MmuINT0107214 @ mm9
Intron Retention
Gene
ENSMUSG00000026950 | Neb
Description
nebulin [Source:MGI Symbol;Acc:MGI:97292]
Coordinates
chr2:52013352-52015089:-
Coord C1 exon
chr2:52014997-52015089
Coord A exon
chr2:52013445-52014996
Coord C2 exon
chr2:52013352-52013444
Length
1552 bp
Sequences
Splice sites
5' ss Seq
TCGGTACTG
5' ss Score
4.52
3' ss Seq
GTATTCTAATTATTCTGCAGGTT
3' ss Score
9.03
Exon sequences
Seq C1 exon
GTCAAGTATAAAGAAGCAATCGGACAAGGAACTCCGATCCCTGACCTGCCCGAAGTGAAACGCGTCAAGGAGACCCAGAAGCACATTAGCTCG
Seq A exon
GTACTGACTCTTACTTGGCATGCATTTGTAAGACCCTCTCAATCGGCACCCTAGTTTCATCCACCCCTTCCTTCTGCTAAAGGCCCCCCCAATACCTGGGGATGCTGTGACTCCTCCCTTGTCCCCCTCAGGTTGCCAGGAGACCTCAGTCTAGCAGTAGCTCACTCCCTAGTACTCCTTGTTATACTCGAACTTCTCCGTTGCCAACTTCCTTTTGAATTCTCTGTCCACTAACCTGAAGAAAACAAAACAAGCCCAGGGGTTCTGTGTTGCATTGGGTTGCAGTAATTTCTGTAATTTTGTTTGATCCAGGTGCTCCACTTGCCTCAGCCACCATGTGCATTCATGGTGTGTACCACCAAGCCAGGCTTAGGTTGAAACTTATTAAGGAAGGAAAGAAGGGAGGGAGGCAGGGAGGGAGGGAGGAAGGAAGGGAGGGAGGGAGGGAGGGAGGGAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAAGGAGAGAGAGACAAGAGATTTAGAAAGTGGGGATCACTTACTGTGTTTTTTTGTTTTGTTTTGTTTTGTTTTAATGTCTATTGATGATAGCCCTAAGAGGAAACATAGATTTAGGGCAGGGACAGAGGACACTGTTCAGTGATGGAGCACATGCCTACCATGCACTCAGGCCCTGAGTTTGGTCCCAACAGTGCAAATAAAACATAAAAATACACACAGGGAAAAAAAGACCAGGCAACAAGCACTGGCTTCCTTGATCCTGTAATCATTCAGACAGAGACGCTCTTCCTGGAAGGCAAAGTCTGTCAGCTCGTATGAGATGTCCAGCTAGGGATCAGCTGAGGCTCAGTAGAGCTGGGAGCGGTGATGCGAGCCTGTGGTCCCAGCACTCAGCAGGCTGAATCAGGATTTCTGGGAGGTTAACACTAGTCAGGGCTAAGTAGCATAAGAGCCTGTCCCAAAAATAGAGGGAGAAATAAAAGGTAAAACGGTAAGAATTGTATTAGGAAATACATAAAATTCTCAATGACTCTGAAGAAGTGAGAACTAGAACACCACATGGTTAGAAAATTCTAAAATAGACATGTGCTTTGAGTACAAATATGTAGGCATAGTTATGCTCCAGGCACTAGCCTGGGTGCAGTAAAATGGTTACTTTGGATTTGGTTTGCTTTTATTTTTGTTTTTTTTGGTTTGGGTTTTTTTTTTTTTTTGATGGGGTGGTTACTGGAAACTGAACCCAAGGCTTTGCACGTGCCAGTCAAAAGGGTTCTCATTGTTTATTAAACTTATTATCGTCATTTAAAGCATTTTAAGAAGATACTAAGTATTGGCTGTGGAAAATGCAAAATTGAGTTTCTAGTTTTCTAGTGGGCAAAATTTCTACAAATATTTATGGACTTCTTTTCCTCTGTCCCTGAGTTCATCTTGCAAAGGCAGCTTGCTTTTATGGGCGCTCAGCAAAGCTCCCTCCCGGAGCTATAATCTGAACCATTTGTGGTGACTCTGCTTTCTGGGTATTCTAATTATTCTGCAG
Seq C2 exon
GTTATGTACAAAGAAAACCCGGGAACAGGCATCCCGACCACTGTCACTCCAGAGATTGAGAGAGTCAAACGCAACCAAGAGAACTTTAGCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026950-Neb:NM_010889:145
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.859 A=NA C2=0.855
Domain overlap (PFAM):
C1:
PF0088013=Nebulin=PD(30.8=25.8),PF0088013=Nebulin=PU(66.7=51.6)
A:
NA
C2:
PF0088013=Nebulin=PD(25.0=19.4),PF0088013=Nebulin=PU(57.1=51.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTATAAAGAAGCAATCGGACAAGGA
R:
CGAGCTAAAGTTCTCTTGGTTGC
Band lengths:
182-1734
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: