MmuINT1024280 @ mm10
Intron Retention
Gene
ENSMUSG00000021806 | Nid2
Description
nidogen 2 [Source:MGI Symbol;Acc:MGI:1298229]
Coordinates
chr14:19807927-19810103:+
Coord C1 exon
chr14:19807927-19808084
Coord A exon
chr14:19808085-19809979
Coord C2 exon
chr14:19809980-19810103
Length
1895 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
CTTCTTGGGTGTCTTAAAAGGAA
3' ss Score
6.27
Exon sequences
Seq C1 exon
CAACTTGTACTGGACAGACTGGAATAGAGAAGCTCCTAAAATTGAAACATCATCTTTAGATGGCGAAAACAGAAGGATTCTGATCAACAAAGATATTGGATTACCCAATGGATTGACCTTTGACCCCTTCTCCAAACTGCTCTGCTGGGCAGATGCAG
Seq A exon
GTAATACTGGATGTGGAGAAAGGTATGCTTCCCTTACAGCTAGCAGTGTGAGCACTATGGGAACAGCACTACAAACCAAATCCTGCCCATCTTTATATCCTTTCGTTTAAATTTCAGTCAGCACAGAATATACCAGATCTGTAAGCTTTAAAAGAACCTTTTACAGTGATTCTTACAGTAAATTTTCTGGGGCTTAGGGAGGAGGCTGGACTGTGTAGCATGTCTGTCCTGACCCCTGACCCCACTGTGTAGCATGTCTGTCCTGACCCCTGACCCCACTGTGTAGCATGTCTGTCCTGACCCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCTCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCGTGTCTGTCCTGCACCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCGTGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGACCCCTGACCCCACTGTGTAGCATGTCTGTCCTGACCCCTGACCCCACTGTGTAGCATGTCTGTCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCGTGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGCCCCCTGACCCCACTGTGTAGCATGTCTGTCCTGACCCCTGACCCCACTGTGTAGCATGTCTGTCCTGACCCCTGACCCCACTGTGTAGCATGTCTGTCCTGACCCCACTGTGTAGCATGTCTGTCCTGACCCCACTGAACACCTGGAAACTTTGAAGTCTGACGTACTGGCCGCTGCTGCCACTTGGCTGAGCTGAGGTTAGTCTCCCTTCTGGGCCATTGTTATCACTTGGTGTGCTGCGATCCTTTGACAAATGCTGAGAGAGGATGTCCTCCCTCAGGATTGCCTTTGCTTAACCCCAGGATTATCTATTCTGTGGTGTGCTTTGCATTACCGAAAACCCTTAAAGACACTGTGTATGAGTGTGTGTGTGTGTGTGTGTGTGTCTCTCTCTCTCTCATTCTACTAAAGAAAGGAAGTTCTCAAACTTACAAAATATGTAGCTGGGCGTTTTTCACAATCCAGTCGTCAGAATATTACATTTTTAAAAGGTATATGAAATTCAGTCTTCATAAGAAATATGAAATTTGAAAATTCTTGAATTCTATAGGATTTTTTTTTCAAAAATTCAAAGGATTACCATGTAAAAATAACCACTACCATTATCTTTTTCTTATACCTAGAATTTATAAATATATATATTGGCCAATCTGGATGTTATGTTTTCAACTTAGAAATTTAGACTTAAAATTATAAAAATTCTTATCTTTAATGACCCCCCTTGGAAAGACACTGCCAGATTTCAATATATTAGATTCTTCCACAAAAAAGATTGAAGTTTGATTCTCAAAACTAGAGTTCTGCTGTACCAGGTGGAGAGGAATCGTAGGCCAGGATTTACAGATGCTAATGTGGACTGCAATGGGCTTAAAATGCCACATGTTGAAATTCTGCCTCTATTCCCTGGAGAAGGACCTGGCAGCTCATTTTTACCAGTGGTTTGCTCAGGGCATGAAGGGAACTCATTTTCCTTCTTGGGTGTCTTAAAAG
Seq C2 exon
GAACCAAAAAACTGGAGTGTACACTACCCGATGGAACTGGACGACGTGTCATCCAAAACCACCTCAATTACCCCTTCAGCATCGTCAGCTATGCAGATCACTTCTACCACACGGACTGGCGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021806:ENSMUST00000022340:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=WD(100=79.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAACTTGTACTGGACAGACTGGA
R:
GCCAGTCCGTGTGGTAGAAGT
Band lengths:
278-2173
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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