MmuINT0040108 @ mm10
Intron Retention
Gene
ENSMUSG00000031274 | Col4a5
Description
collagen, type IV, alpha 5 [Source:MGI Symbol;Acc:MGI:88456]
Coordinates
chrX:141616547-141618268:+
Coord C1 exon
chrX:141616547-141616644
Coord A exon
chrX:141616645-141618117
Coord C2 exon
chrX:141618118-141618268
Length
1473 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGA
5' ss Score
4.3
3' ss Seq
TTGTCATGTGTATGCTTAAGGGA
3' ss Score
4.38
Exon sequences
Seq C1 exon
GTTTTCCAGGAATTCCGGGACCTCCAGGAGCTCCTGGGGCCCCTGGAAGAATGGGTCCAGATGGGCCTCCTGGGCCACCAGGCTTCCCAGGACCAAAG
Seq A exon
GTCTGAAACAATTTCTTAAAGGATATATTTATTTTTATTTTTTATGTGTATCAGTGATTTGTCTGCATGTGTATATATGTGTAGCACATGGGTGCCTGGTGTGGTGACGGTGGAGGCCAGGAGTGGGGCTCAGATGCCCTAGAGCTGAAGTCGCAGACAGTTGTTAACTACCATGTGGGTGCTGGGAATCGAACCTGGGTTCTCTACAAGAGCACTCAACTTCTGAGCCATCTCCAGCCCCAGTCTAGAACATTTTAAACTAGCCCTTTTTCACAAAGACAGTCTTCTCTACTGTCCTTCGATCCAGTTCCTATTCGTCTTAGACATTGTCCCAAGTCTTTATTATATTGATAATACTTAGCTATATTTTCATTTAAAAATAACCAATCCCAAACCATCTTTAATAGAACTTAACACCCAGATCCAAAGTCTCTGACATTGTTTTAGACTGCTAGGTTTTTGGATTACGTGAAAGAATCCAATGATCAGCTTGGCCTATGTTTATGTAGACAAACAGTAACCCATTTCATACTTTTACATGTGTGATGATTGGTAAGATTGTGTTGGATATATCAAGCCCTTCCTGTATTGTTTCCTCTGTTCCAATTCCATTAAATATACATAAACCAAATCACTGCTATTTGGTAATACTAATAAATAACTCCCTTTATATTTTTCCACTGTAACTTATTTAACCTTAAACACTTTTCAGTCAGCCTTCAGCAAACTGCTAAAGCATGTAATTATACCTACTCTTCCTGAATTCCGTGCTTAAATGATCTAATCTCAGTGGATTTCATCCTTATTACTTGTTTTCCTCATGGAAAAACAGCTGACAGACTCTCATAAAAAAAAAATGCATCTCTTTTGGCTTGTTTTTATTTCATGATGAACATTTTCAAATAAACACAAAAGCCCAAGAAATGATCTAATGAACTTTGACAGATGTGTCAGTCAGGTACAAAACTGCTAAGATTATAGTAACACTTCCTTGATCTTTTCCTGTTTTTCAGGAAGGGGGTGGTCTCACTTAACCCAAATCTCAAGATTACATCATTTCACTTACAAATGCTTTGCCATTCATATGTAACTAAATGAAAATTGTATGCAGAAACCACAATGACATTATACTACTTAAGTCATGTTAAAACTAATTCTTTGCATTATCTGATCCTCAGTCCTCTTCACATTCCCTCACTTGTGTAGAGTGTGGTTTAATCCCTTGTTTTCAGTTAACTTTTGTACTTTGAAAACAATCCAACTCATTTAATTTGCTCTCACTAAACCCTATTTCTGTCCCTTCCAGATATTCTCTCTAACACACCCATCATTTTTTAAATTTGACTATCCTCTTCTTAATATGGAAGAAAAAATATTACTTTGTATTCGATGCTTTAAATTCTCTGTAGTAAATGGTAAGCGTCAGGAAAGTCACGGGACTTTTCCTTGTGTTTTGTCATGTGTATGCTTAAG
Seq C2 exon
GGAGAGCCAGGATTTGGGTTACCTGGGCCACCTGGGCCACCAGGATTCCCAGGTTTCAAAGGAACACCTGGTCCAAAAGGTGATCGTGGTTTCCCAGGACCTTCAGGTCCTCCAGGACGCACTGGCTTGGATGGGCTACCTGGACCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031274:ENSMUST00000112931:28
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=FE(55.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(24.1=27.5),PF0139113=Collagen=PU(69.7=90.2),PF0139113=Collagen=PU(9.5=11.8)
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:
AGGAATTCCGGGACCTCCAG
R:
TTTGGTCCAGGTAGCCCATCC
Band lengths:
240-1713
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