MmuINT0038834 @ mm9
Intron Retention
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:113832292-113834584:+
Coord C1 exon
chr3:113832292-113832345
Coord A exon
chr3:113832346-113834476
Coord C2 exon
chr3:113834477-113834584
Length
2131 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
AATGTTACTGTGCATTTTAGGGC
3' ss Score
8.75
Exon sequences
Seq C1 exon
GGTGAAGATGGCTTTCCAGGATTCAAAGGTGACATGGGTCTTAAAGGTGACAGA
Seq A exon
GTGAGTAAAAAGAAATTTTAATCCATACATTTTTAATACACTGCATGTTTTAGTTAAGTCTTCTACTGCTGAGATAAAGCACCATGGTCGAAAGAAACTTGAAAAGAAAGGGGTTTATTTTCCTTACAGTTACAGGGAAATGACTGTCACTAATAGATGTTAGGGAAGACTCGAAGCAGGGGAGGAACTTGGAGGCAGGAGCTGATACAGAGGTCGTGAAAGAGTGCTGCTCACTGCCTTCCTCTTAACAGCTTGGTCGGTTTGCTTTCTTACTGCACCCAGGACTATTGTCCCAGTAGTCGAACAAATGTTCCACATCCATCTTCAATAAAGAAAATAAACGTAAAATACACAGATCAATTTGGTATGGATACTTTCTCAACTGAAGTTCTTTTTCCAGAATGACTCTAGCTTGCTTCAAACCAACATACACATTAGATAACACAATGTACACGTATATTATTTCTTAGCATTAAATACAGAACACAGAGGTTAAATGAAATATTGAAGACAGATCACTTCAGTTATGTAAAGAATGGACAATATAACGTTTGTATAAACAGTATAGTGACAGGGTATTACTATATGTTATTTTAAATTTTATAGGAGCACACAAATGTATGTATGTATGTATTGTATGTATGTATGTATTGTATGTATGTATGTATTGTATTGTATATATGTATGTATATATGTATGTATGTATGTATGTATGTATGTATGTATGCATGCATGCATGCATGCCCATTAGGTTATTCTCTAATAAAACCATCATATTAAAAGCATAGATGTAATGGAGAAAGAACTTAAAACATCTGACTTCTAGTAATTTGACAGCTTTGTGTTAGATGCTAGATAATTTTACTCAACTATACATTAAAAATACTCTTTATGCATTCTTTTCCTTCCACTTTGCTTGAGTTTTTGTTTGGGGACAGCGACTTATTTTTTAGTCATAGCTAGACTTGCACTCCCTATCCTGCCCTGGTTGGCATCAAACTCACAAAGACCATGCACCTCTGCCTTCTGAGTGCTGAGATTAAAGCCATGAACCACCCTGCATGCTTGATGTGCTTTTAAGAAAAGCTGTGCTTAATAGAGATTTCAGGTTATGTGTACTAAATACATTTCTTTGTAGTTTTGAATATGTAATTCTGTATTTTGAAAATGCTAGACAAGCATTCTCCTACTGAGTTATACAGCCAAATACATTTTGATATGTCTCACCTCAACAATGGAATCATTAAGCGCCAACCTGATCAACGTCTATATAAAATAGAGAATCACTGTTCATGGCAGTTTCAGAATAGTATGGTCAAATGAGTAGAAGAAAAGAATGTGGTTTTATTTTAATTTTGTGGATTTATTATGACTCTGATGCTTGACTGTCATACTGTGCAACTTTCATGCATCTTAATTTTTATGATTTTTCAGTATTTCAGAGTGTGAAGTTAGTGTTTTTTTACACCTTTTATATCTGGAAATAATTTTATTTTGAAATAGATTGCCTGACTTGTAGCACATTAAATTCATTCCAGAGAAGATTTATTTTATAACTCATATAAGTGTACAACCTATGTGAGCAAAGAAACAAACCTCAGAGTAGTTGGGATTCTGTGAACTACATGTGAAGGCCATACATTATGGGAGACGATTCGTTTAAAATTCAGCTGCTAATGTGTTCACTACAATTTTTCAAAGTCCCAAATGAAGATTTTTGCGTTATCAATGATAGTTTACAAAACTGCTTTCTAATCTCTGTTCTTCATTCTTTCTCTGTCTCTCCTCCTCTTCTTTTCCTTCCTACCCTCCTCACTCCTTCTCTCCCTCCCTCTCCCATTTCTTTCTCCTCTCTCTTTCATCCCACATATATGAAGCTATTTGGTAGTATATATGTTACCACCAAGCTCTCCACAACTTCTTCAATATTATGCCACATTCATGTATTTACTTAGTAATGAAATGCTGGTTGATGTCAGACTATTTCAACACCTTTCTCAAAAGTAGGCAAAACAGCAAACGAAACATAATGCAATGAACCAAGATTCAAAAATCCTGATTCTCTAAGAATCTCTGCGTTACGTATCTGTAGGTGTTTTAAATGGATACACAATGTTACTGTGCATTTTAG
Seq C2 exon
GGCGAGGTGGGTCAAGTTGGCCCAAGAGGAGAAGATGGCCCTGAAGGCCCCAAAGGCCGTGCAGGCCCAACTGGAGACCCAGGTCCCTCTGGCCAAGCAGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966-Col11a1:NM_007729:29
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(24.6=100),PF0139113=Collagen=PU(3.3=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(11.6=22.2),PF0139113=Collagen=FE(58.3=100)
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: