MmuINT0040173 @ mm9
Intron Retention
Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:137606653-137607358:-
Coord C1 exon
chrX:137607212-137607358
Coord A exon
chrX:137606770-137607211
Coord C2 exon
chrX:137606653-137606769
Length
442 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GTGCATTTTCTCTCTTACAGGTT
3' ss Score
12.55
Exon sequences
Seq C1 exon
GCTTTTCCGGCCCACAGGGAGCTCCAGGACACACACCAATTGCTGAAGCTATGCAGGTTCCTCCAGGACCTTTGGGTCTGCCAGGCATTGATGGTATCCCAGGCCTCATAGGAGACCCTGGGTCTCAAGGCTCTGTGGGTCTGCAAG
Seq A exon
GTAAGAATGGCACCAGAGAACAGGTACTCACTGGGAAGCTGAAAGGCCTTGGTTGAGAGACTGAAGCTACTGGCTTGACACAGGTCTGAGAAAGTGCCTTCATCAAACATTTCCCAAGCTACTTCCCGAAGCTCCCAAACTCTTTGCCAGGGAAGGAAAAAGCTAGAAAGCCAGTGGGGCAGTGGTTATACTTGTCTTCAGAGAACATGTGAATCTCTCCCCTAGACAGCTTGCCATTTCTAAAGAGTGTTTGGAGCTAGAGAAGACGTGAGTGACAAAGGAGAACACAGGGTAGTGGAGAAAGCAAAAGACTCTGGACAGGAAATGTGGTTTCCAAGTCTTAGCTTTGCCCCAATAGGAGTAAGTTGTTATTCTCCCTGTGACTTCACATGAGACTTCCATATTGAGTGCTCCTCTGCCTTGTGCATTTTCTCTCTTACAG
Seq C2 exon
GTTCCAAAGGCCTACCTGGCATCCCTGGTAAGGATGGCCCCAGTGGGCTTCCAGGCCCATCTGGAATCCTTGGTGATCCTGGTCTCCCTGGACTACAAGGACCTCCAGGATTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273-Col4a6:NM_053185:41
Average complexity
IR-S
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(19.7=24.0),PF0139113=Collagen=PU(54.2=64.0)
A:
NA
C2:
PF0139113=Collagen=PD(44.1=65.0),PF0139113=Collagen=PU(61.0=90.0)
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:
GCTTTTCCGGCCCACAGG
R:
TCAAATCCTGGAGGTCCTTGT
Band lengths:
262-704
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: