MmuINT0009481 @ mm9
Intron Retention
Gene
ENSMUSG00000030607 | Acan
Description
aggrecan [Source:MGI Symbol;Acc:MGI:99602]
Coordinates
chr7:86257560-86258723:+
Coord C1 exon
chr7:86257560-86257704
Coord A exon
chr7:86257705-86258540
Coord C2 exon
chr7:86258541-86258723
Length
836 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
AAAAGGCATTTGTCCCTCAGTGG
3' ss Score
3.36
Exon sequences
Seq C1 exon
CAATTTGAGAAGTGGCGTCCAAACCAGCCTGACAACTTCTTTGCCACCGGAGAGGACTGTGTGGTGATGATCTGGCATGAGAGAGGCGAATGGAACGACGTCCCCTGCAATTACCAGCTGCCCTTCACGTGTAAAAAGGGCACCG
Seq A exon
GTAAGAGAGGCTCAGGAGGAGACCCAGGGGGGAGAATAAGACCTCCAGCTGCAAGGGAGCCACTTGCTATGTGACCTGAGCGAGTTCTCTTGTCTCCTAGCTTCTGGGGGCTATGGGAGCCTCCTCAAGAAGCACATGGATGCTCATGTGAGGGTCTCTCATGGCACCAGCATCACAAGGCCAGGGGCAAGAACAAGATGACTCCTGGGGACCTTTCACAGGGACAAAGAGGAGATGAAAGTCATGGGCTAGAGGACAGGATCCTCAACACCATGCATGATGTCCCTCAGATGTCAGCAATAGAAAGTCACCCATAATGGCCCCTGGGTGGACCACCCTTTCTTTGGGGCTCCAAAATTGCTAATCACAGAATCAAAGCTGTCAGGCCTAGATGTTTCAACTTTAAGGGCATGGGCTTCACAGTGTTTAGAGAACCTGGCCTGGTGCTCCTACTCAGAGCCTGTGTCCCCTGGCCTTCTTTGGGCCCCACTTTCCCTGGCTTTAGACATTTTCATAAAGAAGTCACAGATGTCTTACCAGATGGTCCTCTTTCCCCATCTTCCCCCCCCCCCCATTTTTATCTTCTCCCCATTGTTCAAGGCCATTTTTATATTCCCTTCCTGCCTCCCAGTGCCACCGAGGAATCCGGATGTTAGAACTTAATATCTCAGGATTCTTAGCCCTGCATCTTTCCAGTGGACCAGGCTCAGCACTGGGTAGCACAGCCTAATCCCTTCTCATCATACTGTGGGCTCTGGGATAACCTTGTCTCTGCCTACATGGGCTATCACAGAAGATCTCGTGAGACCCCTTGCTAAAAGGCATTTGTCCCTCAG
Seq C2 exon
TGGCCTGTGGAGACCCCCCAGTGGTGGAGCATGCTAGAACCCTCGGGCAGAAGAAAGATCGCTACGAGATCAGCTCCCTGGTGCGGTACCAGTGCACTGAGGGCTTTGTCCAGCGCCACGTGCCCACCATCCGGTGCCAGCCCAGCGGGCACTGGGAAGAGCCTCGAATCACCTGCACAGACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030607-Acan:NM_007424:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.161
Domain overlap (PFAM):
C1:
PF0005916=Lectin_C=PD(42.5=91.8)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAATTTGAGAAGTGGCGTCCA
R:
GTCTGTGCAGGTGATTCGAGG
Band lengths:
327-1163
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: