MmuINT0039011 @ mm9
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61353956-61355730:-
Coord C1 exon
chr10:61355704-61355730
Coord A exon
chr10:61354013-61355703
Coord C2 exon
chr10:61353956-61354012
Length
1691 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TCTGCTGCCTTCCAAACCAGGAG
3' ss Score
8.08
Exon sequences
Seq C1 exon
GGTCAGTGTGGAGAGTACCCACACAGG
Seq A exon
GTAAGTGATACTTCAAGCCAAGGGTGTTCTATGGGCTATCCTGAAGCCCAGCCACTACCAGGGTTGGAGGATAGGAGAGTTGAGGGTCAGGGAGTTGGGGGAGGAACCTGCTACACTGTGTGTAAGGTGAAGTCTGCTCATCTGGAGATCATTGTGTCCATTTGCAAGGAGCTGGCCTCTTTTGGCCTTGTCTGCTGAACAAGTGTCCGAGAGTCACTTAAATGTGTGTGTGTTGCTTTGCCCTCTGTTGGTCGGGAGGGGTGCATGGGTCTGTGTGTTGCCTCTGCCCTGTGTGTGATGTGTATGTCATGGGGGGGGGGGGCAGTTCTGAACAAATAGGAGGAACTTCTGAGTTAGTCGTGGTTTCAGATGCCCCAGATCTCCAGGAGGTTTGGGGCAGTGTACATCTTGCCTGTTAGGAACACAGGAAGCCTGCCTCAAGGTTCACTTGTGCACTTGACAGCAGCGCTCTTGCTGGGGACAGAGAGGGACAGAGCCCTTCCCTGATTCCTTCCTGAAGCTTCAGTGAAACAACCTGAAGACCACATGTATCATGCTCAGGTCTGGGCAGCAAGTATGAAGAAGAGCATCTTAGGTGGCCCTTCCAGCTCTAGGGACCTCAGTATACCACACACACACAATCTGTTGTCCTGGCTGCCATTACAGCTGGGCAGGGTAGAGCTTAGGGGTGGAGCTCATCACAGACCACCACCAACCCTCACTCCACTCCACCCCTACCTCAACACAAACCAGGCTCACAATGTATTTGACTTTTCATGGTCTCTGGGATGGTGTGGCTACTATGCCCAGCCTCTGCCCAGCCTCTGAGAACACAGAAACCCATGCCAGTCCCTGACATCTGGGTCCTTGGATCAGAGAGAGGCTATGCTAGGTTTGGTGTATAAGAGGCCCAGACCAGCAGCCTCACAGGCAGAGCTGGTTTGTCAGTGGGGTATGCTTCAGGGCTGCAGGACTCTGCTATTCCCACCAGCCCGATCTGATACAGCACCAGAAAGCCAGCTGTGTTTATTTGAAATGATAGTCTCACAAGGTGGTTTTATTATCCAAAAGAAATACAGCATCCCCCACCCCTACGCTCACCCCCACCCCCATCCCCCACCCCTACGCTCACCCCCATCCCCCACCTCTACGCCCCACCCTACCCCCATCCCCCACCCCTACGCCCCACCCTACCCCCATCCCCACCAGCCCAGCACAGCGACAATACAACTGCTGGAGCTTCTGCAGTGTGCCACCCAGCCAGTAGAAATGCTCAGGTCGGGGAGAGAGGGATCTCTGCCCCTCAACTCTGCACGAGAGAACAGAGAAGGAGACAGTGATAGAAGGGTCCAGAAGCGGAGTCTGAGGACTGCATTCAGGCAGGGATGGAAGATTTAAATACCCAACCGGCAGGCAAGCTGATTTAGAAGACACTATGAGTAGCAGGTTACTTGTTTGGGTAGGCGGGAGGAGGGATAGGCGGAGTGGGGAGTGGGGAGGGGTGGGTAGGCAGAGGGGGGAGCATTGACTGGTCTCCAAAGAGCCTGGCTAATCCCTACCTCTTGTCTAGCAGGAAAGGAAAGGGCTAGACAATGAGTGGGAAGTCCCCTGTTATCAGGCAGGGTTACTAGGAGGGCCTGTGGGCTTTCTCTTGATCCATGTGACTCCGTCTCTGCTGCCTTCCAAACCAG
Seq C2 exon
GAGTACCCAGGCGGCATGCTAGCAGCTCTGCGCTCCAACCCGATAATGTCCCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806-Col13a1:NM_007731:13
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=0.825
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.1=55.6),PF0139113=Collagen=FE(9.1=100)
A:
NA
C2:
PF0139113=Collagen=PU(1.6=5.3)
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: