGATATCAGCATCATGATCCTCATCTGTCTGAACATGGTGACCATGATGGTGGAAACGGATGACCAGAGCGATTATGTGACAAGCATTTTGTCACGCATCAACCTGGTGTTCATCGTCCTGTTCACCGGCGAGTGTGTGCTCAAGCTCATCTCGCTCCGCCATTATTATTTCACCATTGGATGGAACATTTTCGATTTTGTGGTGGTCATCCTCTCCATTGTAG
Seq A exon
GTAAGATCTGTGCAAAGTCTGGCAAATTCCTCCTGATAAAAGTGGAGGTTGAAAACAGGAATTTAGAGTGGAAGGCATCTCACTACTCAAAGTCAATATGTTGGCATGTGTTTTTGAGTTGTATTTGTTTTTCTTCCAAAATTAGGCTTCTAATTTATACAAATATTTTATCCCATTGCATCACATATTTATTTGACCATTAATAAGATCTCCTTTATTGAGATATATTAAATAGATTGATGTGGTGAACCAAAATTTAAAAAGTGCTTTTAGGTGGTTGAGATTAAACACTCTATACGCTATCCAGATCAATGATTCTCAATCTGTAGGTCGCAACACTTTGGGGATTGAATAGCCCTTTCATAGGGGTCACCTAAGACCATTAGAAATCATAGGTATTTGCATTAAGATTCATAGCAGTAGCAAAGTTACAATTATTAAGAAGCAACAAAATAACTTTATGATTGGTGGTCACCACAATATGAGAAACTGTATTAAAGGGTTGCAGCATTAGGAAGGTTTAGATCCACTGATCTAGATGATTCTGGTAAGAGGGGTACTGAGAATCTGGTCTGAAGGTCAGGAAAGACATTACATTAGAGATGTAGTTAATGGGGTCACCAGCATGCAGAGTAGAACATGGATAGAAGTAAATGGGAAATGCAAGTAGACTAACAGTAGTTTCTTGTGGCTTTCATACAGAAATTTTCAATATTTCCAGAAGGAAACTGGTAGCATGGAACATCTCTTTCTTAGTCCTATCCTACAAATTGTGTAGTACATAAGAGCCTCATGAAGGTAACTCATCTCACTGCAGATACCAACAATGCTTCAGAGAAGTGAAGAAGTCCCTGTATGGGAACTTCATTCCTAATTAAGATGAAATCATTGCAAATTTTCAAGCATAGGACTCAGTTGGAATGATCTGTGTGCTATTCCCCCCTCTGAATAAATAGGCCTTACATCTAAAATCCAACCCATATGTTATATGTAATTTTTAATTCCAACAATAATCATGTAAATAGCATCAAAAAGAGAGAGGCCGAAAGAGACAGAGATAGAGACTGAGATAGAGAAGGCTGACTAAAGAGAATGATGCTTTTGTGCTTTGCATACAATGATGCATTTGGGTATTTTGGTTGGTTGAATAGGTAGGTTTTTGTTGTTGTTATTGCTGTTGGCAGTGGTGGTGGTGATGGTGGTGGTGGTGATGATGGTGGTGGTGGTGATAGTGGTGGTGATGGTAGTGGTGGTGGTGGTGGTGGTGGTGTGTGTGTGTGTTTGTGTTGGAAGTACTCTTTAATGGAGTCTTTATTTAAAGGACAGAGGGGGGAGCTGAGAAATGCAGTGGCATCTAAAGCACTTAGTGTGCAAGCTTGAGAACGAGAGAACAGATTCCCAGCACCAGTGTAAATCCTGGCCAAGGGTGACACCTTATAAAGAAGGCTCTTGGAACCCCTCAAATTATCTGGCAAGCTACCAGAGAGCTCTGTGTTCAATTGAGAAGTCCTGAGCACAGAGACTGCAATGGAGGAGTTAGGGCAAGGACTGAAGGAGCTGAAGGGGTTTGCAACCCCACAGGAGGAACAACAATATCAACCAACCAGAGCTCCCAAAGCTCCCAGAGCTCCCAGGGCCTAAACCACCAACCAAAGAGTACACATGGAGCATGGCTCCAGCCACATATGTAGCAGAGGATGGCCTTGTCATTCATCAATGGAAAGGGAGGCCCTTGGTCCTGTGATGGCTCGATGACCCCGCAAAAGAAATGCTAGGGCCCTGAGGTGGGAGTTGATGGGATGGTGGGGGAACACCCTTATAGAGGCAGGGGGTTTGGGAGGGGAAAATGAGAAGGGGGATAACATTTGAAATGTAAATAAATAAAATAACCAATAAAAATTTTAAAAATTGAAAATAAATACATAAAGTAGAAAGCAATCAAAGAGACTCCCAGCATCAGCCTCAGGTAAGACACACACACACACACACACACACACACACACACACACACACACACACTCACGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCACATGCCACATGAACATACATGTGCCAAAAAACCCAAAATCACAGGGAGAAAAAAAGCTGTAAAAATTAAAAAATTGAGATTTTGCTACAGGAGAGGAAAAGAACATCAACCCTGGAGTGTTTTGCAAACACACAGGCACATGCACGGACAATTCTGTAATAATATTAGTTCATATGAGGATGAAAACAGCATGAAACACTCCAAGACTTCAGATTAGTGAAGTGTGAAAAAGAAAAGTTTGGTTCAACAAGTTTAGAGAAAAAACATCATATTCATATATTGTTGGCTGTTGACATTGAAGCAAATTTTCGTATTTATTTCTGATGAGATTTTAAGTTAACCATAGCATATCAATACTCTTCGGGCCAGGCGTGGTGGTACATGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCAGATTTCTGAGTTCTAGGCCAGCCTGGTCTAGACTGAGTTCCAGGACAGCTAGAGCTACACAGAAAAACCCTGTCTCGAAAAACCAAAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATGCTCTTGGGGGGGCGAGCTGTACTATGATTCTTAAATTTTAATCTATTGCTGAGGCTGAGTAAAAGCTAAAGTTAACTTTTATTATACATCGTATAATTCTATAAACACTCAGTTTTCCATATGTATGTATTAAATATCTGAAAATTCAAACACAGATCAAAAGTATTTTTAAGAACCATGCTCCTCTCCTGACCATTTTTAATATAATGAACGGTAGCAACTGTTCTGTTTTGGATTTTTTGTTTTTGTTTGTTTGTTTGTTTGTTTGTTTTCTTGTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTTTAATTTGGTTTGGTTTTTCAAGTCAGGGTTCCTCTATGTAGCCTTGGCTGTCCTGAAACTCGTTCTGTAGACCAGGCTACCATCACACTAACAGAGATCCCCTCCCTCTGCCTTTGAGTACTGGGATCCACCTCCACTCAGCCTTACTTGGTTTTTGTTGTTGTTGTTGTTGTTGTTGTTTAGTTAGGATTGGATTTCTGGAATATCACAGCAACTCTTCACATGGTACTTTCATTGTTAAATGTGATGAACATTTTAAATATAATTCAAAACTTTCAATAAAATGGTATAGACAAATTGTATGCAAATGTGCTGCCATATGATATAAAGGGCTTTCAGTCCTTGAATTTTGATGTTCTAAGGAGGAGAGGTGCATCCTGGGACAAATCAGCTGCAGATACTGGAAAATGATTGGAATATATTTGTACCATACCCAAGATTACAAAATTGAATCTTAATACTCTGAAATTGACATTGGAACTTTAATAACTCAAATATTTTAATAAATGATTAGTTGATGACTTCTTCACTGATTGATAGTTTAATTATCTTCCCACAG
Seq C2 exon
GGATGTTTCTTGCGGAGCTAATAGAAAAGTATTTTGTGTCTCCTACCCTGTTCCGAGTCATCCGCCTGGCCAGGATTGGACGAATCCTACGCCTGATCAAAGGTGCCAAGGGGATCCGCACGCTGCTCTTTGCTCTGATGATGTCCCTTCCTGCGCTGTTTAACATCGGCCTCCTGCTTTTTCTCGTCATGTTCATCTACGCCATCTTTGGGATGTCCAACTTTGCCTATGTTAAGAGGGAAGTTGGGATTGATGACATGTTCAACTTTGAGACCTTCGGCAACAGCATGATCTGCCTGTTCCAAATCACCACCTCTGCGGGCTGGGATGGACTGCTGGCCCCCATCCTCAACAGCAAACCCCCTGACTGTGACCCTAATAAAGTTAACCCTGGAAGCTCGGTGAAGGGAGACTGTGGGAACCCATCTGTGGGGATTTTCTTTTTTGTCAGCTACATCATCATATCCTTCCTGGTTGTGGTGAACATGTACATTGCTGTCATCCTGGAGAACTTCAGCGTTGCCACAGAAGAAAGTGCAGAGCCTCTGAGTGAGGACGACTTTGAGATGTTCTACGAGGTCTGGGAGAAGTTCGACCCTGACGCCACCCAGTTCATGGAATTTGAAAAATTATCTCAGTTTGCAGCTGCTCTAGAACCCCCTCTCAATTTGCCACAACCAAACAAACTTCAGCTCATTGCCATGGACCTGCCCATGGTGAGTGGAGACCGCATCCACTGCCTGGACATCTTATTTGCTTTTACAAAGCGGGTGTTGGGTGAGAGTGGAGAGATGGATGCTCTTCGAATCCAGATGGAAGAGCGGTTCATGGCTTCCAACCCCTCCAAGGTCTCTTATCAGCCCATCACTACTACATTAAAACGCAAACAAGAGGAGGTGTCAGCTGTTATCATTCAGCGAGCTTATAGGCGCCACCTTTTGAAGCGAACAGTAAAACAAGCTTCATTCACATACAATAAGAACAAACTCAAAGGTGGGGCTAATCTTCTTGTAAAAGAAGACATGCTCATTGACAGAATAAACGAAAACTCTATTACGGAGAAAACTGACCTGACAATGTCCACAGCAGCTTGTCCGCCCTCCTACGATCGGGTGACAAAGCCAATCGTGGAGAAACACGAGCAGGAAGGGAAGGATGAAAAAGCCAAAGGGAAATGAACAAAAACAACAAAAAAAAATAATAAATTGGGTGACAAATTGTTTACAGCCTGTGAAGTCAAAAGGACTCCTTTAAGAAGTCAATGCCAAACTGACTGTTTTTACACAAATTCACTTTAAGGTCAGTGCCTCAATAAGACAGTGACCCCCTTGTCGGCAAACTCTGTGACTGTGTAAAGGGGAGATAACCTTGACAGGAGGGTACTGTTCTAACTACCAGCTGACACTGCTGAAGACAAGAGACAAATGGCTATGCAGACTGTAGGGATCAGTCTAAAGGGGTGCAGAGCTATAATTTGGGGGTTAATGTGAAACACTTTAGTGTAGTAACTCTATCCACCGTTTGCATTTCAACTGCCACATTTGTCAGGTTTTTTACAAACTCTGTTAGTGGATTCATCTTTTTTTTAATCCATGTGTTGTTTGTTACATGTGACTATTTTTGTAAGCAGGGTTTCTGTTGGGAAATAGACTAAAGGAACTCTTTTCCCGGTGTGTCACCTGGGAGTGTTGACATCCTTATGGCCCTCCCGTCTGCACAACGGTGTGGTTTCGCATGAGGGCATGTTGCACCTTAGGATCATGCATGAGAAAAAGTCGAAAGGAAAGCAAAGACAGTTCTTCAACAGTTCTATGTCATCTGTGTTTCTGCGGGGGGAGGGGGCGGTACGGAGGTGATCGCTAGATCGTGGGCTTTGCTGAGCTGGGTTTGTCAAAATCTAGTCCTTAGTCCAAGGAGATTGTTCAGACAGGTCATCAAGTCTTAGGAGGTGCAAACTTCATTCAAATGTCTGGAGTCACGCTACATTTCTGTTCACTGTCTCTGAAAGGTCTCTAAATTATGACTCTGACTCCCTACCCCCAACCCTAGCAGAGCGAATTGACCAAAAGAACCCTTTATAAATCCCCGCTTCCTCCTGCACTTTGTTTAGCCATCTTCAGCTCTCAGCAAGGTTGACACTGTATGTGTTAATGAAATGCTATTTATTATGTAAATAGTCATTTTACTCTGTGGTGCACGTTTGAGCAAACAAATAATGACGTAAGCACAGTATTTATTGCATCAAATATGTACCACGAGAAATGTAGAGTGCAAGCTGTCCACCGGAAATATACTGTACTCTGTACCATTGTAGATAGTGTGGATGCTGCCAATGCATGTCGATATTACCACGTTGCGGTATCTAGTTTCTCTCAGCACTCAGAATCTCACTCACGAGAAACCATAGGTCAGTGGCTAAGTCAAGGAAACTGTTCAGCAGACTTCATTTCTTTAAGTCATTAAGCAATAGTTTGCAGCACTTTAACAATGTTTGGGTTGTTTTTAAAATTTAAGTGGATAACGTTCAATGTATAGCCAGACTGTACATACGTGTTCAAAAGACAACACTACTGCTTAACCTGTTAAAAACATGTTTAGAGTTTTATAAGCAAATATAAATACTGTACAAAGTCACTTTCTTTTACTTTTCAGCATTATGTACATATGAAGAGGAAATTATCTTCAGGTTGATATCACAATCACTTTTCTTACTTTCTGTCCACAGCAGTTTTTCATGGAAGATATTTGCTAACTAAGAAATGAAACTATGACTGGGTAGTGGTAGATCTCTGCTTTTTTATTACAATTGTTAATTTTGGATTATTTCATAATTTTAAGGGGCAAAATACACTCACAACTTCACATCCAAATTATGATTTGCAATTGGAAAAGGTATAACATTTGATTTATATTTATTGTAGTGTTTGTGCTAACAGATGACCAGAGTGCTTTTTTTTCTCATTTTTTTCTTTATTTCCCCAATTTCTGTTTATTTTTCTTTGCTTTGAAATCATGCTTCTTTAGATTGTTCTAAATATAAATGTGGGCTTCAGAATTTCTTTTCCTCAAAATCAGAGAGGATTACACTTATATAGTCAATTACATCAAGATATTTGTGTTTCTTACAGAAGCAGACCGTAGGCACCTCTTTTTCTTAAAAAAAAAATATTTAGGCAAACCGTATTCATGAACTGCATGTTGGAAAATGCTACTATTAGCCCAAAATGATGCTAATCACAATTAAAAAATGTGCAAATCTAATAAAATTAATTTTTTATTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064329-Scn1a:NM_018733:26
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.122
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=42.5),PF0061222=IQ=WD(100=5.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: