MmuINT1007452 @ mm10
Intron Retention
Gene
ENSMUSG00000058806 | Col13a1
Description
collagen, type XIII, alpha 1 [Source:MGI Symbol;Acc:MGI:1277201]
Coordinates
chr10:61890079-61891264:-
Coord C1 exon
chr10:61891208-61891264
Coord A exon
chr10:61890145-61891207
Coord C2 exon
chr10:61890079-61890144
Length
1063 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
3' ss Seq
CAACTTCTATCTTTCCTCAGCTG
3' ss Score
8.38
Exon sequences
Seq C1 exon
GAGTACCCAGGCGGCATGCTAGCAGCTCTGCGCTCCAACCCGATAATGTCCCTAAAG
Seq A exon
GTTTGTCGGTTCTCGATGGGCTCCAGCCCCCTCTTGGCTGAGACGCTTCCTGGACACAGAGCTCAACATGGCACATCTCTGGGCCCCAGCGTGGGAGGACGGGGCTCTGCATGGCTCAGTGTGTGGCAGCTGTCCCTAGAGGGTGTAGCAGGAAGAACCTTAGGAGGGCCCCCAGATGGGCCCCTAATTCTCTGCTGAGTGTGTTCTCATCAGAGATGGATGGCAATCCTTAACATCCAACCCTCCCAAGGCCTCTGGTGAACTGAGGGGCCTTAAACACGGGTCTTTGTCTTCATATGGATTCTAACCTTCAAGATCTGCCTACCAGATGAGACAAGAAGCAGCAGAAATTACCCCAAATGAAAAGGCTGTTGTGATCGCAAGCTGCCTGTCCTCCCTAGAAGTGGTTGGCCATTCCCAAGGCATCTTTACTGAGTGTGCCAGCCCCAGAGTGAAGCCTCAGCAGCACTTTTGAGTGTGCCACACAAGCCGCACCCTCGGCCAACTCAGCCCCCGGGAGCCAGGCTTCGCCTCCCTTGACCATGGCCTCAGATTCGCTGACATCAGCCTTTTTTAGTCCCACCAAAAAGGAACCCACAGGGGACCACACGCCAGCCTGGCTCCACGCACCAATTTAGCTCATCCTGTGGCTCTCAAGGCTCAGCCCAGTAGCCGCTGTCCACCCAGCAGGCCCGGGTGGGGCAGTGCAGTGTTGGGTGGCATATCACATGGCCTGAGCAGACTGGCATGGCTTCCGCAGTGAGCTTGGCCAGGGAGAGCCCTGCTTCTGGAACTCACAGGGGCTGCTAACCAGTCTCCAGAGCTGAGGAAGGACACTTCTAAGAGAGCCTAAGGCGAGATCAGCATTGTGGTGTCTTGCCCCTTGAGCTGAGCCTCCGGGGTGGCCTTCCCCCAATCTATCCTACTGCCATGTTTACACTGACCGCTCCTCTTCTTCTTCTCTTCTCTCCACTTGGCCTTCTTGGTGACTTCCTGCATCATTCTGAATACCTGCGACCTCTGGCCTTTGCCCTCTGGCCTTCCAACTTCTATCTTTCCTCAG
Seq C2 exon
CTGTTGCCTCTACTCAATTCAGTGCGGCTGGCTCCACCCCCAGTCATTAAAAGGCGGACCTTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058806:ENSMUST00000105454:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.803 A=NA C2=0.909
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(1.6=5.3)
A:
NA
C2:
PF0139113=Collagen=PU(4.6=13.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
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
- 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