MmuINT0040275 @ mm10
Intron Retention
Gene
ENSMUSG00000026042 | Col5a2
Description
collagen, type V, alpha 2 [Source:MGI Symbol;Acc:MGI:88458]
Coordinates
chr1:45393053-45394435:-
Coord C1 exon
chr1:45394382-45394435
Coord A exon
chr1:45393107-45394381
Coord C2 exon
chr1:45393053-45393106
Length
1275 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
TATGTTCTTTTAATTAACAGGGT
3' ss Score
8.9
Exon sequences
Seq C1 exon
GGTGGCATAGGAGAGAAAGGTGCTGAAGGAACAGCAGGAAATGACGGGGCAAGG
Seq A exon
GTAAGAGAAAGGGGAAAGGGTATTTTCTACCATGGGCTACGATCCTACATTTCTGCTCATTACCCTACAAACTTGCTGTAAGTTTTAACAACAATGTTATTCATGCTGTCTTATAGTCAAGGCTACTAGAATGATGCAATTTGAGACTGGATGTAGATTGACAGTGGCTACTTATTTTACTTATCTTCCATTAGATCCGTAGAAAAATGTAAAGTCCTTCCTGAAGGAATGAAAGGAAACACACAGTGCTCTCCCTGTATCTATGGCACTTAGGGAATTATGTATAATAGATCAGGGCAAATACAATGATTGTTCTGTTTGTAGTAAGTGCAATACATTGTCATTTTCTATAAGGAAAAAAGTAACAACATGCCTTCTTTGTTTTAAGAACACCACCCCTGTACTAATAGGGAACTTACATTTTCTATCCATATAAACAACAAAGTGATTTTACACAGCTTAGAAAAATTATGAGAAAAATATGTTTTCCATTATATATTTGGAGAAAAAACTTTTTTTCTTAAGAACATACAATTAATAAGTCAATTTTATTCTTTATGTTTTCTTTCAAATGTATGCATATATACATATACATTTATAACTTTAATGACAAAATAATATTGAGATACCTATGAAGAAGAAACAGAAAACTGACAGAGAACTTGTTCATAAAGAACTGCCAACAATCCATTTGAATGTTGCGATTATGTGCTGTGAAGCTCCAGGCCCTGCCCCAGGTGTTAGCTCACGTTATGAACAGCACCAACAGCAATGAACCTTGACTGCAAATGTCTATTTCATGAACACTGAAGACGTGTTTAGTGTAATTGAATTTTAAATAAAAGAATTACACTTTGTAATAATATTAAAATTTGAAAATATTGCAAAGGTAATTCTAATTTTCAATTTATACCCAGCATTCAAACTAGAGACTAACAAAACTAAACAGATTATAGAAGCAAGGGTATATTAACAAAATGCTGCTAATTTAGACTTAATTTGAAGACAGTTTCATATACTGAGAAGAGGTTTTTTTTTTTTTTTTGAAAGAGGTCAAAATATTTTGTAGAGAAAAATCTCATTGCTAGAATATGCATGACATGGCAAAAGTCCTGAAAGTATAGAGGGGATGTCATCTATGATAGATAATGACATAATTGCTTGCAAAAGCAATCGTGCTATAAAAAAATAGCTGTTTTGTTTTCTTATTTAATTAAACATGAACATTTCTGTACATACTTTTCCTCATCATACTTATGTTCTTTTAATTAACAG
Seq C2 exon
GGTCTTCCAGGTCCCTTGGGACCTCCAGGTCCTGCAGGCCCTACTGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026042:ENSMUST00000086430:35
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=PU(9.5=44.4)
A:
NA
C2:
PF0139113=Collagen=FE(25.0=100),PF0139113=Collagen=PU(3.3=11.1)
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