MmuINT0042446 @ mm9
Intron Retention
Gene
ENSMUSG00000042401 | Crtac1
Description
cartilage acidic protein 1 [Source:MGI Symbol;Acc:MGI:1920082]
Coordinates
chr19:42372144-42372873:-
Coord C1 exon
chr19:42372773-42372873
Coord A exon
chr19:42372313-42372772
Coord C2 exon
chr19:42372144-42372312
Length
460 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
TGCCACCTTCCTCCCTCCAGGGC
3' ss Score
11.79
Exon sequences
Seq C1 exon
GGGGCGTAGTGACCGACTTCGATGGTGATGGGATGCTGGATCTCATCTTGTCACATGGAGAGTCCATGGCTCAGCCACTGTCTGTCTTCCGGGGAAATCAG
Seq A exon
GTATGCACTGACCTCAGGCCCTTTAGCTCCCAGCCTGGTTGTGCTCCCAGGGACCCATGTGTGCGTTAGGGCACAGGAACCCGGGGCTCACTGGCCAACATGATAGAGAACCTAGTACCTGGAAACACCTAAGTTCCCAGCAGGAAGGACCACTTCCGGGAGAACCCCTTGCCAGAAGGACCACTTCCGGGAGAATTCCTTGCTCAGCCCTCTGCCATCTGCCACAGGAACTTCTTGGCCCCAAACCTTGGCCCACAGTCTCTTGGCTCTTTCCCTCCTCCCTGAAGCAAGCTTTGCCCATGTTCCTCTTCTTTTTTCTCTTCTGCGCCTCTCCTTTTCCACCCGTTCTCCCTCTTCCCTGTCTCCTCATCCCCTTCCTCCTCCCCTCCCTCTCTCCCAGCATTCCTACCTCCCGGCTCTATGCCACCCTGGCTGATGCCTGCCACCTTCCTCCCTCCAG
Seq C2 exon
GGCTTCAGCAACAACTGGTTGCGTGTGGTACCTCGCACCCGGTTCGGGGCCTTTGCCAGGGGCGCCAAGGTTGTACTCTACACCAAGAAGAGTGGGGCGCACCTACGGATCATTGATGGGGGTTCCGGCTACCTGTGTGAAATGGAGCCTGTGGCACATTTTGGCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042401-Crtac1:NM_145123:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.088 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0183918=FG-GAP=FE(84.6=100)
A:
NA
C2:
PF0183918=FG-GAP=PD(2.6=1.8),PF075937=UnbV_ASPIC=PU(55.7=68.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGCGTAGTGACCGACTTC
R:
CCAGGCCAAAATGTGCCACAG
Band lengths:
270-730
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: