MmuINT0038878 @ mm9
Intron Retention
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:113800745-113802035:+
Coord C1 exon
chr3:113800745-113800807
Coord A exon
chr3:113800808-113801993
Coord C2 exon
chr3:113801994-113802035
Length
1186 bp
Sequences
Splice sites
5' ss Seq
CCCGTAAGT
5' ss Score
9.09
3' ss Seq
ACGGCTATTTTTTGTTATAGGGG
3' ss Score
7.86
Exon sequences
Seq C1 exon
ATAAATGGACATGGTGCATATGGAGAGAAAGGGCAGAAGGGGGAACCGGCTGTGGTTGAACCC
Seq A exon
GTAAGTGCTTTGGCATTTGTTTTAAAGATTGCTACAATCATTTAATTTATGAATTGTCATTTCCTTGTCATTATATAAGACCCTACATTTTCAATGAAAATTCTGATGTTTATAATTTACCCCAAAACAGGTGGGTAGTAATGCCTTTTCTGGAAAGCAAAATTTCAGTAAAATAAAATTATCACACATTTATGGAATTTGGAATTTTGAAAGTGGCTGGAATTTTTTCTGGTCCAATTTTTTTGTTTACAAATCTGAATTTACATGTTTTATTCTGTGATCTCAAATGGTTGGTAGTTGAGATATAATGGCTGTAGGTCTTCAGTCTGTGATTTTACTGATATTTGTTTACTGATAATTACCATATTAGAAATGTTATTAAAAGTACATTATACAATAACAAAATAAAATGAATGGATAAGGAGTTGAGAGAGAGAACTGAGTAGATCACAACAGACAGGAGTGTTAGGGAGACGAAGTAGTGACTGTGGTCCGTATGTATGGCATTTTTGTGTGAAACTTTAAGACAAGAATATTCTCTAAAATTTTGTTTTGTTTACTTGCATGATTATCTGAAACTATGATTGTATCAATGCTATGAACTCTCAAGGTATTGTTAAGAGGTATATATTTTCAAGAAGCAATTTATAAAAAAAAACAGTTTTCATTGACCAGCTACCTGGGGAAAGCAGTTTATTGGAGCTGTAGGTTGGTTTAAGGGTTCACTTCAGACACATGTATTTCTTTCAGTAAACACAAATAAATATATTTTATTGGAATTAAAGTGTTTAGGTATTTTCTTTCATTAGTTCATTCATCAATTCATCCATTAGTATAGCAAATATTTATCATGATCCTGTATTTTTGTTTGTTCGGTTGTGTTTTGTTATAAATTAAGTAATTAAGTTCTAGGGAAGCGCTTACTAAGGCATCTCTGCTATACTCTCGACAGAAGCACTTAGCATATTCTTTCTCCTTAATATCATTTGTCTGAGTATTTATTTTACTTTCAATTAGTTCGTATATTCACTAATAGCAAAGGTTATGTCTTCTATTATTTCAAATTATTTTATCTTCCCATAAAACCACGTTTTAATTGTTTTATATCATATGAATTTGGAATTTGCTTTAAAACTATTATAGTTAGTCGAAAGGCTAAAAGCTACACGGCTATTTTTTGTTATAG
Seq C2 exon
GGGATGCTTGTTGAAGGACCACCTGGGCCAGCAGGACCAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966-Col11a1:NM_007729:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(1.7=4.8)
A:
NA
C2:
PF0139113=Collagen=FE(22.0=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: