MmuINT0040105 @ mm10
Intron Retention
Gene
ENSMUSG00000031274 | Col4a5
Description
collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456]
Coordinates
chrX:141613489-141615122:+
Coord C1 exon
chrX:141613489-141613657
Coord A exon
chrX:141613658-141615029
Coord C2 exon
chrX:141615030-141615122
Length
1372 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
AGTGTTCCATTTGTTTTCAGGTC
3' ss Score
10.4
Exon sequences
Seq C1 exon
GGTGGAATTACTTTTAAGGGTGAAAGAGGTCCTCCTGGGAGCCCAGGTTTACCAGGTCTCCCAGGAAATATGGGACCTACAGGCCCAGTTGGTTTTGGGCCTCCAGGCCCCATAGGCGAAAAAGGCATACAAGGTGTGGCAGGAAATCCAGGCCAGCCGGGATTACCAG
Seq A exon
GTATGTTTACCTTTGTTGTCTTTTCTATTTTAAAAGTAGACAGACACATAGACAGATAGACAGACAGATAGATATAAAAAGTTTAAAAAATTCCTGGGAAATGTGTTTCTCTAGCCATCTATATGCTTATAGGAAGGGAATAGATTGTTTTTGTTTAAAGTGAGATTTCTTGTTAACTTAGTCTAAGTTTGTAGTGTTTTTTGTATTTCGTTCTTGAATATATGTTAGTGTAGTTGTATCCATGTAACTGGGAAGGATATGCACATAACTATTTTATTAATATTTTTGAAATGATATTATAATTATAAATTTTTCTGCCTTACCTTTATCCCTCTAACTCCTCCCATCTCACATGTAACCCCTTGCTCTCTTTCCAAGTTAAATCCCTTTACTTCAAATATTCTTTTACATATGTGTGTGTTCCTACATGTACATTCCTAAACACAGCACACACACACATACACACTCCTAAATACATAAAAACAACCTGCTTGGTCTGTATAGCATTACCTTTATGTATATGTTTTGAGTGTCAAAAACATGCACCATAATTTTGGAGACAGGGTCCCTCACTGAACCCGGAGTTCATTGATATTGCTAGGCTGGCTAGCCAGTACTATCCAAGATACCCTCAGGATATGGGTTATGTGGTGCTATAGCTACAGTTTTATTCATATTCAGCAGGCACTTTGCTGATGGAGCTACCATCCCATCCCAATTTATGTTCTGATGCTCAAGGGAAGGAGAAGATAGGTGTTCCAGATGAATGAGGAGATGTGGGGGGGGGAAGAGGGAGAGATTTTTTTCCTATGTTTTTTGTTGTTGTTGTACTATCCACATCCTCTTCTGTTGGATGATAATGGTCCATATTGTGCAAAGGCAGACCCTCCTTCCTTAAAGCACTGATTTAAATTCCTATGTCTTCTGGAATCATGGGCCATAGGCATAAAGCAGAGATAATTATTTTATCAGCTATCTAAATATCCTTTAATCTAGTCACCCTGACATCTAAAGTTAGTTATCAAACATCCTCAATCATGGAAGTACCTAAAATTCATTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCTTCCTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCCTTCTTCCTTCCTTCCTTCCTTCCTTCCTTTCTTCCTTCCTCTCTCTCTCTCTTTTCCTTTCTTTCTTTCTTTTTTTTTGAAATTTTATCTTTCTCTTTGCTATCTTCCTAGAATATGCAAAATGGGATTGTAATTATTAGTCAAGTAAATGATTCTCACTTGGAGTGTTCCATTTGTTTTCAG
Seq C2 exon
GTCCTAAAGGAGATCCAGGCCAGACCATAACCCAGCCAGGAAAGCCTGGTTTGCCAGGTAGTCCAGGCAGAGATGGTGAAGTGGGTCTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031274:ENSMUST00000112931:25
Average complexity
IR
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(21.8=21.1),PF0139113=Collagen=PU(85.0=89.5)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=25.0),PF0139113=Collagen=PU(45.8=68.8)
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:
GGTGGAATTACTTTTAAGGGTGAA
R:
GACCCACTTCACCATCTCTGC
Band lengths:
256-1628
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types