MmuINT0040179 @ mm10
Intron Retention
Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:141223996-141225689:-
Coord C1 exon
chrX:141225621-141225689
Coord A exon
chrX:141224032-141225620
Coord C2 exon
chrX:141223996-141224031
Length
1589 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
TCTCTATTTCTATTTCTCAGGGA
3' ss Score
9.74
Exon sequences
Seq C1 exon
GGGCTGCCTGGTCACAAAGGTGCCAAAGGAGAGCCTGTTCCTTTTCAAGGCAGCATTACAGGAATAAGG
Seq A exon
GTAAGAGTTTCTAAAGCAGGCAGCGGAGTGGGTGGGAATCAAGGTTTCCTCACACCAAGCCATTTCCAAAACTAAGAAACCTGTGCGCCTGCTTAAGGAGCAGCACCAGCTGACTTTCAAAGGATTCCAAGTTTTTTGGTGGTAGAAACATTTGCAGAAATGTTTGTAGCTATGCTGTCTAGAAATTTGTTTTCCAGGATCTGCACCAAAACTAAGAGAGAATTTGGCAATGAGTTTGCATGGCTATTTTCTTTGACAAGCCAAAACGTTTTCTAGAGGCACATGCTTTTGTGTTTCCTCTAAAGCCTTAATACCTATGCACCTTAGTTTGAGTCTGTATATATCCTTATACAGCTTAGTATGGCTACTGCCCCAGCATCTGGGTTCCTTCTCTAGACTCCTGAAAGTCTACAAATACTTGCCTGTCAACTTTCAACTGATTGGAATCTAATCTCTTGTCAATAATATCATTTTATTGAGCCTTCCTCTATTTGCTAACTGGTAGCTTTATGTGTCCTCAATAAACCCTGGTTCCAAATGATTGACCCTACTCGTCTGCAGACTGGGAAAGAATCCATCACTACCTTGATAGCAAATAGGAATTTATGTGCCTGCATTTGGAGGGGAGAATACACCAAGCTTACTGAGATAATTGACACTACTCTCCCATCACTGTACAGGGCCTGGAACCTTAGAAACTGGCCATAAAAGCAGAGATGGGGATGGAACATCTGGATAACTACAGAAGAAGGAAATTTGGGTTCTTGACTTGGATGCCATAGCAGAAGATAGAACATTAAAGTTGGCAAGGGCCTCTTGGCTTTTGAATTCATGTCACTCATTAGACAGATTTAAAATCTAAGGCTATATAACTTACTCAGAGCCAGATGGCCAGTTCTCTGAAGAACTAAACCTCAGGCAGTGTTCTTTCCATGCTACAGGGAGCTTAGAGGTTTTTACTGTAAGTCAAGTGATGTAAGACTAGCAGGTGTCAAAGCACAGCCATTGTCTTAGCAAACATTGATTAAATGATTTTTCCAGAAATCAAAGAAACCTTGGATCCAGTGGAACACAGCAATTTCCACAAGATGGTTATATTACAGATTCATACAGTGGCTTAAGATGCCTCAAAGTAATTAAAACGTAATCAGAGTCTGTATGCTCTGTTGATTTTCCCTTGAAATGTCTGATTTGCATTGTATACATATAAGCACAGATTCTCTGGGGATGAAGGCACAAGGGAAGGTAGCTTTGCTTTCCTCCAAAAGGAGCAGAAAATCACCAGCCTGCAGAAGCCTTTTCTAATTGATAAGTTCCTAGCAAATGTGAAAATTAATTAATCTAGGTTAAGTAGGAAATCTTGTTCAGCCAAGGCTATAATATTTGTTTTCTAGAGTCCAGAATGTTCATAGGGAAAAAGTAAATGGGTAGATACAGCCAATTTATGCATTATTTAAAACACAAGACCTTGATAGGGGCCCAAGTTGCCGTAATTTGTTTCTATCCCCTTGAATCTCAGGTTGGTTGTCTGAAACCCTTTGGGCTTAATTTTTAATCTCTTCCGTGTGTTCTCTATTTCTATTTCTCAG
Seq C2 exon
GGAGATCCTGGGCTGCCTGGACTAGATGGAATCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273:ENSMUST00000101205:7
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(21.0=56.5),PF0139113=Collagen=PU(10.3=26.1)
A:
NA
C2:
PF0139113=Collagen=FE(19.0=100)
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