MmuINT0038871 @ mm9
Intron Retention
Gene
ENSMUSG00000027966 | Col11a1
Description
collagen, type XI, alpha 1 [Source:MGI Symbol;Acc:MGI:88446]
Coordinates
chr3:113909572-113911278:+
Coord C1 exon
chr3:113909572-113909625
Coord A exon
chr3:113909626-113911028
Coord C2 exon
chr3:113911029-113911278
Length
1403 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
CTCACTCAATTTGCTTGTAGGGT
3' ss Score
7.27
Exon sequences
Seq C1 exon
GGACCTACTGGCCAGAAGGGTGACAGTGGTATGCCAGGGCCTCCCGGGCCTCCA
Seq A exon
GTAAGTGTATATTAGCAAGAATGATGCTCTCTTAGAAGGCATGTGGGTGCAGGAAATAGTTTCTCTGGACTTGTATAACAAGGGGAAGAAATATTCTGTCCAAAGTACTAATGTTGTAGGAAAATCCAGTGTGGTTCCTCAGATTATCACCCTACATGTCAAGATTTGGGTTTTAACTGATATCATTTCTTACATATAAATATTTCTTAATTGTATTCTACAATAAACTTATTAAGATTTCAAGGTAATTATGTATACTTTCATCACGTTTACTGAAACTAACAGAATATATGCCCCACAAAATGAACACGCACACACACACACACACACACACTTCAGGATTAAAAATGAAAGCTCAGATCCCATAGCTAAATAAATGTCATTTATTAGGAATGTTATTTTTCTGAAGTGTTTGTATTAAAATGTAGAACTATATGTACGACACTGTATTCTGTTTTTTTTTTTTTTCTAGTTAAAGTGTCTCTAACTGTATGTGTGGTCATTTAGTCCAGCCACAGGGCAAAATACAACCAGAATGTCCCTGTGGAAACTGGAAATCCTAGACCAAAGTGTCACAGGGTTGGTTTCTTCTGAAAGGCATGGGAGGAGAAATTATTTTAAACTCTCGTCTTATATACAACATCCTTTTCTTAGATTGCCAACCTTGCCTAGATCTGTGTTCATGTGATCATATTTTTTCTTTTCATAAGAATATCAGTGATACTTCACTAGGTCTACCCCGGTGACTTCAGCTTACCAAATCATATATTCCGTCATCCAAATTATAAGAAAGGTTGAAATCTTAGTTATTGTGCTGAGGGTTAGAGATATTAAGTGCACATATAGGTGGAGCATGATTTGACCAGGGAGGTTATGGGTTAACTCTTTAATGTGGTTCTGTGCTCACACATCAGCAAATTCAACTAGTGGCATTTACTTTCAGAGTAATATAGAATAATGTAAGTTATGCATGTTTTAATATGATAATGGGGCAGATTTTTTGGTACTCTTTCAGAAAGTAAGCTATTATTGAATAAATAAAATTTGGATAGCCTCAGAGCTTTGGAACAGTGTTCTAGTCCCCAGAGATTCTGATATCTAGTCATGGATATAGCTATACAAATCAACATTAGTCAATAAATACGAGTAACCTATGCAGTATGTCACCAAAATTTCATACTATGGTAATTTACAGATACTGTACCAATAATTATCTGCTTTGTAAACCTACCTCAATATCTCTACTATACTCTTTTAAAAATATATCTTTTCATCTATTACATATCATTAATTTAGCAATTGATAGTTAAGCCAATTAATTTCTGAAAAGAATGTAAGTAGTAAATAAACTCACAGAATATCTTATTTTTCAAAATAATGACACTCACTCAATTTGCTTGTAG
Seq C2 exon
GGTCCTCCTGGAGAAGTGATACAGCCTTTGCCTATTTTGTCACCAAAAAAGACCAGAAGACACACTGAAAGCATCCAGGGTGATGCAGGAGATAATATTCTTGACTACTCAGATGGCATGGAGGAGATATTTGGTTCCCTCAATTCTCTGAAACAAGACATTGAACACATGAAGTTTCCCATGGGCACACAGACCAACCCAGCACGAACATGCAAAGACCTGCAACTCAGCCATCCCGACTTCCCAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027966-Col11a1:NM_007729:62
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=0.845
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.7=9.5),PF0141013=COLFI=PU(12.7=32.1)
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:
CCTACTGGCCAGAAGGGTGA
R:
GAAGTCGGGATGGCTGAGTTG
Band lengths:
294-1697
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: