MmuINT0040445 @ mm9
Intron Retention
Gene
ENSMUSG00000032572 | Col6a4
Description
collagen, type VI, alpha 4 [Source:MGI Symbol;Acc:MGI:1915803]
Coordinates
chr9:105923097-105925255:-
Coord C1 exon
chr9:105925205-105925255
Coord A exon
chr9:105923133-105925204
Coord C2 exon
chr9:105923097-105923132
Length
2072 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTTATCATTTCTGACCCTAGGGT
3' ss Score
9.04
Exon sequences
Seq C1 exon
GGTCTTTTCGGTCCAGACGGCCATGGTTATCCGGGAAGAAAAGGCAGGAAG
Seq A exon
GTGAGCTCCTGCCAAGAGCATTCCAATATCAAGTCACGTTCCGAGTTTTACTAGAATATAGTGACTGTATGTCAGGAATGGTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCCTTTCTTCCTTCCTTCCTTCCTTTTTATAGCTTGACAGAGTTCCCTTACTGAGAAATCAGACTGGGCTCATCCCTCACTTCCCTGCCTTTCTCCCTTCACATTCTCTATACTCACAGGCTCCCAATGATAGATTCAACCAGCTATAGGTTAAGACATCTGAGAAAAATCTGCATGTGTACTGAACATGTACGAACCCATTATCCCCTAAATAGCTCAAGGTGATGTCTGTTTCACAGCACCCGTAGTTGTAGGTGTTCTGTGTCATCTGGAGACTAAAGTCTAGTAGAGGGTGTGCATATGTCACATGTATGTGCTTGGCAGCACCGTATTACGTCAGGGCGTTGACTGTGCTCAGATTTCTGTACCTTTGGGGGATATTGGAATCAACCTTCTGAAGATATTGAGGGGCAGCTGTAATTCTTTATTTCTTTTAAAAATACATAATATTTTAACTTTTTCTTTGAGAATTTCATACTCTCATTTTATTCCTTCCTCCTATCTCCCCACTCCAGCTCCTTGATCTCCTTCTGACATCGTCTCCTTTCCAAGTCTTTAAAACTTGCTAAGTCTGATTATCCCTGCCCATATGTGTGTGGGAGCATCTACTGGAGTTATAATTTCTAGGTGGTGTAGGGGGAATTGTAAAAACTATTTATGGATTGTCGACCTCTGGGATTGAAATGTGGCCTCTTGATGACCTTTCTCAGAGGAATGTTGAGGAAAATGTATTCACTGGTCATTGAACGTTATATAAACATGTCCAATATATAGAGAGCTGTATACCTAATGAAAACTGGTTTTCCTTCTAGCGGCCATCAACTTAATAATTCCTCAGCCCTGAATATCTTTTGCAGGAAGGCTTTATAGAAAGCAGCAAGTGGGAGGTGAATGTTTCTAGCCTGGCAAGCATCTAATTGGAGAGCACCTATGGCCTGTAGCATAATTGGCTGGTGCTGGGAGTCAAACCATAAACTTAATTTCTGCTTCCCTCTGCATTGGTGGTTGTTATGCAGGGGGCAGGCTTGTTGGCAATTAACTTGGAAATGCTGGATTGTTGGGGAAAACTAACCTGGAGATGCTGGTCTGTTGGAGTTAGCCTAGAAACTGGAGCTAGGCTTGGGTTTTGTTGTGGGGTAATTTGGAAACCAATGCTAGGTACCGACCTGTTAGTTTACCTGAGTTCAAGTTTTCTAAAATGGAGTCTGAACTTAAAAGATTTGTTCTCTCACTCTAACATTTACTTATTTGTGTGTGCAAGAGCATAGGAGAGTGGACTGCCTGCTCGATTTGTTTTCTCCCTCTACTACCTTTGGTCTCAGGGACTGAACTCAGGTCGGTAGGCTTGGTGGTGAGTGTCTTTCCCCCACAGGACCATCTCACCAGCTCATTTTTAATTTCCTGGTCCCCACTCTGGAATCCTGGTCCATTTCTGAGATGCTATTTACTTCTTTGGTCACTTGCTTCTTTGGGAATGCAAGTTCAGTGTGGGTCTTGGTTTTGTGCATAGCTGAGTCCCCAGTGATTACAGGACCACTTGGCAAACAGCAAGGGATAACTAAATGTCTGTGGGATGGGCGATCATTTTGAAGCATGCCTGTGCCTCTGACGGTTCCATGCTGGGTCCTAACATTCAGATTGATGCTCCTGCCTTGCTTTCTGTTGTCACAGATCTCAGGGGCTTTAGACTGAGAAATAAAATGCACAAGAAGGAAGTTTCATTAGACCCTGCATCAAAGATGCTTAAAATTGTAAAAACTATTTATAAATTGTTGATCTCTGGAATTAAAATGTGGCCTTTTGATGACCGTTTCTCTTTCCTGGAGGAATGTTGAAGAAAAACTTAAATTACCTGGCACTGAATGTTTTCTTATCATTTCTGACCCTAG
Seq C2 exon
GGTGAACCTGGGTTCCCTGGCTATCCTGGTGTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032572-Col6a4:NM_026763:26
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(12.9=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
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: