MmuINT0040175 @ mm10
Intron Retention
Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:141168594-141169750:-
Coord C1 exon
chrX:141169559-141169750
Coord A exon
chrX:141168881-141169558
Coord C2 exon
chrX:141168594-141168880
Length
678 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TGTCCATCTTCTCTTCCCAGGAT
3' ss Score
10.97
Exon sequences
Seq C1 exon
GAGCTCCGGGAAATCAGGGCCCCATTGGGCAGCCTGGGATGCCTGGGCACGGTGTGAGAGTGGGCTACACACTAGTAAAACACAGTCAGTCAGAACAGGTGCCACTATGCCCCACTGGGATGAGCCGGCTCTGGGTGGGTTACAGCTTGCTCTTCGTGGAGGGGCAGGAGAAAGCCCATAACCAGGATCTGG
Seq A exon
GTAAGTACAGCTAGTCCTTGCTCCCTGACCCTACAAGGATTGAGAACTGACCACTTTTCTTCTCACAGCCCTTTCGACTCATGGTTATGAAATAGGCCACAGCTCTGGGGTCAAAAGGATTTTGATTCAAATGCTGGTCCTACTGCTTCAAAGCCACAGGCCCTGGGTAAATTATTCAACCTCTCCAAGCTTTCATCCTCCCTCAATGGGACTAAGCTATTTCTACTATCTGTCACATAGAGTGCTGTAAGGAATTCATGAATCACCCAATGTACAATATATTTAAGCCTCCATTAAGTATTAGTGATTAGTAATAACAATAGTAACATGACCTACAGGGCATTGATGATTGCCCAAGGATTAATTGCATTAGCAGCAGGTGTGCTACCTCTTAGATGTGAATTCTGTCTACTAAATGTAGGTTTTACAAAGCAGATTAATTAGGGAGTAATTATTCACTTTATCAAAAGATTCTCATCATTATTCAACTCCCCTGGTAACTTTATGATACAATTTGATCCTCAGACTCCAGCACCTACCAAAGTCATAGGACTGTAAGAGCGCTGTACTCTCCGAGCAAGCATTTAGAAGGAAATTCACATCTTTGGCTACTCCAGGCCTTGTGCCTCTGCCCTTTAGCCAGCACTTAGCTGATTCTTGTCCATCTTCTCTTCCCAG
Seq C2 exon
GATTTGCTGGCTCCTGCCTGCCCCGATTCAGCACCATGCCCTTCATATACTGCAACATCAATGAAGTGTGCCACTATGCCAGACGCAATGATAAATCTTACTGGCTCTCCACTACTGCCCCCATTCCCATGATGCCTGTGGGCCAGACCCAGATTCCCCAGTATATCAGCCGCTGCTCTGTATGTGAGGCACCCTCACAAGCCATTGCTGTACACAGTCAGGACATCATTGTCCCACAGTGCCCTCTGGGCTGGCACAGCCTCTGGATCGGATACTCCTTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273:ENSMUST00000101205:43
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.328 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(37.3=33.8),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(25.9=31.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTCAGTCAGAACAGGTGCC
R:
GGCACTGTGGGACAATGATGT
Band lengths:
353-1031
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