MmuINT0108514 @ mm10
Intron Retention
Gene
ENSMUSG00000021806 | Nid2
Description
nidogen 2 [Source:MGI Symbol;Acc:MGI:1298229]
Coordinates
chr14:19805843-19808084:+
Coord C1 exon
chr14:19805843-19806014
Coord A exon
chr14:19806015-19807926
Coord C2 exon
chr14:19807927-19808084
Length
1912 bp
Sequences
Splice sites
5' ss Seq
AGGGTTAGC
5' ss Score
1.46
3' ss Seq
ATCTTAAAATTTATCCACAGCAA
3' ss Score
6.88
Exon sequences
Seq C1 exon
GTTTGATAAGCCCGGAAGGACTTGCCATCGACCACTTCCGTAGAACAATGTACTGGACAGATAGTGGCCTGGATAAGATAGAGCGGGCCGAACTGGATGGTTCCGAGCGGAAAGTCCTCTTCCACACAGATCTGGTGAATCCACGAGCCATCACTGTGGATCCAATCCGAGG
Seq A exon
GTTAGCTGGCTTTCTTTGGTCTCTCATGCAGATCTGTTTTGGAGACCCTGGCTCTTATATATGTCATGGGAAGGTCTAGATAGACCAGAATAAAAACTCAAATACAGTAATTCACCAGATATGTAGACCCGCTGCTGGGTGTCAAGCATTCTTGTAGGCAAAAATCAGGGGTTTTTTTTGTTTTTTGTTTTGAGCTTGCATGCATTGTACAAGGCATTCGGAAGTAAGATGACATTCAGTAAAGATGTTAGTTAGTCTGGGATGGGATGTGTCACACGGAGAAGCCAGACCCCATCATGGAGAATCCAGAGGATGCCTGGGTCAGACGATCATTAGGCAGGGCCTTGGAAAAGGATGGGTCTGCAGAGGGAGTTGTTTCCTTCAGCCGTTCCCTGAGCAGAAACACCACAGCAGGGTTTTTGGGTTTTTTTTTGTTTCTGTTTTTTTCTGGATGGAGAGTGTACAACGTCAAGATAAAAATGTTCTCTCTGTGGCAGTGCCAAGGCCGTCAACTGGGGTATCCAGGCCTGGGTCAGAGGTCCCAGGATTACTGAGCTGCAGCGTCCACAAACACAGTTACAGAGAAACCCTTCAAGGTGTGAAGGTTCTTCCTGAAAGTTCTACACAGGAAGGTTCCTTATCTGCGGGACTTAATTAACCCTTGAGGCTCCTCTTTGATGGTCCCTGGTACTTAGTCTGACCGGTCAGGGACTGAACAATGGCACCTTGTTCGGTCATTAGGCTCCAAGATCTAGAGTCTAGAGGACAATGTCACAGCAGTGTGCATGCATGTAATGTGAGCCCCTCCTCGCAGCTCCAAGGAGACTGCTCACTGTGTGGTTCTCGGCCTGCCACAAGTAGAAACTGCTCTCTGGCTCTCACTGCCACCCACAAGGAGTGACTGCCACACAGAGGAAACTGTTTCTCTCCCTCTTGCTAGGGCTCCCTGTGGTTCAACCAAAAGATATCTATGGCTTTCATGGAAGTGCCACTGTTTCTGCTCTGTAACCCTGTTTCCATATGCATAACTCATCTCCAACTAATGAGATCCTACTTTCTGAGTATTTTGTATGTTAGGTCAGAGTCTGTCTGTCCAGGTCATTGCCAGGTGTAGGATAGCTAAGTTTCCCTTCCAACACTTAGTGTTGTCCCAGGAAACTCTCCCTTGATCCCACTGAGTTTCTTATAACAGGTCCCATAGCTTCTACCACAGATTTTTTTCTAACAAATACATTTCTTTGGATTCTAGGCCCAAGATCTAATTCAAGATTTCAACAAATTAAGGGTTTCTGGGCAAATGCATCGGGTTTGTGAGAGGCAAGGATCTAGACAGTTAATAGATAATGACTTCCCACAGAGTTACGATTGTCAGAAAGCCATGGCAGCCTAAGGCAACATTATTAACTGTGAGTGAGGTATCTGGGTGAGGTAATGTCAAAAAGCGACAGCCAAAGGTACTAGCCAGGCAAGGCCAGCATGATCCAGACTTTCTTGGAAAGGTCCCTTTCCAAACTCTTGTGGACTGCTGGCAGGCCCCAGGCTATTGTTGGCCATTGGGCAAGAGGTAGCTTGCTGTATAAAATCCAACTTCCCCTGGGGAGCAAGAAAAGGCACTGGACAGAAGCCAATTTAAAAAAACAAAACAAACAAACAAATAGTGAAAGTGATTTTATGACTTCTACCGTACCATTCACCAGGAGCAAGACACTAAACTCAGCCAAATTCAAGGGAATTAAGGCCGAGAATACCAGGAGGAGACAATCAGCCAGTGGTGGCCAGTGTGGCTGATGCACAGGGTGTGAGGCAGGGAGCGATGCTGAAGGTTATACATTCGAAACAAGAGCCCTACTACTAAGCTATATGCCACAACCCCTGCACAGTTGTTCATAACAATCTTAAAATTTATCCACAG
Seq C2 exon
CAACTTGTACTGGACAGACTGGAATAGAGAAGCTCCTAAAATTGAAACATCATCTTTAGATGGCGAAAACAGAAGGATTCTGATCAACAAAGATATTGGATTACCCAATGGATTGACCTTTGACCCCTTCTCCAAACTGCTCTGCTGGGCAGATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021806:ENSMUST00000022340:17
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=0.019
Domain overlap (PFAM):
C1:
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)
A:
NA
C2:
PF0005812=Ldl_recept_b=WD(100=79.6)
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:
CGGAAGGACTTGCCATCGAC
R:
TGCCCAGCAGAGCAGTTTG
Band lengths:
311-2223
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