MmuINT0039031 @ mm10
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61860440-61862113:-
Coord C1 exon
chr10:61862015-61862113
Coord A exon
chr10:61860485-61862014
Coord C2 exon
chr10:61860440-61860484
Length
1530 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGG
5' ss Score
5.42
3' ss Seq
GGATGGTTTTATTCCCACAGGGA
3' ss Score
7.74
Exon sequences
Seq C1 exon
GGTCTAGACGGCCCAACTGGGGAGAAAGGAGAACCAGGTGACGAAGGGAGGCCTGGAGCGACAGGATTGCCTGGGCCCATCGGGCTCCCGGGATTCACA
Seq A exon
GTAAGGCGAGAGGACCGGGTGTCAAGGGTGTCCACGGGCAGCTTCAGATGAGAGTGCAGGAGCAAGGGACTCCTCACTGGGGCCAACAGCCTAAGAGTGCCCGGCACCGTGCCAAGCTTACCCTAACCTGGGTCTGGCAGCTGCCCTGGGCTCCTGATTGGGTCCAGAACTCTAGCCTCTTCAGTACACAATGTGGTGGCTCCTGTCTCTAGCTGCTACTTAGCTGGAGCGCTGGAGACTCGGACATAGAAATACCCCCTTAGACCTAGAAAGAGACCGGCATGCATGCATGCCTTAGAGGGACACATTTCCTCATGGGGTGTGCAGTTCTGCCAGCCTAGCCGCATCAGTGAGCTGCACGTCCCAGAAAAGCGGGGGGGAGGGGGGGGGCGAATTGAGCAAGGAAACAAGGCAGACACCTGGGTGAACACGAGGGTGACATCCTACCTCTACCCACACATACCCATACAAACACACCTCCACAGAAACACACCAACATGCCTACACACCAAGACCCCCACCACACAAACACACTCTCACACAAACATACCCACACACCAACATACCCACACACACAAACCCAAAAGAAGTAAAGAACCTCAAGAGGTCAGATGTGTGACTCAGCAGACCCCGAAAGTGACTCTATACCCAGCTGGCTCAAGCCGGTGGGTGGCTCATAGCTTTACAGTGTGCCCACTTTCACGATGAAAGCTGAGCTACTGGGTTTGGTGTGGTCTCGTCCTCATCCACTTCCACCATTGTCTCCCCTCCCCACTGAAATCTGAGCCATAGTCACTTTCCTGCAATGTACCACAAACCATCACAAACAGCAGCTTAAGATGGCCCACCTGTATCGCTATATATTCTGCACCTCAGTGGCTGAGGCCTGCCATAGCTGGGTTCCCCAACCAGGGTCTCCTAAGGCCTCAGTCAAATCAGTGGTCATCTGTGTTCTTACTGGAGCCTCTGATCCTCTCCCAAACCACTGGCCATAAAAGGACTAAGTTCCCAGCACCTATGATTCTCTGACACATGGCCCCTCTCTATAGTGGACAGTCCACTTCATATTAGCTTACTTCTTAAAGAAAGGGCCTTTCTAGAGTCTAGAACTAGCAAGATGGAGCCATGTGCATGCATGTGTCTATGTGTGTATATATATACACAAGTCTTAGCATGTGTTATATTTTCCTATGTATTACACATGTATGTGATGATGTGTAACATAGTCACAGGAGTGGCAGGCATCATGAGGCCACAAGTCTCTTTCAAGACTGAGAAACAAGTCACAGTACCACCTTGTAGCTTGTCTGCCACAGGACACATAGTACGAGCCCCTCCCTGACAACCAGAGCCTGAGATCTGTGAAGATGGTTGTCACGGGGCCATCTTGGTCCTGTCCTGCAGGCTAGATACCTATGTAGCCTCTCCAGGAACAGCCCAGTCCTTGTAGCTTGTCACAGATGTGAGGGTAAACCTGTGGACAACCTCCTGGTTACCTGCTCTCACAGTGGGATGGTTTTATTCCCACAG
Seq C2 exon
GGAGAGAAAGGAGAAGCTGGGGAGAAAGGCGACCCGGGAGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806:ENSMUST00000105454:31
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(42.3=90.9),PF0139113=Collagen=PU(29.4=60.6)
A:
NA
C2:
PF0139113=Collagen=FE(22.6=100),PF0139113=Collagen=PU(0.1=0.0)
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