MmuINT0040112 @ mm9
Intron Retention
Gene
ENSMUSG00000031274 | Col4a5
Description
collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456]
Coordinates
chrX:138064519-138065905:+
Coord C1 exon
chrX:138064519-138064686
Coord A exon
chrX:138064687-138065815
Coord C2 exon
chrX:138065816-138065905
Length
1129 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
GTAACTGATATTTTCCAAAGGTG
3' ss Score
5.88
Exon sequences
Seq C1 exon
GCTTACATGGGATTCCAGGAGAGAAGGGGGACCCAGGACCTCCTGGGTTTGATGTTCCAGGACTCCCTGGAGAGAGAGGTAGTCCAGGGCTCCCTGGAGCCCCTGGTCTTATAGGACCTCCAGGATCACCTGGTGTCCCTGGAAAAGCAGGTGTCCCTGGATTTCCAG
Seq A exon
GTAATGTTTAATAATCTGTCTGACTGTGAATCAATGAAACTAATATTTATATGACTGACAAAACATTTTCATACTAAATTTTATGACTTTACACTATCTATTAAGGAAGACTGTTAAATGTATGAGTATTGAAAACTCCGTTGGTGTTTGTGCTATACTTTTTTTATACTGTGTGATAGTACCAGTAATATATTACTATATAATAAAGGATCCAAAGTATGATGGTTGAAAGTAACTTTTCAAACATTTTGCTTAAGATTCTGTGGGTCAGAAATCAAAGGGTGCCTTTAACAGATTATTTTCTATAATTCATATGACTCCAATAAGAATGATTAGAGTTGCAGAATCTAACTCTATGGTGACTCTTTTCTGACACTTGGGTATTCTTTAGCTCATGTGACATCTAATCATTCATAATGCCCCATTCTCATCTTTTTTTCATCCTTCCATTGCAAGTGGCTTCCCAAAGTAAGAATTTCCTGAGACAAAAATGAGGTCCTGAAGAGATATTTTAGTGGTTACAAGAACTGGCTGCTCTTTCAGAGAACTGGGGTTGGATTCCCAGTGCTGACAAGGCAGCTCCCAACTCCCTGTAATTCCAGGTCCAGGGATCAAGTGCCCTCTTCTAGTCTCTGGGGGGTACTACAAGCACGTGAGGCACAGCACAGACATATTCAGCCAAAATACCCATACACATAAAATGAAAATAAAAACGTGCTTTTGGAGGGAGGGAGGGAGGGAGGGAGGGAGAGAGGGACAGAAGGAAAGTGGCGAGATGGAAGGAGGGAGGAAGGAAAGGAAGGAGTCATGGAGGGAGGTAGGGAGAGAGGTAAGGGGGAGAGGGATAGGGGGAGGGGAGGGGGAGGGGGAGAGGGAGAAAGTTAGTTTCAGGGCACCCTGGTTGGTGAATTCTTAATATGTAGTGCTATCTTCTGTGGAGAACAGTTACCACAGTGAGTATCTGTGCGTTTTGTTCAGGCGTGAGTGCTAAGCTTCCAGTAAGAAAGGGGAAAATCTCACTGTGCCTTCCTTTCATTCCTAAATAGCTTTCCAAAGGATATCTTTAAAAGTCTATCTTATCTTTCCAAAGTCCAAACCCAGGAAATTTAGTAACTGATATTTTCCAAAG
Seq C2 exon
GTGTCAAAGGCGAAATGGGTATGATGGGACCTCCAGGCCCACCTGGACCTTTGGGAATTCCTGGCAGGAGTGGTGCTCCTGGTCTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031274-Col4a5:NM_007736:32
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=PD(42.2=61.4),PF0139113=Collagen=PU(64.4=66.7)
A:
NA
C2:
PF0139113=Collagen=PD(33.9=64.5),PF0139113=Collagen=PU(42.9=87.1)
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:
GCTTACATGGGATTCCAGGAGA
R:
TTAAGACCAGGAGCACCACTC
Band lengths:
256-1385
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: