MmuINT0039479 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180730165-180731212:+
Coord C1 exon
chr2:180730165-180730329
Coord A exon
chr2:180730330-180731059
Coord C2 exon
chr2:180731060-180731212
Length
730 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
CACACACTTCCCTAAAGCAGGTG
3' ss Score
4.82
Exon sequences
Seq C1 exon
GCCTTGCTCTAACCCATGTGCTGGAGCAGAACCTGAAGCCAGCAGCCGGTGTCCGTCCAGAGGCAGCCAAAGTGTTGATTCTGGTGACAGATGGCAAGTCCCAGGATGATGTGCGCACAGCTGCCAGGATCCTTAAGGATCAGGACATTGATGTCTTTGTTGTGG
Seq A exon
GTGAGCTGGCACAGTGCCTGGGCCCTGGGTTCGAATGCACATGGCTAGGGTGGACTCTAGATCACAGACACATCTGCACTCTGGCTTTACCATCTCTGGCTAGAAACTTGGGTACATGATAACTGCTGGCCTGCAGCATCCACACCCATAGGGGCCAGAGGGTGAGCCCTGCTCCATAGAGGTGCATGGCTACACCTTCCAGCAACATCTGCAAAATTTGTCCCTGTCTCCCTTGCCGTGACACTCCCCAACTCCCTGCCACCCTCCAACTCATACTGCAAGTAACCTTCAAACTGGTCCCCTGCCTGGCAGCTGCCATTGTGTCTGACAGCTCTTCCCCCTTCCCCGTTTGCTCCTCAAGTAAGGAGTGTCCCTGGTGCTCTCTGGGACGTCAACCACATTTACTGCACTGTTTGATGGGAAGGAAACTCCAAGTGTAGGGGGTTGTTCCAGGAGCCCCTCTCTTCCAGGAACCCCCTCTCTTATGGGTGGGTACCTGACACCAGCATCCACATAGTCTGGCCTGCTTCCCAGTTCCCAGAGCTAAGCACACTGGCCTCCCCTGGCCCATTCCTGTGTTCCACTGAGACCCCGTGAAATCTAGGACATACAGCTTCAGTTTTGCCCTCCCCCATGATGGGAACTCTGGTAGGTCCCTCCCCTGTGGTCTTGTCTGTAAATAGAATGAGAGTCTCGGAGTGGCATGTTGACACACACTTCCCTAAAGCAG
Seq C2 exon
GTGTGAAGAATGTCGATGAGGCTGAGCTGAAGCTCCTGGCGTCCCAGCCACTGGACATCACTGTCCACAACGTGCTGGACTTCCCTCAGCTGGACACCCTAGCTCCTCTGCTCAGCCGACTCATTTGCCAAAAAATTCAGGGCAGAGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(31.8=100),PF0385310=YjeF_N=FE(55.0=100)
A:
NA
C2:
PF0009223=VWA=PD(21.4=71.2),PF0385310=YjeF_N=PD(41.0=78.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCTCTAACCCATGTGCTGG
R:
TTTGGCAAATGAGTCGGCTGA
Band lengths:
294-1024
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: