MmuINT0040448 @ mm9
Intron Retention
Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:105920185-105921797:-
Coord C1 exon
chr9:105921735-105921797
Coord A exon
chr9:105920221-105921734
Coord C2 exon
chr9:105920185-105920220
Length
1514 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATG
5' ss Score
5.46
3' ss Seq
CATGCTTCTGTTCTTTCCAGGGC
3' ss Score
11.56
Exon sequences
Seq C1 exon
GGCAATTCTGGATTTCCTGGGCTTGCTGGAACTCCAGGTGACCAAGGCCCACCGGGAAAAATG
Seq A exon
GTAATGAGTACCTTTCCTTCTATATTTTTAACCTTGTGCCAAGGTGAGAAAGAGCTTGATAAGAGGCCTCGCTGAAGGAGAAACAAACATCTGGGACATTTGGCAGGCTCAAGGGAACTGGCAAACTACTTAGAAAGCACTAACTTCAAACCCTACATAGCATTCTAGATGTAGTGTTTCTGAATATAGAGGTGATCTTGGCGTAGATAGAGATTTATGGATCTTCCTAAATACATAGATTAATACATAAAACTTACCAGTGAATGAGCTTATCAATGCAAACATGATGACCAATACATAAAGCCAGAAGGAAATCCTCATTAGATATGCCATCCATACAATCTGAGCTGATAATGCTGCAAGACTAGAAGAATTTTTAGAATACACTGGGATGTAGAGAGACTCTGAAGGTTTGCCCTGTGTCCTGTTTTAGAGACAGCATGGAATAGTTTGCTTCCCTGTGAGAAACCACTGACCACAAGCGAGTTGGGGAGGAATGTGTTTATTTGGATTATAGATTATAGTCTATCATTGAGGGAAGTCAGAGCAGGGACTCAAGGCAGGAAGGAACTTGATGGCCAGGACTGAAGCAGAGACCATAGAGGAATGCTGCTTACTGGCTTGCTCCCCACCGGGGATGGTAGCATCCCAGGCCCATCTGTTTAAGGGTGATACTACCCACAGTTGGTTGGGAACTTATCTGTTGGCAATGAAGAAAATTTCTCATGGACATGTCCATAGGCCAATCTGAGACAATTCCTCACTTGAGATTCATCCTTCTGAGATATGCCAAGGTTTGTATTAAGCCGGTAAAAAACTAGCCAGTGTGTGTCTGTCACTCTGTGAGGAATAACATATTCATCAGCCAGAAGGGGACATCGGCATGTCCCTCACTGGAGTTTGGAGTATTTATTAGAGGGAATCAACTAAGTCAGAAAAACCAAACACCACAGAGGTAGTTCATAGTCATCTGATGATGAAGTACTGACTTAGTGGGTCTCAGTACAGTGACCTGCCCTAGACTTCAGGTTACCACTGTGTAGAGACTACACAAAGTCAACGACTGGCTAGGCTCCCAGGGGGGCTGGAGCCAGACAGTGGTAACTGGAAGACTTCTGGGAGGGTTCCTTCACTACGAGGGTCGAAACAGGGTGGGGATGAGAGGCGTGGAAGAGCAGGAACAGGGGGATACCAGGATGTAGTTTAGAATAGCATGTGGCAGGACCTGGGATCTTGAATACCAGTTTTTGAATTTGAACTTGAAGTATAAGTTGGTTTCAAAATTACTTGGTCTTCCAAGAGTTTATGTCTCATCCTCCTGGGCTTCCTGGATTCTGAGATTTAGGATATACCACTCAGGTACTTTGACCTCCTTACTGGGCTGGGCAGAACTCCAGGGCCAGGAGAGGAGGGCAGTGTATGTGCCCTGGTGAGCACTCAGTATCTCCAGTTGCTTATAAAAAAGTGTTAGGAATCAGAACCCACGGTTCTAACCATGCTTCTGTTCTTTCCAG
Seq C2 exon
GGCACCAAAGGCTCGAAAGGCTTGGCAGATAGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572-Col6a4:NM_026763:29
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=0.667
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(32.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(16.1=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: