MmuINT0039023 @ mm9
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61330579-61332325:-
Coord C1 exon
chr10:61332272-61332325
Coord A exon
chr10:61330624-61332271
Coord C2 exon
chr10:61330579-61330623
Length
1648 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
TCACTGTTATCATGCAACAGGGG
3' ss Score
5.37
Exon sequences
Seq C1 exon
GGAGAAGCTGGTGTTGATGGCCAGGCTGGGCCCCCAGGACAGCAAGGAGACAAG
Seq A exon
GTAGAGTCCCCCTCACTCTCCTGCAGGATGAGGGTGATCTTGGGTGTTTGAACACAGTTCAGAAAACCAGCCATCCCTGAACCCCAGTGCTGATCCCATGCTAGCTAGCTACAACCCCTGCATTCCAAGACTGTGGGCATGAAGAGCCTGCCTGGAAACTGGGACTCTTTAGCTGAGGAAGGAGTCTGAACTCTAGCTTCTAGTCGCTTCCCGCACCACAGATTTAGACAGAGAAGTCCCTTCTGTCCCTGCCTCCTGCACAGGCACATGGTAACCAAACTCAGGAGGGATAGGGGGCAGATCCTCAGAGGGACAGTGGCAGGGTCGTCTGGAGCTGACAGAGCATTCCGTTTCCCTTCATCTTTGACTTGGTGTATGAGTCAGAGTTCTCTAGAGTTACAGGACTTATGGAATGTCTCTATGTAGTAAAGGAAATTATTGAAATGACAATCTGGAGTCCAGCTAACAATGGTCAGCTGTGAATGGGAAGTTCAAGAATCTAGTAGTTGCTCAGTCCCTTGAAACCAGGTGTTTCAGCTGGCCTTCTGTAGAAGCTGGAATCCTGAAGAAGTAGGCTCCAACAGATGTGCTGGCAAGTAAGTGCAAAGAAGGAAGCCTTCCTTCTTCCATTGTCCTTACATAGGCCTCCAGCAGAAGGTACATCACAGATTAAAGTTGTGCACCACCACGCCTGGGCCTAAGCTGTTCTTTACTTAGAACTTGCTCTGTCCCAGGCTGGCCTTGAATTCAGAGATCTGCAAGTCTCTGTCTCCTGCGTTCTGGGATTAAAGGCATATACCACCATGCCTGAGCCTAAGCTTTTCATGGCCGCCATGCTTCAAGATCCAGATCAAGGGCTTGTGTCCTCCAGCCTCAAGATCTGGATCACAGGTGTGCCCTCCATTTCTGGATTGTAGTTCATTCCAGATACAGTCAAGGTGGCTCTGGGAAAAAAAATCACACGTGGTGTTTTGTCTTCAATGTTCACATTATTCCCAGGAAACTGAGATGTGTGGTTTGTGCTTCACTTGACACCACTATCCCACTTAGTCCACATTACCTGGTCCTGTTTCCATAGGAACAACCTCCAGCCCCTGGCCCACCTTAAGACATCAGTATCCCTCTAGCTGCTCCCCCCTGACACCCCTGGCCTCTGGGTTTCACCCTGTACTCCCTTCTGTCCCACGGAGAGTGGTCCCTGGAAGTGGGATCTCTGTGGCCATCACTGAACAGCGGCCATTGAGCCCTGCTGCCAGGACAGGATGGAAATCAGAAGAAGCAAGGGCTAGATCCCTGCTACCAAGGACGAGACTGGTTTGCGTTACCAGGGAAAGGTAGCCAAGGGGACAGTCAGGAGTCAGTGACAACTAACCCAGCAGAAAAGAAGGGACATCATTAAGTATAAAATGAGTAGAGCCCCAAGGATCTCGAACCCAGGGGAAGAAGAGTGAGGGCAGGTGTTAGGGATGTTTCTGGAAGGGAGAGGAACCTGCACTGAAATCAACAGGAAAGCTTGTGTTCTGGTGGCTTGGGCCAAGATAAGCGAGCTCTTGGCCCCTCCATGGCCCTTAGGGTGTAGCTCCCCTGAGGACACTGGGTGTTCTTGCATCCGGCCTTACCAACTCATTTCACTGTTATCATGCAACAG
Seq C2 exon
GGGCAGCCAGGAGCAGCTGGTGAACAGGGACCCTCTGGCCCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806-Col13a1:NM_007731:24
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(28.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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: