MmuINT0038868 @ mm9
Intron Retention
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:113797435-113798211:+
Coord C1 exon
chr3:113797435-113797551
Coord A exon
chr3:113797552-113798118
Coord C2 exon
chr3:113798119-113798211
Length
567 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
TCTTCTGAATTTATCATCAGGCA
3' ss Score
6.42
Exon sequences
Seq C1 exon
TATGCACCTGAGGATATAATCGAGTATGACTATGAATATGGGGAGACAGACTATAAAGAGGCTGAGAGTGTAACAGAGATGCCTACTTTTACTGAAGAAACAGTAGCACAAACAGAG
Seq A exon
GTAAAACCAAGAACTGTCTGTTGTATGTGGTGTCCACTCTTCATCGTCCTTCAGACTTACCGAATACCTATCACTCGCTTCTGTGAATTAATAACATGTTATATTTGACAGAGACACCTGGAGGAGAGCTGACCATGTTTGCATTTTCATTTCCTTCCTTTTATCCATACGCTTTATTTTCTTTCTCACTACATGTTTTCCATTCCATCTTTCATGACATTTTACAGAAAAAGAAATCCAATTACACAAAGAAGAAGAGGACATTGACCACTAACTCAAAGAAAAAAACTAAAAAGTTCACATCCCCCAAATCTGAAAAATTTGCATCCAAGAAGAAGAAACGTAATCCAGCCACAGCCAAAGCCAAACTAGGGGTCCAGGTAGCGAGAAAAAGCAATCAAGATCTGTCCTAGATGAGATGGAAGATCTCTGATGAGTCTTAGACTTAACCCAATTAGATCAATTCCAATTTGGCTAACACTGTAATGCAATTAAATCATGATTTTTCACTCACTTGAGATTACATTACAGATTTTCTAACCCTTGTTCTTCTGAATTTATCATCAG
Seq C2 exon
GCAAATATTGTGGATGATTTTCAAGACTACAACTATGGAACAATGGAACCTTACCAGACTGAGACTCCTAGGCGGGTATCAGGATCGAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966-Col11a1:NM_007729:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.756 A=NA C2=0.895
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCACCTGAGGATATAATCGAGT
R:
CATTCGATCCTGATACCCGCC
Band lengths:
206-773
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: