MmuINT0039475 @ mm9
Intron Retention
Gene
ENSMUSG00000016356 | Col20a1
Description
collagen, type XX, alpha 1 [Source:MGI Symbol;Acc:MGI:1920618]
Coordinates
chr2:180750960-180752245:+
Coord C1 exon
chr2:180750960-180751037
Coord A exon
chr2:180751038-180752023
Coord C2 exon
chr2:180752024-180752245
Length
986 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAT
5' ss Score
6.6
3' ss Seq
CTGCCCTTCTCTCTCACCAGGAT
3' ss Score
12.64
Exon sequences
Seq C1 exon
GTGAGCCTGTGACTATCAGCCACACAAGCAACCCTAGACTGCAGGAGGTGCAGACCCCAGAATCCCTGGAGTGAGCAG
Seq A exon
GTGAATTTCTGTCATTGTGCCAGCCATGGTACAAGAAGGAGGGATAGCTGGAGGGAGGGGAGCTCTGCTGAACAATGATAGAGTGGAAGATGGTGCTGCTTCTATCTGAGAAGAGGTCCTGCCCTCGAGAATGGGGTGGAGCTGATACTTGTGAGGCTGGTTGTCCTGCAGACCCTGCTTGGGCCTGCAAGTGTGAGGAGCCACAGTGAGGAGGAGAGGTTTGAGCTGCGGGAGTGTGGGTGCTCACGGGTCTTGGAGAAGCCCTATAATGGGAGGGGTGCTTACAGAGGATGGATCTCAGGTATGTATTCCAGTGAACACCTGATGTGGTGAGAGCACCTGAGGTCACAGACAGAGCACTCTGGAGGCTCTGAGTGTGTGTGAAAGACTTGGAAGTAGGCAGACAGGGTGCAGCACCAGATGACCTCTTCCCGTTCTCAGAATGTGCTGAGCAAGCTTCCCATGTACAAACCTGCCTGAGGAGGTGTTTCTAGGTGCAAGTGTGGGGTAGGGTACAATGAACACAGGTGGAGTGTGAGTACAGATAAACCCAGGTGAGCTCTGTGAACACAAGACCAGGTGAGCACAGGTGAGCATGGGTGGCACAGCTGGCACAGGTGGGTTCAGGTGGCACAGCTGGCACAGGTGGGTGCAAAAACATTGTCCTCAAGTAGATGATGGAGCTGGAGGCATGTGGGAGCAGATTTGGCAGGCACAGGGGCTCAGGGGTGTGTGTGACAGAGAGAGTGTCAGGAGTAGGGAGCCAGCTATGGACAAGCTAGAGCCCTGTGAGTACAGCCTTGTCCCTGCTTCTGAGACCAGAGAACAATTCAAGGGTCTGCTTTGTTTCATGTCACAACAAAAGCTGGGGTGTGGAGACCTCAGCTTCTTTTACTTTGGGGAAGCCTGAGCTCACTGTGCCAGGAGGCTGGGCCACAGGTCTCCTAGACTACAGTCCAGCTGTGTCTGCCCTTCTCTCTCACCAG
Seq C2 exon
GATCTTCCCTCCGCCACTTCAAATTGCCCTGGCCTTCCCCAGCACCATCATCCATAATTTTGTCTCAGCACTAAGAACAACTGTGTGCTGGAGGGGCAGAGAAGGAAACCCAGAGGAAGACCCCGAGGTGGCAGGAGCTGGAAGGGAGGAGGGCGGTGCTCCTCCTTCAAGCCCCTTCTTTGTAGCACTTCTAGGTTCAGATAAACTTCTGCTTGCTTGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000016356-Col20a1:NM_028518:35
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTGTGACTATCAGCCACAC
R:
TGACAAGCAAGCAGAAGTTTATCT
Band lengths:
296-1282
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: