MmuINT0172768 @ mm9
Intron Retention
Gene
ENSMUSG00000021614 | Vcan
Description
versican [Source:MGI Symbol;Acc:MGI:102889]
Coordinates
chr13:89794915-89797290:-
Coord C1 exon
chr13:89797108-89797290
Coord A exon
chr13:89796964-89797107
Coord C2 exon
chr13:89794915-89796963
Length
144 bp
Sequences
Splice sites
5' ss Seq
ACCGTAAGT
5' ss Score
10.43
3' ss Seq
CTTTGTTTTCTTCCATGTAGCAT
3' ss Score
9.39
Exon sequences
Seq C1 exon
TTGCTTGCGGCCAACCCCCTGTTGTAGAAAATGCCAAGACCTTTGGAAAGATGAAACCACGCTATGAAATCAACTCCTTGATTAGATATCACTGCAAAGATGGTTTCATTCAGCGACACCTTCCAACTATCCGGTGCCTAGGAAACGGGAGATGGGCAATGCCTAAAATAACCTGCATGAACC
Seq A exon
GTAAGTGGTCCTTTAGAAAGAACGGACAGCGTTGCTTTAACAGATACTAGACACCTACATTTTACCGCTGTGGTATCCGTAGTTTAGGGTATGGAGCAAGTAATACTGTTGTGTTTTCTTCTTTCTTTGTTTTCTTCCATGTAG
Seq C2 exon
CATCTGCATACCAAAGGACTTATTCTAAGAAATACTTAAAAAATTCCTCATCCGCAAAGGACAATTCTATAAATACATCAAAACATGAGCATCGCTGGAGCCGGAGGCGGCAGGAAACCAGGCGCTGATCCTTAAAATGGCGAACATGTGCTTCACTCATCATTTCAGCCAAAGTCCTGCCTTTCCGTGCCTTTCCTATCACCTCAAGAAGAATTAGAAGTTGGTTTGGATTATGGGACTGCCGTCTGGTCATTTGGGGTGGCTGTACTCTTAAAATATTTTCAATGAAACATGGAATTTTGAAAAAGCGAATAAAATGAAAGAAAATGAACGAAGAAGATAACCATTTTCAGCCTATCTAATTTCTTTAGTTCTCTCAATGCCTCCAGTGCAGACTGTTTCCTGTACACCAGCCTACTGTACTATTTTAAAAAAACGCAATTTCAGCACCGATGGCCATGTAAATAAGATGATTTAATGTTGATTTTAATCCTGTATATAAAATAAAACATCACACTCAGTTCAGGCATATTTAATGATGATTATGCAGCTTTCAAGGTCTTTAATCGTTGGTTTGGCTGCTTTGCTATAGCTTGCTTAGGCTGGAAATGGTTTTGTCTACCCTTTGACTGTCAGCAAGTTTGAGGACGGCTTTTCTGGACAGCCAGCAAACAGCATCTTGCAGGTCTCTGCACGTGTGTCAGCCGCGGGAGCCACACTGATGCCTGGCTGATTCCTGGCTGATGAAACTCTCGCTCGGAGCTCCAGGGTGTAACTCCGCTTTGTCATGTTCCCTTTTCTTCACTTACACGAAGCGCCTGAATGGAGGACTTTTCTATGACCTGGAACATTTTTTTAGGGGTCAAATTGCTAACTATTAACTCAACCAGGTTTCATTTACAATGGCTTTCTTAACACTAACCCTGGTAAGGTAACAGATCAAGATATTTGGAATGGATATAGATCAAGGGTTGAGGAGGGTGGGGGAGGGGGTTTTCTTAAAACAACAACACTCGTGCAAAAAAAAAAAACATTTTGTACATATAACCATTTTAATTCTTTATAAAAAATTTGAATGTTCATGTATGAATGCTGCAACTGCGGAGCACACGTAAATAAATGAAGTAAGCCATACGGATTTAATTTATTGGATGTTATTTTCCCCAAGACCTGAAATCAATGTAGTATGCTAGTAATTTCTCAGTGTTACCTTTTATATTTTCTTCACAGTTTAAAACCTTATAATATAGGTACTTCCTTCTAAGTGTTTATTACGGAGAATGGAAATGTGTTTAGCTATCCATAAGTGGTATTTGCCCATCCCAAGCAAGTGTGAAAATGTAGAATAGTGTGGCCATTGCTTACTGTTAGATGGAGTGTATGTGCTGACGTTTTCACTTCACCCTTCACCCCTTGCATTTGAATAGTGGTTGCTGAAGATGACATGGGAATCATTATCTAGATAATTTAAGGCTCAAAGTTAAAACTGCTCTCAGAAAGAAGGCATTTAAGGCTCATCCATTCCCTTCATTTACAACTAACAGAAAAGGCAAATAAAACCTGAACAGAAACCAGCTTTGAAATGACACAATGAAAGCAAGCATTGAAGCATCGTGCGGTGTCCCATAAGTATGGTCAGACTTTATGTTTTATACATCAGGTCAAAATATATATTCAGCAAAGAAGAGTAGAGGAAGAGCAGACTGGAGTTGGTCCTATGTTGACTGTTTCCCATGAATGCTACTTTAGCTTAGAGGGAATGACTGTGCTCACAAGCATACATAGTGTCTTAGACATGGTCCTGGGTCTCAGCAGTAAATGTAATTCATCCTAATGTGTACTAGAGCACAGAAAATCACTGTGTTGACTTACTAGGGCTTTTTTTCTTTTTCATTACAATGCACATAATACTTCCCTGTATTTATATTATAACATGTATAGTGTAAAATGTGAATGGCTTTTTTTGTGAATGAAAATCTAAAATCTTTGTAACTTTTTATATCTGCTTTTGTTTCACCAAAGAAACCTAAAAATTCTTCTTTTACTACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021614-Vcan:NM_019389:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.571
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=91.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAGGAAACGGGAGATGGGCAA
R:
AGGTGATAGGAAAGGCACGGA
Band lengths:
249-393
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: