MmuINT0039874 @ mm9
Intron Retention
Gene
ENSMUSG00000031502 | Col4a1
Description
collagen, type IV, alpha 1 [Source:MGI Symbol;Acc:MGI:88454]
Coordinates
chr8:11242782-11244403:-
Coord C1 exon
chr8:11244341-11244403
Coord A exon
chr8:11242818-11244340
Coord C2 exon
chr8:11242782-11242817
Length
1523 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TAAAATGCTCTCTCTTACAGGGT
3' ss Score
11.36
Exon sequences
Seq C1 exon
GGCTCACCAGGGTTGCCAGGACTCCAGGGACCCGTGGGTCCTCCGGGATTTACTGGACCACCG
Seq A exon
GTGAGTTTTGAGGATAGTCCCATGGAGAGGAGACGTGGAACACATTGAAGCTGACTGAGACTGTCCCCCTTGTGGCTCACACCTCCAGCCCCCAACCCCCAGAGCTGTGGGAAAAAGGATGCTTTATACGGTGGACCCTCCAGACATCCTGGGACAGATGGGACAGATCACCTGTCGGTGTGCCAGGGCTACTAGATACCCATATGTCAAGCCACTGGGGAAGTGGGACTGAAGGTCACCAGCAGGGGCTCTGCCCTTTGTGCAGAGGAGAGGTGCTGTAGAGTCAGAGGTGCCTCAGGATTAGGTCAGGTCAGTTAGGAGCCAGGCGCAGACCTGGGGAAGACTCTGAGAGGGATTGAGCACCTGGGGGGGGGGGGGTGCTCAGGAAGAAGCCCCGCCCCTGGTCTCTGTAAGGCTGACATTCTTTGCAGAAGGAGAGAGACTTTTCCTCACTCCTTCATTTTGACAACACTGAAAGGTTAGCATTAAAAGACTTATCTACTAAGAATCAAGAGTGCGAGGAATGGTCAGAGGTGACGGAGTTCGTGGCCTGCACACAGCCTGCCTGAGCATCCTCTCAGAGAGCCTCGGACTTATACCTTAAATTCAATCATTTTCTTTTCGTTTTTATATTGTTTTTCTCCGCATGTGTGAACAGGATCCACCCGCCTTCCTATGGATCAGTGAGCTTGTTTTTATATTCCAGAATGGCTGGCTTCCTTTTTGAAAAAGTGACTATAGGATTCTGAATTTTTCTTGCAAATGTGGGGTTATCTTTTTTGTTTGTTTGTTTGGTGTCAGCATAATCTATTCTCTAGAAGAGTCACCTTTTCCCCCCTGAGGTCTGAAGTGGACTTATGTCAAAAATGGACAGTGCTGTTCTCATGTGGGCAACTCCAGCTTGGAGCCTAGGCTGGTGCCCCCAGGCTACTGGTACCCAAGGACAGGCTGCAGCCTTTGAGGGACTTCTGCCCTCCTCATAATTATCCTGACTCATAACTGGCTATTCTCAAAGCTTAAAAGGTGTGTGTCGCACACATCATCCTGCCAACAACAGAGTGCAGAGGACTGTGTGTGTGTGTCAGACTTTGCTAGGACACAATTCTAGAAGGATACAGTTCACAAGGAGGAAAGATTCGTCTTGGCTCACAGTTTCAGGGGGTTGAACGCATGACCCAAGGTTCTGTGGTTTGTGAGCCTGTGAGAAGGTAGAACACTGTGGTGGGGAGCATGAGGTATAGTTGAGACATACTGAGGACTCGCGGCGGGGGGGGGGGGGGGGGAGACAAAATGCCTCCTTCAAAGGAACAACCCTAGTGACTCATCCTTCAAACCCTCCCCCTTCCCCCACCGCAAGAACTCACCAATGGTTAGGCACCCTGGTGATGCGGTCACCTCTCCATAGTGCCCACAAAAGACGGAGTGTGTATGTGTGTGTATGTGTGTGTGTGTATAGGGATGATCTTCCAGATCACAGCTGGCTGGTTTTGAATACTATTTAATTAAAATGCTCTCTCTTACAG
Seq C2 exon
GGTCCTCCAGGCCCTCCTGGACCTCCTGGAGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031502-Col4a1:NM_009931:10
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(33.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.6=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: