MmuINT0038860 @ mm9
Intron Retention
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:113888800-113889499:+
Coord C1 exon
chr3:113888800-113888853
Coord A exon
chr3:113888854-113889445
Coord C2 exon
chr3:113889446-113889499
Length
592 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGT
5' ss Score
9.07
3' ss Seq
ATTTTCACTGTCCATTACAGGGG
3' ss Score
8.97
Exon sequences
Seq C1 exon
GGACCCGTTGGGTTTCCTGGAGATCCTGGTCCACCTGGAGAACCTGGTCCTGCA
Seq A exon
GTAAGTGTCATGTAGGAATAAAAGGATGCTTGGGTGGGGCTGTTCCCTCAGTCTTAAGCAACATTTGTTTTTTTTTTTTTAAAAAATATATTAAAAGTGAACTACAGTCAGAATGCCAAATGAAGAAAACAGTGATTGCATTGATGACAATATCTATTTAACTGATGACTCTTGCACCTTGGTTATATGACTCTCCTCTTCATTTGGACAACTATTGAGACTTTTTTAGAATACAGAAGGAGCATCTATACTTCTATTTACAAAGTTCAAAACTTTTATTTCCTAATCTTGTTTACTATGTAAATCCTACCTGGAATTGTTTCATGTCTGTTCCTGATGAAAGGAAGCACTGGGGATCTACACTAACTGTGTCTTCAAACATTCCTTATATCAAAAGAGAACTTTACAATCAATTGATATGGAAAGAGCAAGGAGCACCATAATCTAAAAAAATATGTGTTATAATATTGTTTGTCCATGTGATCACAGTTTATTTCAACAGTCTACCAAGACAGTCTGTACAAGTGTTGTGTCTTTACAATAATAAATTATAACAAGAAATATTTGGGTTAATTTTCACTGTCCATTACAG
Seq C2 exon
GGGCAAGATGGTGTTGGAGGTGACAAGGGTGAAGATGGAGATCCAGGACAACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966-Col11a1:NM_007729:52
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=FE(18.7=100)
A:
NA
C2:
PF0139113=Collagen=PD(9.9=50.0)
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:
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: