MmuINT0040163 @ mm10
Intron Retention
Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:141182816-141183592:-
Coord C1 exon
chrX:141183529-141183592
Coord A exon
chrX:141182891-141183528
Coord C2 exon
chrX:141182816-141182890
Length
638 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
AATATTTTTCATACCTGCAGGAG
3' ss Score
8.98
Exon sequences
Seq C1 exon
GGTTCACAGGGGCTCACTGGGACTTCTGGCCTCCTGGGAGCAACTGGTATCCCAGGTTTAAAAG
Seq A exon
GTAAGGAACATTTTGTCTTCTGATGTGTTTGCCTAGACCAAGGTGATGTTCTACCAATCCACAACTCAGGAGTAGTGGGAGCTGTGTTAAGGGAGAAAATGAATTTTGTTTGTATTTCCCGTTTGGCTAAACACACTCTTCACTCCTTGTTCTTCAAAGACATTGCAAACAACAGTGTCACATGCCAAAATCTCTTCCCCGGGCTTTCATGGACAATAAACAAACAAACAAACAAATCAACATTCCATTCGCTTCGTATTTTGATACACCGAAACAGCAACATAGAACTTCACCTCGAAACACCTCTTCCCCTGATGAGCACAGCCCCATAGGCAGGACCAATTCTCTTGTTTAAATGAATCACCATTCCATTCTGGTAGTATTTCAGGGCTCACTTACCATCTTCTCACATGTGCTGGACCATGTTTCCAGTACAGGGGTGCTGTGTATAAATCATCTCATTCTAGTAGCTTGTTAGCATCCCGGGTCCTTTTACCCAGTGGATGCTTTTGTCAAGAAGCCCCTCTGACTGTTTTGAATCTGAATCGAGGGGGAAAATATATTGAAAAGACTGGGTGAAAAAAATGAATAATTGTTTCTTCTGACCATTTGAAAAATAATATTTTTCATACCTGCAG
Seq C2 exon
GAGATCAAGGCCAAACACTTGGCATTTCTGGAAGCCCAGGACCCAAGGGACAGCCTGGAGAATTAGGTTTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273:ENSMUST00000101205:32
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(31.8=100)
A:
NA
C2:
PF0139113=Collagen=PD(9.1=23.1),PF0139113=Collagen=PU(29.7=73.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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