MmuINT0039008 @ mm9
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61356782-61358108:-
Coord C1 exon
chr10:61358082-61358108
Coord A exon
chr10:61356809-61358081
Coord C2 exon
chr10:61356782-61356808
Length
1273 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
TTTTTTTTTTTCTCCCACAGGGC
3' ss Score
13.98
Exon sequences
Seq C1 exon
GGCCACCCCGGACCTAAAGGGGAGATG
Seq A exon
GTAAGCCCCTCTACTTCCTTTCCTTCACTCGATAGGTAGGGGACCAGCCTTGTCAGCCTGCCTGTCACTATCAGCAGGCCCTAGATCCTCATTCCATACAGGGAGACGTGGCAAGCCTTTTCTCTCCTGCACAGGAGACATCCAAGGTATCAGGCAAGCCTTTTCCAACGTGATGATAGAACACTCTCCAGGTCGGGGTGGGGTGGTGCCAGTCCTAGGTGGCCTTTTACTTTTCCACAGTGCCTTCCCCTGAGCTGTCCTAGGACTCTCCAGCCCAGCCACTGGGAGCCCGCTCAGAGTTTCCTAGTTTCAAGGTAGATCCAGTTATGAGTCGGAAGCAGGGGGAGGAGCCTTTTCTACATCTTGCCATACTGAGGCCACACATCCAGATACCCAGAGGCCCAGAGACCGGCACTCTGGAGGTTCCTCACAGACCAGCATAGGGTTCTGAGCTGCCTCAGAAGCTCAGGCAAGGGTTCAGATTTACAATGTGTTAGACTGGAAAAGACTAGCCTTTCGTGGCCTCACCCTGAGCTGTGTGTGAACACTGCTGTTCTCTTGGCACTGGGAGGCAGAGGTGATGCCAGCCTCTTTCTCCTCTGGCCCAGTAAAGGTCTGCAGAGCCTTCCCTCGAAGGGCCAACCCACACATGCTTCTGTCCTGTACATCAGTATGGGCCTCCTTAACCAGGGCTTTCTCCTGAAAGCTTACCAGACACTCAACCCTACTCCCTAGAACCAAAGGATACGACAACCTCGACAGCAATGCCAAGTCCCCTTATGCCTTCCAGGGAGCTCAAACCATGGATTAGGGGATCCAATCCAGCTTCCTGTCTTTACCACAGGCCTCACACAGTGTGTCTTCAGCACTAGCCTACCCCACCCATGCCCCCCAAACCTTTCTGGTTCAGTGGCCAGGAGAACAGGAGGCAGGCTATGCTGGGGTCTCTGGGGATCCCAAGTGAAGGATGTAAGGTCCTTCAGAGCAAAACACCCCAACACCCAAGCCTCCCATGTACAGGGGTCTTTGAGACATCAGTGACTGGAGGAAAAGCTGAGGGGGTCAGGGAGCGACTGGCCACACCCACTGAGGCTTGGCGTAGAGGGTCATCCCATCTTGGATGAGTTGGACATAGGCCACTGTGACCTGTAAGGCTTTGGGACATTCTGGGAAGCTCTAAGAAGCCCAGGATCTGTCCCCAACCCATCCAGGTATGTGTCTGTGATTTACCCACCCACTGACACCTGTGTTTTTTTTTTTTTTTCTCCCACAG
Seq C2 exon
GGCCTGGTGGGTCCTCGAGGACAACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806-Col13a1:NM_007731:10
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(13.1=100)
A:
NA
C2:
PF0139113=Collagen=FE(12.9=100),PF0139113=Collagen=PU(9.1=88.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
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: