MmuINT0108513 @ mm9
Intron Retention
Gene
ENSMUSG00000021806 | Nid2
Description
nidogen 2 [Source:MGI Symbol;Acc:MGI:1298229]
Coordinates
chr14:20624520-20625236:+
Coord C1 exon
chr14:20624520-20624649
Coord A exon
chr14:20624650-20625064
Coord C2 exon
chr14:20625065-20625236
Length
415 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
TGTCTTACTTTTATTTCCAGGTT
3' ss Score
10.09
Exon sequences
Seq C1 exon
GGCTCCATAGTTGTGGGGATTGACTATGACTGCCGGGAGAGGATGGTCTACTGGACAGACGTTGCTGGTCGGACCATCAGCCGTGCCAGCTTGGAGGCAGGAGCCGAACCCGAGACCATCATTACCTCAG
Seq A exon
GTCAGCAGCTCCTCCCATGGATACTTGGCGGTACCTTGTGTGTTGCTTCCGTTGGCCTGTTTGGTCCCAGTTTCTCCCACGCTCATCTAAAGGGAAGGTTAAGTTCTCTGCTGGTGACTTTAGAAAGGTGGTTTAGGATAGGATGAATGAACTGCCACTCCAAGAGTGGTTCGCAGTGAGACTGCAGGGTCTGGCAGTTTAGATTGCCTGTCCCTAGCACCACGGATGCCAGGTGCCATCAGGGCAGCAAGGTCCAGCACAGAAGAGACTGGATATGGTTTAAAAAGTTAGCCTTCGTCCTGGGGCTTAAGGCTTTTCTGTTCTATGCTCTGGATTCTGTAAGCTGCTCAGCAGACGGGGAACTTGATTTCGCCTTCTACACCAGCCAATGCTCCTGTCTTACTTTTATTTCCAG
Seq C2 exon
GTTTGATAAGCCCGGAAGGACTTGCCATCGACCACTTCCGTAGAACAATGTACTGGACAGATAGTGGCCTGGATAAGATAGAGCGGGCCGAACTGGATGGTTCCGAGCGGAAAGTCCTCTTCCACACAGATCTGGTGAATCCACGAGCCATCACTGTGGATCCAATCCGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021806-Nid2:NM_008695:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PU(71.4=68.2)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(26.2=19.0),PF0005812=Ldl_recept_b=WD(100=70.7),PF0005812=Ldl_recept_b=PU(0.1=0.0)
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:
GGCTCCATAGTTGTGGGGATTG
R:
TTGGATCCACAGTGATGGCTC
Band lengths:
295-710
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: