MmuINT0139644 @ mm10
Intron Retention
Gene
ENSMUSG00000075318 | Scn2a
Description
sodium channel, voltage-gated, type II, alpha [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65711707-65713841:+
Coord C1 exon
chr2:65711707-65711945
Coord A exon
chr2:65711946-65713667
Coord C2 exon
chr2:65713668-65713841
Length
1722 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
TAACTACATTGCTCATATAGGTC
3' ss Score
7.2
Exon sequences
Seq C1 exon
AACTTGAAGAATCCAGACAGAAATGCCCTCCATGCTGGTATAAATTTGCTAATATGTGCCTGATTTGGGACTGTTGTAAGCCATGGCTAAAGGTAAAACATGTTGTCAATCTGGTAGTGATGGATCCATTCGTTGACCTGGCCATCACCATCTGCATTGTGTTAAATACACTCTTCATGGCCATGGAGCACTACCCGATGACGGAGCAGTTCAGCAGTGTGCTGTCTGTTGGGAATTTG
Seq A exon
GTAAGACTCCTTGATGGTTCATCTTTCTACAGATTGCTTTTATTAATTTTATGTGTCACTGTCAAATAAGTTAACAGTTAATTGACTTTGTTCACCAAAGACACGAAAACATTTTTGCATGGGTTTTAAAGAATAAAAACAGGTTCCTACTTGAACTCAGTACAAAGGATTCAGAGGTTTTATGTGTAATTTGATTTAAAAGTGAATCTAAATCATTTCTTTATTGTAATGATAATTGCAATCAGGCATAATGACACATACCTGTGATCTCAGCAGTTGGGAGACAAAGGCAGGAAGATCACAAATTCTAGGCCATCTCTGCTACATAGAGAGATCCTGCCTCACTCAAAGCAAACAGAGAAAGAAACAAAAGAAAAATTAGGGCCATGAGATGGCTCCCCAAGAAGGAGCTTTCAGCAAGCCTAATGACCTAAATTGGACACTTGACCCCAAAAGCTGGAAGAGAACCAACTTCTGTAAGTTATCCATTGACCTTCACAAACATACCATTTAACACATGTGCTCCCACATACACACAAGACAAATAAATAAAACAAGATTAATAAATAAGACAAAATCTAAAAACAAGATTATGCTAGGAATAGTGGGAAAATAAGTATGTAACATATATACATATATATGCATACATATTACATTTATACATATATATAATATGAAAGGCTAATTAAGTTCTCATGTGCCTTATAACAAATATATTAAAGCATAATATACTTCTTAGACTTGAACACACACACATATATATGGTATTCATAGTATAGTATGTATATAGTATTTTATACTTTTTATTCTTTATTATGTCCTAATGACACGCTTGACATATTTCACAAATTATATATATATGTATATATCTGAGGACTCTCAAGTGAGTCAAATGATAAAGTATGTACAGTGAACACATTTCATATCAAGTTCTGAATTAAATATTATATACACTCCATCCTTTTCTGTCCTTCCTTCCCCAACTTTCTCAATGGACACCATTTTGATTTAACAGTTCACTTGAGAAAAAAGATATTGTGGAACAGCAAGTGTAGAATAAGAAGTGTTCCTGAAGAAACCTTGATCAATGTTTTCTGCCCTATTGGGTACATACCTTTTTGTAGCTTGAGGAAAGAAAATTTCACACAGAAACAACCTGTTTGACTTGTAATTGTCCCTTGCCTTAAACTCGAATTGGTCTTCTTTGGATTATTGGTATGTCTTTAAGAAAAATTATAATCAAAGATGATTTCTTTTAGCAAATCTAAGTTTTTGATTGGTTTATTCGACTACTACAGTTGGATGAGACACAGTAGCTTGGTTATCCCTATGTTTATTATAGTTTGCGTCAAGCCGCCTTAGCTCCAGTTCTTCTGCAGAGCTATGAAGAGACCAACCTATTCTACGTGGCAACTGAAGTCTGTGCTTCTGGGCAAACACTTGGTGAAGCTTTAGAGAACTAGAGAGAGCAAGCACAGTAGAGAGCAGTGTGTCCAGTGCAACTTTGTCGCAAAATCAGGGAGTTCATTTCATTACCTGAATAATAAACCTTAAGTATTATGAACAGTTATATAATGTGTTAAATATAAAACATGCAAGGACATCCATTGTTTGAACACAAACCAACCTTTAAGATTCAGAATTTATGTTTGATCTACTGTTCGTTACATTGCTTCGTTTTGAGAGCAGGTACTCCTGTAATTAACTACATTGCTCATATAG
Seq C2 exon
GTCTTCACTGGGATCTTCACCGCAGAAATGTTTCTCAAGATAATAGCCATGGATCCATATTATTACTTTCAAGAAGGCTGGAATATCTTTGATGGCTTTATAGTGAGCCTTAGTTTAATGGAACTCGGCTTGGCGAATGTGGAAGGACTGTCAGTTCTCCGATCTTTCCGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318:ENSMUST00000028377:14
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=PU(1.6=3.8)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.0=100)
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:
ACAGAAATGCCCTCCATGCTG
R:
CGCCAAGCCGAGTTCCATTAA
Band lengths:
358-2080
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types