MmuINT0039030 @ mm9
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61324763-61325519:-
Coord C1 exon
chr10:61325376-61325519
Coord A exon
chr10:61324862-61325375
Coord C2 exon
chr10:61324763-61324861
Length
514 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
AGCTCTTTGTCAATCTATAGGGT
3' ss Score
7.28
Exon sequences
Seq C1 exon
GGGCCTCGAGGAAAACCAGGAGATATGGGGCCGGCTGGTCCTCAAGGACCCCCAGGAAAGGATGGGCCTCCAGGAATGAAGGGAGAAGTCGGACCCCCAGGAAGTCCAGGGGAGAAAGGGGAGACAGGACAAGCAGGCCCCCAG
Seq A exon
GTAAGTGTCTAGACATCTGGCATCCTGCATGCACCACCTCCATCCTGACACAACCTCTGCATGCCACCAGCTGTTCCAGAGTTCAGAAAACCAAGAGTCACTTGCAGCTACCTGCCATGCCACTCACCGTATAAATGCTGGTGTCCTATAGTGTCCCCACTCAGGGGACCTGAGTCCTGTGCCAGCCATCTGTGTTCTTGGGAAAGTCACTGAGCCTTGCAGAGCCTCTGTTTCTCATGGCCTGTGAAAAAAACACAGCAGGGCTGTGAACCTGCCTCTACAGAAGCATGTGGAAGCCCTACATCAGAAGAGTTTGCATGAATGGAAAGAACCCCTTGCCCTTTCTAGCTAGGCTGCTGACTTAGTTGAGCCTCAGTAGTGCCATCTGTGAAATGGCACCACCCTCGACAGCCACCCTTGGAGGGAGTCATGCATGTATGCATGCCATAGATGGCACATTTTCTCAGTATGGTGACTAGGAGCTTCACTGACAGAGCTCTTTGTCAATCTATAG
Seq C2 exon
GGTCTAGACGGCCCAACTGGGGAGAAAGGAGAACCAGGTGACGAAGGGAGGCCTGGAGCGACAGGATTGCCTGGGCCCATCGGGCTCCCGGGATTCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806-Col13a1:NM_007731:30
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=PD(37.7=47.9),PF0139113=Collagen=PU(57.9=91.7),PF0139113=Collagen=PU(9.1=16.7)
A:
NA
C2:
PF0139113=Collagen=PD(42.3=90.9),PF0139113=Collagen=PU(29.4=60.6)
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:
GCCTCGAGGAAAACCAGGAGA
R:
TGTGAATCCCGGGAGCCC
Band lengths:
241-755
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: