MmuINT0108509 @ mm10
Intron Retention
Gene
ENSMUSG00000021806 | Nid2
Description
nidogen 2 [Source:MGI Symbol;Acc:MGI:1298229]
Coordinates
chr14:19797164-19798645:+
Coord C1 exon
chr14:19797164-19797283
Coord A exon
chr14:19797284-19798396
Coord C2 exon
chr14:19798397-19798645
Length
1113 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
CTCCTTTATGTCTCCCTCAGACA
3' ss Score
9.23
Exon sequences
Seq C1 exon
ATGTTGATGAATGTGCGGAAAACCGATGTCATGAGGCAGCTATCTGCTACAATACCCCCGGGTCCTTCTCCTGCCGTTGCCAGCCTGGGTATCGAGGGGACGGGTTTCACTGCACCTCTG
Seq A exon
GTAAGTGATGGAAGACCTGAGTAAACTCGGGAATCTCCCAGCTCCTTCCCTCCTATTTTCCTCCCTGCCCAAGATGGAACCTGGACTGAGGCCTGATGGGGGGCACTTTCCAGGCTCTGGATTCTTCTCAGTAGACTCCTGATGTCCACTGACCGCTAGCTGGTTGTGAGCTTCTTGGAGTCTCACCCACCCTGTGGCTGCTCTGGTTCACTACCCGAGTGATGTGCTTTGCTGGGTGTTGTTTGGGGACCCATTGAGGGGAAGCTTATTCAGTAGGAGCCTCATGCACTGGTGAGCCCAAGTCAGCACTCGTGGTGACTGCTTTCATGGGCCTTGGCCAACATACAGCAACATGGCTGCTACTGACCTGGGCTGCTTAGACTTAAGACTCTGGGTCCCAAAGAGTGGATGGAGTTAACTTGTCCTCTCCAGAGTCTCCCAGAACGCCAGGCAGTTTATTCTTCATTTTGCCCAGATATCAGCTGGCCCCAAGGCTGAGGAACAAACTGGACTAGCTTACATTTGTATTTATGTAGGGATGTACGGGGCAAATGGAGGGAATTCATAGTAACTAGGTAGTTGGTAGCAAAGCCCGAATAAGAACTCAGGACTCTAAAATGTGAGTGTCAGGCTGGCGAGATGGCTCAGTGGTTAAGAGACTGAGCTCTTCTGAAGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCACCCTTAATAAGCTCTGACTCCCTCTTCTGGTGCATCTGAAGTCAGTTACAGTGTATTTATGTATAATAATAAATAAATCTTTGGGGTGCAGCAAGTAGGGACTGAACGAGTGGAGTTGACTGGATAGAGCGAGGCTGACAGGAGCGAGCAGAGGTCCTAAAAATTCAATTCCTAACAACCACATGAAGGCTCACAACCATCTGTACAGCTTCATTGTACTCACATACATAAAATAAATAAAGAAATCTTTAAAATGTTAGTGTCTTACTGTTTTTCAATGTCATAGTAACTTTCGATTGTATGGAAGAAACACTCAGTACAGAAGACTTTATGGGGGCCTGGTTAGTGTGGATGGGTTGCAGGACCTTTTATTTCTCCTTTATGTCTCCCTCAG
Seq C2 exon
ACACGGTTCCGGAAGATTCCATCTCAGGACTGAAGCCCTGTGAATACCAGCAGCGCTATGCTCAGACACAGCACGCCTACCCTGGGTCACGGATCCACATCCCCCAGTGTGATGACCAGGGAAACTTCGTGCCACTGCAGTGCCACGGCAGCACTGGCTTCTGCTGGTGTGTGGACCGAAATGGCCACGAAGTCCCTGGCACGCAGACTCCACCCGGCTCCACCCCGCCCCACTGTGGACCACCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021806:ENSMUST00000022340:12
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=0.226
Domain overlap (PFAM):
C1:
PF0764510=EGF_CA=WD(100=92.7)
A:
NA
C2:
PF0008613=Thyroglobulin_1=WD(100=78.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGCGGAAAACCGATGTCAT
R:
GAGGTGGTCCACAGTGGGG
Band lengths:
355-1468
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