MmuINT0039781 @ mm9
Intron Retention
Gene
ENSMUSG00000022483 | Col2a1
Description
collagen, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:88452]
Coordinates
chr15:97829706-97831037:-
Coord C1 exon
chr15:97830834-97831037
Coord A exon
chr15:97829723-97830833
Coord C2 exon
chr15:97829706-97829722
Length
1111 bp
Sequences
Splice sites
5' ss Seq
GTGGTCGTA
5' ss Score
-11.41
3' ss Seq
TTCTCTGTCTTCCCTTGCAGGAA
3' ss Score
14.73
Exon sequences
Seq C1 exon
AGGAGGCTGGCAGCTGTCTGCAGAATGGGCAGAGGTATAAAGATAAGGATGTATGGAAGCCCTCATCTTGCCGCATCTGTGTGTGTGACACTGGGAATGTCCTCTGCGATGACATTATCTGTGAAGACCCAGACTGCCTCAACCCCGAGATCCCCTTCGGAGAGTGCTGTCCCATCTGCCCAGCTGACCTCGCCACTGCCAGTG
Seq A exon
GTCGTAATTTATTTATTTATTATTCAACATAAATAAATTACTCGGAGACACAGCAAATGCCTTCCGTGGGTTTTGGCCTTCTCTTTGAAGCGGAGAAGCTGCTAATCAATCTATTTGATCCCACCAGCAGGGGCACAAAGGCAAGGCCACTTCTCGGTTCCACCAGGTTGAAGGCTGGTGAGCCTGAATCACTACAGAGACCCTCCCTCACCTAACACCCCAGGAGGATGCGTACAGAAACACAATTATGCTTCCACAAAAGTTTTCCCTCCTGAGTCAAGTCGGCTAATTAATTTAAGAAAAGCCAAAGGGGTAGCTGGGCTCTGGGAGTTGAAAGGATGATCGTGCCCCTGCAAGCTGCTGTGGTTACCCACTCCCAGCTAGAACCAGTGCTAACAAAGAAGAGTACAGCTGACCCCTTCCCAGCACCCACGCAAGTGTCCCATCTCCCTACGGAGAGCGTGGGGGATGCCCGCACAGGCTCATGGTTCCCTTCCTACTCCTATGGAGAAGAGGGCTGAACTGGAATCGAGAAGTCGCCTTTCCTGCATGCTTCCCCCACACTGTTGCCTGGTATGGCGCAGATTCTCAGAGGGAGGCGCCCATACCAGTGCGGTGTGAGGACCCAGTGGAGCTTGCTGCTGTGGTGGGGGAGGGGCGTATGGGTCTGGGATGGCCCTGGCTGCAATGCTCTTTGTAACACCTGTGTCCCGCTCTCTTTTGTGCTTACGTCAAGGAGACTCCACGCTAATGTAAGGCTGGCTTCCTTAGACTCTTCTTTGGGAGGGCACGGGTTGGGAAGGACTGCCTGACCTCTGGGTCTTCTGCGCTTTGCCCTCCAACCCCTGGTTGCCTCCTCCCCTGCTCTCCGCCATATTCCTGTACACTATGCATGCTTCTTGACTAATGAGGTAGAGGCACCTCTGTCCCTTCTAAGTCCCCAGCCACAAAAGGGCTCCGTGATCCTAACCCCACCACAGAGGGATTCCGGGGACAGAGGGATGCGCTTCCTTCCTCGGTTGTGGCCCTTTCCTTTCTGATCCTTCGAAGAGAGTTTGAGTGTCAAATTATCATCCCTGTCTCACTTCTCCTTCTCTGTCTTCCCTTGCAG
Seq C2 exon
GAAAATTAGGGCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022483-Col2a1:NM_031163:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.767
Domain overlap (PFAM):
C1:
PF148281=Amnionless=FE(90.7=100),PF0009313=VWC=WD(100=79.7),PF0139113=Collagen=PU(3.4=2.9)
A:
NA
C2:
PF148281=Amnionless=PD(2.7=33.3),PF0139113=Collagen=FE(11.4=100)
Main Inclusion Isoform:
NA
Associated events
Conservation
Rat
(rn6)
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: