MmuINT0039562 @ mm9
Intron Retention
Gene
ENSMUSG00000063564 | Col23a1
Description
collagen, type XXIII, alpha 1 [Source:MGI Symbol;Acc:MGI:2653243]
Coordinates
chr11:51387934-51390406:+
Coord C1 exon
chr11:51387934-51387960
Coord A exon
chr11:51387961-51390352
Coord C2 exon
chr11:51390353-51390406
Length
2392 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
ACCTCTCATCCATCTGTCAGGGG
3' ss Score
6.92
Exon sequences
Seq C1 exon
GGCAGACCTGGAGAACCAGGACTCGAT
Seq A exon
GTAAGTTTTGTGTGATTGACTGTGAGTGCCCGGGCCCTCCTGTGTGTGTCTTCTGCTCTCAGGTTGTTGTCCAGGCTTATAGCAACCTAGTTAGCTCAAGTGTGGCCCATCCGGAAGGCTGCTGCTGGCTGGTTCCCCTGTGTCCTCAGTGCAGAGTATAACGACATTCCCTAGAGTACTGCAGATGGATGATAAGCTGACAACAAAGGAACAGTAGAACACTGGTGATCCTAATGTATGAGTAGAGAAAAGATGGATGAGCTGATGGACTGGCAGATGGTAGAGGATGGACAGAGAGACAGACTTATGGGCAGGAAGACAATGGATGATGGCTGAAAGAAATTAATGGATGGTGACTGAAGGGGGAGAATGATGAGGAGATGGTGGGGAATGAATTAATGGATGGATGGTGGCTAGATGGGTGAAAATGGATTGATGAACAAGAATGATAGCTGAGGGATGGTGGATGGGTGGATGGATGGATGGGTGGATGGATGGATGGATGGGTGGGTGGATGGATGATGGATGGATGGGTGGGTGGGTGGGTGGATGGATGGATGGATGGGTGGGTGGATGGATGATGGATGGATGGATGGGTGGGTGGGTGGATGGATGGATGGGTGGGTGGGTGGATGGATGGATGGATGGGTGGGTGGATGGATGATGGATGGATGGGTGGGTGGGTGGATGGATGGATGGATGAGTGGGTGGGTGGATGGATGATGGATAGATGGATGGGTGGATGGATGGATGGATGGGTGGGTGGGTGGGTGGATGGATGGATGGATGAGTGGGTGGGTGGATGGATGGATGGAAAGGTAGATGGGTGGGTATATAGATGGATGATACACTGTAAAGGGGAGGTGAGGAGAGCAGCAAGGAGGCTGATGCAATATATTTATGACAGTGATGAGACCTCAGTTAGGGTGGTATTGTGAGAAGGAAGCAACAGGAAGTATTAGCTTAATGTTGACCACATCAGGCCTCCTTTGGTAACACAACATAAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAATTCAATCTTGCTTAAAATGACTCAAATTGAAAAATCTAGGGATTAACCACATGTATCCAGGGCACAGCTGTGTCAACACCGCCCAGCCATCTCCCTCTCTGGTCTTTGCCTTCCCATTGTGGAAATCACCAGAGATCTGGTCCAGCCAGCCCCTCCAGACAAGTAGCTTCCTGGACCCAAATACAGTAAGAAGATTTGGCTCTCTTTAGTCAACCCTGAGCCATCTTGGGGTTATGAGAGTGCAGCTTCCCCTCTGACCAGGCTCAATCCCCTGCTGCCTGGAGGTAGTCAGCGAGAGGGATGGAGGAGTCTTGAGAAGTCATGAGGCAGGGAAAGAGACTGAGACTGATGCAGGGCTGCTAGTCCTCCAAGGTGTACCCAGACTGAAAGAAGAGAGTGCTGTTGCCATGGTGAGCAAACATAGGCCAGGAAGAGAGGGACCAGCCAGGCTCCTGACTGGGAGGGTCACCTTCTACTGATGTGACAGAGCTGGAAAGTAACTTGCTGAACCCCACTCAAGTTCTGGACCCAGGAAGGCTAATTGGATATGTGACTGTGGGTGACCTCCTCTGCTTCCTAGAAGACCTGGAGCTTAGTGTGGCATTTAAAAGCCCTGCCATTTTCTCTAACAAGCCCCATCCCATTTCCACCCAGCTGGATGGTGACCTTGCTCAAAAGCTCCCTGTGGTACCTGCCCCTTGTCGGAACAACCTAGTGCCCTGCCACATCTGACTCCTACGCCTGTGTCTGAGCACGCTTGCCATCCACACTCCCTAGCCTGCCCCAGGAGACATCAGGGAGGAAACACACCAAACCCTTGTCTGTCCCAGCATCCAGTCTGCAGCCTGGACTCGGCCGGATGCTTGGAGATTAGATTAAGAGGTGGATATAGACGAAACTGAGCCTAGGACAGACAGCACAAGCGACCTTCTCTCAGTCCATAGAAGATGGACACATGACTTCTGTGGCTTTCCTTTGTCCCAGCCAAGTCTGGGCCAGGACCAGCTGTGTCTGACCATGGCAGGAGAAAAAAAAAAAGAAAGAAAAGAAAAAAAAAGAAGCCTCTTTCCAGTAGCTCTGCCTCCCTCAGGGTTTCTAGCCAGGAGCAGAGCCGGGAGCCCCATCTGGTACCCAGCAGGCACATACGCTAACAACCAGAGCTTGGCAGTTTGTGCCAGTTACATGTGGACAAGGAGCAGCGTGGTGGGTGAGAGAGGAGCGGGAGCATCAGGTCACAGGGAAGTGGGCTCAGGTCACAGGGAAGTGGGCTCAGGTCACAGGGAAGTGGGCTCAACTCTCACTTCAGCCTTAACCTCTCATCCATCTGTCAG
Seq C2 exon
GGGTTCCCTGGACCCAGGGGAGAGAAGGGTGACCGAAGTGAACGTGGAGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000063564-Col23a1:NM_153393:25
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=PU(14.8=88.9)
A:
NA
C2:
PF0139113=Collagen=FE(24.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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:
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: