MmuINT0039517 @ mm9
Intron Retention
Gene
ENSMUSG00000079022 | Col22a1
Description
collagen, type XXII, alpha 1 [Source:MGI Symbol;Acc:MGI:1916950]
Coordinates
chr15:71700541-71702270:-
Coord C1 exon
chr15:71702235-71702270
Coord A exon
chr15:71700595-71702234
Coord C2 exon
chr15:71700541-71700594
Length
1640 bp
Sequences
Splice sites
5' ss Seq
CCGGTACAG
5' ss Score
5.65
3' ss Seq
CTGTCTTTCTTTTTCATCAGGGA
3' ss Score
11.14
Exon sequences
Seq C1 exon
GGTCCCTCAGGACGACCAGGAGATAAAGGACCCCCG
Seq A exon
GTACAGTATGCTTTAGATGGAGGATTCTTAGCCCAAGTCTAAATCAGAGGCAATCAAAAGTCACTCGAAATTCCTCATACTAGACAGACTCTCCAAAATAGGAGTATGAGCTTATGGGAACACTGGGGCGGAAGGAAGTGGCAGGTTCAGTTAATCCAACATAACATTGTAAAGTCAGGCACACCGAGACTGGTTTTGTCTGTTAGCATCTTTCCGTTACAGACGTGGAGCCCTGATTAAGTGAATTTAGTCAAATGGTAAGAAAACTAGTTTTTGGATTCTGGCTTTACCCAACCACAGAGCCAGGAACACATGAAAGGTTTTCTTCTTGCCTTGTAATGTGGAGGCAGCCGCAGCTATGATCCATTGTGGAAATTTTTTTGGGCTCATTTTATACTATGCAACAAGAGAGCTCCCAAGATGCATTTCTTCTCAGGAACAGCCACCGGTGTTGGCCATTTTCAAGCATTCACTGTATGCTTGCTGGTGCATCTTCTGCTGCAGGACAACTATATCATATCCAGTCTATGGCTCTGTGCATGTATTTTAAGTCGATATTCACTTGTGGTTTCTGATTAAGGAGGATAAGAAATCTTGTGGATGTTGTGCTAGATGAAGAAACTGAGGCTCAGACCAATTGAGATTTATGGCCATGGGATTTCACGGCAAGTTATGTGGAGTAGAGCTGAGGAGTGTGGGACTCTGGATGAAGGGCAGCTCAAAGACCCCCAAGGAGGCCATTTCAGCTCCTGCAGAGCAGATAGCCAATACCCTGAGAAGATGTCATTTTCCACTTGCAGATCTAAGGAAATAAAGTCCATTGCCTGATGTTTTCTAGAAAATGTCAACATAATGGGAATGATCTTAAGAAAGTGATCAGTGTCAGGCATGAGCTAAGCATTTCATTGACTCTTGTGCAAAGAAAGTTGTTTAACCAATAAGCATGGGGCTGGCTGTGCAATTCAAGGTGTATAGGAAGGCATTCTGGATTGGTGCTCAGGCCTGGCTCTCCATAGGAGCTGTGCCTTCCACTCCAGCAAGGGGCCACAAGGGGCTAATGCATGAGGCTCGTGTCAGGCTCCCACAGAAGGTTTTCCTGAGCTTTGTGTCTATGGGCTGAGCACAAGTCGCCATAGAGTGCATCTTGCTCAGTAAGGTTTGAGCACAGTGCTTTTGACACATGCACTATTGTCAAATTGCAGTTCATGCTGCTGTGATAGCATGCTCTGGCAAAAGCACCGTAAGGAAAAAGTAATTTTTTCTTAATTTAGCTCTGTGTAAGTGTAGTCTGTTGTAGCAGGGAAGACAAGGCAGCAGGAGCGTGAAGCGGGTACTTGTATCCCATCCACAGTTAGGAGACAGGAATGAGTATAAGCTAAGCACTATGATCACCGGTCTCCATTTCCTATAGCTCAGGACCTCCTGACCATGTTTAAGATGAGTCTTTCTCCCATCAGTTAGCATAACTGCGATACTCCCCAAAGATGGCCATTTTCAAGCATTCCAAAAGCCCATCTCTGAGACAATCATACCAGTGATCTCTCTGCATAGCTTATCCTTGTATAGTCATAGCCAGCGGTAGCCAGACAAAGGTGAGCCCTGTCTTCTCACAGTTGGAGCCTGTCTTTCTTTTTCATCAG
Seq C2 exon
GGATCTCGAGGCTTACCTGGATTCCCCGGCCCCCAGGGACCAGCTGGCCAGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000079022-Col22a1:NM_027174:41
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(19.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(29.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
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
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: