MmuINT0040104 @ mm10
Intron Retention
Gene
ENSMUSG00000031274 | Col4a5
Description
collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456]
Coordinates
chrX:141612421-141613657:+
Coord C1 exon
chrX:141612421-141612612
Coord A exon
chrX:141612613-141613488
Coord C2 exon
chrX:141613489-141613657
Length
876 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
TTAAACATTTCCATTTTCAGGGT
3' ss Score
10.87
Exon sequences
Seq C1 exon
GGCATACCTGGACCTCCAGGTGCTCCAGGCTTTCCAGGGTCTAAGGGTGACCCTGGGGATGTCCTCACTCTTCCAGGAATGAAAGGTGACAAAGGAGAGTTGGGTTTCCCTGGAGCTCCAGGGCTTCCTGGTCTACCTGGTAGTCCTGGAAAGGATGGTTTGCCAGGACTCCCTGGCCCCAAAGGAGAGCCT
Seq A exon
GTGAGTTGGATTAATATACTTGCTTTTATGTCAAATTGTCATTTAGTAATGTTTCATACAGGATGAAGTTCTATGTCAATGGTAAAACTTGTACTGGGTTTGTGTGAAGTACCTAAATTCAATTTTCAGTACTCTCTAACCCTCCTAAAGCAATTGGTAAGTTAAAATAAAATAGGAGCCTATTACATAGATGAATACTAATGCCTAAAATAATACGATTTTACAGTGAAATGGTACATTGATACTAGAGTTTCCTTACTGTTTTCCTTCAGTTCTATAAACTCCTTATTAACTCAGTATAGTATTGATTATTACTAACTATGATTAGATGGAGAGGAAGTTAAAATGCTTAGGAGTCAGAGAGGGATTCATTATTCTAAACATCTGTGGGAATTTTTTAAGCATGAAAAAACCCAATTTGTTATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGCGTACAGCCAGATTAAGATACTACAGAGCCAAACACTGAGCGTAAATGAACAGTCTCTTTTTATATTCAACATCCAGTAGAGGATATTTGAATGAGAAATATATTTTAATAGTATAAATAGACAATAACCATCTCATGGTACGGTGTGAGATTTTTGAGAGCAGAGACTTTGATTTACTCATCTTCTCAGCTTATACCACTCACTGGAAGATAGCGTTCTGAGATATTTGTTGAAGGAGGTAATTAGTGAGTAAGTAATCATAGATTCGATAAAAGAACGTAACCCAGTTTTAGCATAACTTTAAAAGGCATACTTATGGCTGAGTCATGCCCCTGATTGTATCCATTTAGACTAATCTACATGACGTTGTTACACCAATGCTTTCTGTCTTAAACATTTCCATTTTCAG
Seq C2 exon
GGTGGAATTACTTTTAAGGGTGAAAGAGGTCCTCCTGGGAGCCCAGGTTTACCAGGTCTCCCAGGAAATATGGGACCTACAGGCCCAGTTGGTTTTGGGCCTCCAGGCCCCATAGGCGAAAAAGGCATACAAGGTGTGGCAGGAAATCCAGGCCAGCCGGGATTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031274:ENSMUST00000112931:24
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(31.2=31.2),PF0139113=Collagen=PU(74.5=64.1)
A:
NA
C2:
PF0139113=Collagen=PD(21.8=21.1),PF0139113=Collagen=PU(85.0=89.5)
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:
CTCCAGGTGCTCCAGGCTTTC
R:
TAATCCCGGCTGGCCTGG
Band lengths:
344-1220
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