MmuINT0009482 @ mm10
Intron Retention
Gene
ENSMUSG00000030607 | Acan
Description
aggrecan [Source:MGI Symbol;Acc:MGI:99602]
Coordinates
chr7:79113655-79115099:+
Coord C1 exon
chr7:79113655-79113837
Coord A exon
chr7:79113838-79114199
Coord C2 exon
chr7:79114200-79115099
Length
362 bp
Sequences
Splice sites
5' ss Seq
ACCGTGAGC
5' ss Score
4.78
3' ss Seq
ACCTCCCTTTCTCGCTGCAGCCA
3' ss Score
9.85
Exon sequences
Seq C1 exon
TGGCCTGTGGAGACCCCCCAGTGGTGGAGCATGCTAGAACCCTCGGGCAGAAGAAAGATCGCTACGAGATCAGCTCCCTGGTGCGGTACCAGTGCACTGAGGGCTTTGTCCAGCGCCACGTGCCCACCATCCGGTGCCAGCCCAGCGGGCACTGGGAAGAGCCTCGAATCACCTGCACAGACC
Seq A exon
GTGAGCATTGTCCCCTGGTCCCTCACCTGGCACAGAGTCAGGTTCCCCCAACGGAGCCTTCTCACTCTCCCCAGAGCATAGTGGGAGCTGGCACTGTTCCATAGGTGCCAAACCATGCTAGGGGCTAAGCCACACAGGGATGGTACTGAGGGTCTGTCCATCAAAAGAACACTGAGCCTAAGGAAGTTTAATGAGAAATCCAACCCAGGGGAGCAGGGTGGGAGCAGCTGTGGGTTATATTCCGGAGCCCACAATGCACAGGGAGGGGCTTCTGTCCATGTGGGAAGGCTGCTCAGAGACTAAGCTTGGCCCTGCCTCCTCCCCTCTCACTGTTGATTTCCCACCTCCCTTTCTCGCTGCAG
Seq C2 exon
CCAACACCTACAAGCACAGGCTACAGAAGCGGAGCATGAGACCCACACGGAGGAGCCGCCCCAGCATGGCCCACTGAGAGGAGCTTCCATAATGTGCCCAGGATGCTGAGCCCAGCGGCCAGCCAGGCTGACCGTGCATCCCACCCACATGGTGTCTTCTTGTCGCTTTTTGTCATATAAGGAATCCATTAAAGAAGGAAAAAAAACCCACATTGTGTGTGCCCCACTCCCCGCATCACCCAAACTGCATCTAATTTATCCCCTTCTCCCCCCCCCCCAAAAAAAAAGAAAAATGCCAAAGCAATTCACTGTAACCCGTGGACTGAGTTTAGAGACTTTTTTTGATTTCCCACCGTGCCTTTCCAGGGACCAGTGCAGGGACAGGGTGAGAAGTAAGGGGTTAAATTAAATAAAGAAGATTCTTTTTTGTTGTTGTTTCCTGACTTTGCCCAAGAACAGTACAATGGTTGGTTACTTCGCCTCCAGGGAGAGCTAGGGGACCAGAGGAGGAGCTGAAAGAAGACAGGACCAGGAAGGGAGGAGTAGGGCGGTCACAGAGCTTGGAGGACTCAGAAGAGGCAAAGTACAGCTTAGTGTGTTGGACAAAAGGAATTGAGGTCTGTGCCATCTGTGAGGGAAGGAGCCTGGGGTAGGGACAGGCTGGCTGAAGAGAAGGCAGAGCCCTCTCCTAGGGACCTTTCATCTGGGTCAACCAACCTAGCAGGTGTCATTTCTCGGCTGGACTGGGTAGGGGCACTTCCTTCCCAGGGGTGCTCCGCCGTCCCCTTCCCTCTCCCCACCCCGGGACGGTGCAGGCACCAGTGTTCCGTGCACCTATTTATATTTTTGAAAACTAAAGATTATGATAATTATAATAATAAAGACATTGGAAGAGATCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030607:ENSMUST00000032835:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.161 A=NA C2=0.792
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.9)
A:
NA
C2:
NO
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:
CTCGAATCACCTGCACAGACC
R:
ACTCAGTCCACGGGTTACAGT
Band lengths:
349-711
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