MmuINT0039421 @ mm10
Intron Retention
Gene
ENSMUSG00000029661 | Col1a2
Description
collagen, type I, alpha 2 [Source:MGI Symbol;Acc:MGI:88468]
Coordinates
chr6:4528306-4529121:+
Coord C1 exon
chr6:4528306-4528413
Coord A exon
chr6:4528414-4529067
Coord C2 exon
chr6:4529068-4529121
Length
654 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCA
5' ss Score
7.87
3' ss Seq
CTCTTGCTTTGTACTTCCAGGGT
3' ss Score
8.91
Exon sequences
Seq C1 exon
GGTGAAGCTGGTGCAGTCGGTGCTCCAGGCAGTGCTGGTGCCTCTGGGCCTGGTGGGCTTCCAGGAGAGAGGGGTGCTGCTGGCATACCTGGGGGCAAAGGAGAAAAG
Seq A exon
GTACCACTCGGTGTTAGACCTTGATACATAATATCCATGAACTCCAGGCAAGAAGGCTGTGCGAGGATGCACAGTTGTTTACCATTCATAGCAGGCGGTCTGGTAGCATTTTGACATCTATATGCACCTCCCTCTGCCACCCAGCACCTACACATGTCTAAACTCACTAATCTGGCAAAATTCCTTGCTACCATGGAATTTCATGCAAGCAGATGGTGTTGAGTAATACATGAGGCTCATTTTAATGCCACTAACAATAATGCCTCATCCTGCCCTAATTAATGGAAGAAGCTATATCAAACAGCTGTTCACCGTGCTATGGCATTCATTATGTTATAAGAGTGACCGGGCACCACAGCCCGTCGCCATGTTGTCTTGTGATTCCAACCTCATCAATTTGAAACTTGCTTCGTGATGAATCAGAGGGATGTTTATTTTTTAGTGTTCGGTAGTCCTCTGAAAGGGGCCAGAAAAGATGAACTTCCGACTGTTTTTCTCATTCAACATCCTACAAAGTGGTGGGAAACTGAAAAACACTGAAATTCTAAAAGGGTGGCCAGCATTATAGAAATTTTTGTCAAAGCACTTTGCAGTTCATTTCCACTCAGAAGTTGAGCAGGAAAGCAAAATGTGGCTCTTGCTTTGTACTTCCAG
Seq C2 exon
GGTGAAACTGGTCTCCGAGGTGACACTGGCAACACTGGTAGAGATGGTGCTCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029661:ENSMUST00000031668:32
Average complexity
IR
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=PD(19.0=44.4),PF0139113=Collagen=PU(44.6=91.7)
A:
NA
C2:
PF0139113=Collagen=FE(23.0=100),PF0139113=Collagen=PU(12.5=61.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types