MmuINT0040484 @ mm9
Intron Retention
Gene
ENSMUSG00000043719 | Col6a6
Description
collagen, type VI, alpha 6 [Source:MGI Symbol;Acc:MGI:2444259]
Coordinates
chr9:105617652-105619066:-
Coord C1 exon
chr9:105619004-105619066
Coord A exon
chr9:105617688-105619003
Coord C2 exon
chr9:105617652-105617687
Length
1316 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TTGCTTACTTCCTTTCCTAGGGT
3' ss Score
9.83
Exon sequences
Seq C1 exon
GTATCTGCTGGGATTCCAGGAGAGCCGGGGTCCCCCGGGGAGCCAGGACCCCCTGGACGGAAG
Seq A exon
GTAAGTGGGAATATTTCCTGTAAGATCTTTACACTTTAGAGCTCAGGGCACAGGCCTGCCACTTTTCAGGTGCACACACCGTCTGCCTTTGCTGCCTGGTGACATATTTCACTATTCCCTGTGTGTTCCAGAAAATGGGGCAAATTAAATATCTCCCTCAGGAAGGAAGAAATATAGGGTGAAGGTGAAAAATCAAGCCAAAATGAGGTTCTCTTCCAAAATATTTTCTTTTACATTCATAGGTTGGTTTATTTGGGAGATGGCACCTTGCAGGTTTCAGAGAGTGAGTTCAAGAGTCAGTTCTCCTCTTCTATCACATGTGTCCTGGTGACTGACCTCAGGTCATCAGGCTTGCTGACTCTACCCTTACCCACTGAGAAGTCTCAGCAGCCTGAGATTCTGCACTCTTCATGAGTGGGTTTGGTTATCCGTCCAGTCACGGTTTCTATCCTACATTCATTCAGTGAATGAAGTATGCATGTGTGTGTGCACATGTGTATATGTGTGTTATGTGTGTGGGGTGTGTGCACATGTGTATGTGCATGTGCACATGCATGAAATGATGAGCAGTGTATGTGATTGAAGTTGTGTTCCTGTGGAACATACCTGGAGATTGTGTGGAGCACCATGGCACTTTTCTCTCAATGTTTCTGTTTGAGAGAAGCCAAGACTTTCTGCTCTAGGATGGGACTGTTAAAAAAAAAAAGCTAAGTCAACTTTGTTCTTTCCACTCCCCACCCTCTCCCCGCCCCATCCTGCCCTTCGCTGCCCCGCCCCCTCCCCACCCCTCCCCACCTGCCCGGACATACACATGTGTATATTCACTCATTTGGGGAGAGATGCTGAGTGAGCTTTTCAGGTGTCTGAGGCTGAGCTGACCCCTTTGTCCATCAGCCGTGGATAGGAATGACCTAAGTTCATCTTGGGCTGCTGTATCACAGCGGAGCTATAATACCAGGTGGGAGCTTCCAAGACTTGGGAGGCAGCTGAGAACAGATGGCTCAACCTTTGCTAGTGGCAAGCTGAACACCTGCTCCAGGGCTCTGTGGACATCCGTCAGGTGGGCAGCTCCCTCAGGTTCTGGGCATCTCTGCCAGGATTTGGGGAAAGTGGCCTTGAAGGTTTGTGTGCACATGCACACCCCTAGTGCCATCTTTCACGAGGCAATGTGTGTCCTAACTGTGTTCTTTGCTCCTTTAACTTTAAAGGAGTAAACCCTTTTCAAAGGGTTCGCAGGGAAGTGTGGGTACACATCCTGGCCTACTGAGGTCTAAGTCTGCAGCCATAAGACAGATTTTGCTTACTTCCTTTCCTAG
Seq C2 exon
GGTGTGAAAGGGGCCCGAGGACTGGCTTCGTTTTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043719-Col6a6:NM_001102607:29
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=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
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: