MmuINT0009484 @ mm9
Intron Retention
Gene
ENSMUSG00000030607 | Acan
Description
aggrecan [Source:MGI Symbol;Acc:MGI:99602]
Coordinates
chr7:86229353-86231322:+
Coord C1 exon
chr7:86229353-86229736
Coord A exon
chr7:86229737-86231147
Coord C2 exon
chr7:86231148-86231322
Length
1411 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAG
5' ss Score
5.73
3' ss Seq
CTGGTCCATGTGTCCCACAGGTA
3' ss Score
10.25
Exon sequences
Seq C1 exon
ACCATGACAACTCACTGAGCGTGAGCATCCCTCAACCATCCCCATTGAAGGTCCTCCTAGGGTCTTCCCTCACCATCCCCTGCTACTTCATCGACCCCATGCATCCTGTGACCACTGCCCCCTCCACTGCCCCCCTCACCCCAAGAATCAAGTGGAGCCGTGTTTCCAAGGAAAAGGAGGTGGTACTGCTGGTGGCCACTGAAGGACAGGTTCGAGTCAACAGCATCTACCAAGACAAGGTGTCGCTCCCCAACTATCCAGCCATCCCCAGCGATGCTACCTTGGAGATCCAGAACCTTCGCTCCAATGACTCTGGGATCTACCGCTGTGAAGTGATGCACGGCATCGAGGACAGCGAAGCCACCCTGGAGGTCATAGTGAAAG
Seq A exon
GTGAAGGGCCTCCCACTGGGGACGCCATGTTGCCTGTAGGAAGAGCTAGAATGATGTCCTCAGCAATGTGCACCTTGGAGACTAGCTCTCCCACTCAGTTCCTCTGCATACCCGTTTTCTCCTTATCGTGCCCTACTATGGGACTGTCTGGCAAATGCTGTTCTCTGTGGGATTGGGACCCTAGGAGTGGGGCACATAAATACATCCTGGTGTTGGCAGCTTGTTTGCCAACAATCTTTCACTTGTTGGGTCTATCAGTGTTTCTTGCTGCTGTGATCAGAGACCTGACAGGAGTCCACGTGAGGGAGGAAGGCGTTACTCTGGCTCACAGTGTGAGGGCATACAGTCCACCATGGTGGGGACAAGATGGTGGTAGGAGTCTGAGGCAGCTAATCATACGGCATCGACAGTCAGGAGGCAGGAAGATGAATCCCACTGTTCACCCAGATCACTCTCCCTTTTTTTCTTTCACTCTGGGACCCTGGACCATGGGATGGTACCATCTACCTTCAGAGTAGGTCTTCCCTCTTCAGTAAAACCCTCACAGACATGCCCACAGGTGTGCTCCTACCCCACAGCAGCCTTGTAAATGTGCCCATTTTGCACATCAGCAAGTGAGTTAAGTGGCATATCTGCCATGATCCTAGAAATGAGTGAAAGTGGGTTCCTAACACGTCATCCAGGCATCATCCCCGCCCGCTCCTCCAACCTTTATTCTCAGCTTCAAAGAAATGATGGAAGATTCACTTCCTGTTCTCCTTTGTCTCTAAGAGGTCTCATCAGGATGCCCCTGAGCCACTGGAGACCTGGAACCCTCATATCTCATTCCCTGGATTGGTGGTGGAGAGGGGGGATTAGAAGGCCTGGAGTGACAAAAGGAAAATCACAAGGAGATAGTTTTTGCTATCGTTCCAATAACTTTCTTATTGTCAGAATTATTAAATGTGTTTTAAGGAGAATGCCTGATGATGGGGTGGTGAGCACCCTGTTAAGGTGGTAGGGTGGGGTGGAGAGGAGACAGGGTTCCAGCAAGAGCAAACTTCAGTTGCTAAGGATCTATTGGCAGCCGATCTGACTGCTTCTGGCAGAGGAAGTTTTCTTTAAGGGTACAGCCCCTGGTGGGTTGGCCGCACTCTGGTAGATGGCCCCACACCCAGGAATACACAGGCACAAGTTGGACTCAGTGGGAGGGGTGGAGGGTTGGAGGTACAGCTGGAAGGGGCCAGGGAGAGAAGTTAGGGTACATATAATCAAAATACGTTTTAAGTATGTATGAAATTCTCAAATCAATAAAAAAATTACAATAAACTATGTCAGCCTAGACCAGACAGTGCCCAAGGTCCCCTGGATCCTGGTCACCATTTCTCAAGGGCTCACACCTAACTTGCTCTCTGGTCCATGTGTCCCACAG
Seq C2 exon
GTATTGTGTTCCACTACAGAGCTATTTCCACACGCTACACCCTGGACTTTGATCGAGCACAGCGGGCTTGCCTACAGAACAGCGCCATCATCGCCACCCCAGAACAACTGCAGGCTGCCTATGAGGATGGCTTCCACCAGTGCGATGCAGGCTGGCTGGCTGACCAGACAGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030607-Acan:NM_007424:3
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:
PF0768612=V-set=WD(100=94.6),PF0019312=Xlink=PU(0.1=0.0)
A:
NA
C2:
PF0019312=Xlink=PU(60.4=98.3)
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:
CTTCATCGACCCCATGCATCC
R:
GCTCGATCAAAGTCCAGGGTG
Band lengths:
357-1768
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: