MmuINT0009479 @ mm10
Intron Retention
Gene
ENSMUSG00000030607 | Acan
Description
aggrecan [Source:MGI Symbol;Acc:MGI:99602]
Coordinates
chr7:79111294-79112037:+
Coord C1 exon
chr7:79111294-79111452
Coord A exon
chr7:79111453-79111954
Coord C2 exon
chr7:79111955-79112037
Length
502 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
AGCCTATCTTCCCATTCCAGAAA
3' ss Score
7.99
Exon sequences
Seq C1 exon
ACCAGGAGCAATGTGAGGAGGGGTGGACTAAGTTCCAGGGTCACTGTTACCGCCACTTTCATGACCGAGAGACCTGGGTGGATGCGGAGAGACGGTGTCGGGAGCAGCAGTCACATCTGAGCAGCATTGTCACTCCTGAGGAACAGGAGTTCGTCAACA
Seq A exon
GTGAGTGTGGGCAGGGGCTGAGGGACAGGACACAGCAGTGAGAGAAAAGAGCCTTGCTGGTCAGAAATGAGCAGTCTTGAGTTCAGGGTTGTAGCTCAGTGGGCAGAGTGTGCCTTGTGTGTACAAGGTCCAGCATGGCAGAAAGGGAGGGAGGGAGACAGAGACAGAGAAAGAGGGTACAGGTTGGGTACACTGCAGGACAGGGAGCTAGAGGAAGGTCAAACGGTCCCACATTTTCTTCAGAGAAGACACAGGTCACAGCAGACCCAGGGCAGACCTTGCCAGTCAGAGCCATCCCAGGTTAAGCCTGTAGCTGTCTCCTGCCTGTATCAGCCTGAGGAGGTGTTCCAGCATATACCACAAGCATGCATGTCCTGAGACCCTTGCAAGGTCCTTAGAAGCCAGTGGCATCCACTTGCCCCCTTCCTCCCTCTCCATGAGTTCCAGCCCCCAGACAGTGCAGGGTACCCAACATAAGTGCAAGCCTATCTTCCCATTCCAG
Seq C2 exon
AAAATGCTCAAGACTACCAGTGGATCGGTCTGAATGACAGGACTATCGAAGGGGACTTCCGCTGGTCTGACGGACACTCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030607:ENSMUST00000032835:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005916=Lectin_C=PU(30.2=59.3)
A:
NA
C2:
PF0005916=Lectin_C=FE(25.5=100)
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:
ACCAGGAGCAATGTGAGGAGG
R:
AGAGAGTGTCCGTCAGACCAG
Band lengths:
241-743
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