MmuINT0040172 @ mm9
Intron Retention
Gene
ENSMUSG00000031273 | Col4a6
Description
collagen, type IV, alpha 6 [Source:MGI Symbol;Acc:MGI:2152695]
Coordinates
chrX:137607212-137609260:-
Coord C1 exon
chrX:137609162-137609260
Coord A exon
chrX:137607359-137609161
Coord C2 exon
chrX:137607212-137607358
Length
1803 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
GTTTCACTACCTGTCTTCAGGCT
3' ss Score
6.94
Exon sequences
Seq C1 exon
GCATGAGAGGGGAACCTGGCCTCATGGGGACTCCTGGCAAGATCGGGCAACCAGGAGACCCAGGATTTCCTGGGATGAAGGGGAAGGCGGGGCCAAGAG
Seq A exon
GTGAGTGCAGGGCCAAGCCTGAGCCTCAGAGGGAAGGGGTACAGCATGAAGTTGAGGTTTTTCGGAAGCCATGTTGTCTACCACACCACAAAACCAAGTAGGGTATCATGCTCCCAAGCCCAGGAGGTAGTTTCCCTCCTTTGGAGATACCACCATGCCAATCTACTGCCAGAACTGAAGGTCCCTACCATTGGTACCTGACCTCCCTCTGTATTACTTCTGCATTGCACCTAGACCACTAAGCTCACTTTCTAAGTTCAAAAAAGAAACAAAATTCTTTCTATCCTCGAGCCAAATGTCAACTATTCAGTCTATCAGCCACCCCAGAGGGCTCCTTCTCCTAGCATGCCTTGTATCTGCTCACTTTCTATCAGTTCTGCTGCTCCCTTGAGGTCTAAGCCATCAGCAGTTCTCATGTAGCACCCTTCCTCCCCCAACAACAATTATTTGTCCCATATAGTCGCCGGTAAAAAGCAAACCATTCTATTCATGGCATAGACAGGAACCATGGCCCACAAAATCCTGTGTGACCCCTCCCTCTTTATCTCATGCCAGCTCATGTCCCTTTTACTGTCCATTGACATCTGAAATATTGTCCCAATTATCCTTTCTGCCCTCCTCCCCTTCCTACTAGTTCCCTTTCCCCTAATTAGCCCCTCCTCTGTTTTTATGTCAGATATGATGTTCTCCAATTGTATCCATTTGCTTGTACATGGCGTGCTTCACTTTTCATCCTGACTGAAGAAAGTTCCTTCATGTATATGTGTCCTATTTCCTTTGTCCATTCATCTGTTAATGGACATTTAGGTTGTTCCCAAACCTTGGTTATTGTGAATACTACAGGGATAAACATAAATGTGTATGCTGGCTTGGAGTCCTACTGGGAATGGTACAGCTGGATCATATGGAAATTCTAGTTTTAGAGTTTTCTAAGGAGTCCTAATATTGATGCCTGCACTAGTTTACCTTCCTGTCAGTACTGTATATGTTTTCTGATGCTTGCTTGCCCTTCAATCTTTAAATGTCTAGCTCCCCCTGATACGTCTGATGTTTGAATAGTTTCAGTGTAACTGTCATTGGTTATAAGAAGCCACTGGTAGCTCTGAAGCAGACCCCTTTACCCAAACCACTCCCTGCTCCCTCTCATTGTCACTACAGCACTTATTTCCTCCCCAGTCCTTCTTATAAGATTTGAACAATGGGGTTAACGGTATTTGCCAAATGGTGCTTTGTTCATCTTCATCACTAGGCCTTAGGCTCTATAAAGGTCTATCACTGCTCTTGTTTCTCATCTCCCAGAATCTTGGCAGATAGTAAGGACCCAAGAATTACTTTATTAATGAATTAGTGAACAAGCTATTCTATTTGTAAAGTGGCTGACTTGGGTGGGTCTCTTAGACTGGGATGCCAACTGCACCTCTGAAGTTGAATACATCGATCGCTACAGTATCTTTGGTAGTGCATTCTGACCAGTGTGTAAGTTATAACTGCTTCATCCCTGACCCAAAGCTCAGCTTGCTAGAGTTGCAGTAGAGATTTCCTAACTGCTTTCCACCTAGTGAATTCTATACTGGGATATGGGGAGCCACAATAAGTATGACTTGCTCCCTGCCTTGCCTACAGGCACTAAGAAGAAGATGGGAAAGGAGGTTCTATCAAGGGTTGTGTATTCTATACTGGAGGCCTCAAGTGGGGATTGTGAGCACAAAAAGAAAGAAAATAGTTGGCGACTGCCAGGCAGAGAGAAGGCTGCCTTTGTTACTCCTCCAGCCTGACAGGTGCTGTTTCACTACCTGTCTTCAG
Seq C2 exon
GCTTTTCCGGCCCACAGGGAGCTCCAGGACACACACCAATTGCTGAAGCTATGCAGGTTCCTCCAGGACCTTTGGGTCTGCCAGGCATTGATGGTATCCCAGGCCTCATAGGAGACCCTGGGTCTCAAGGCTCTGTGGGTCTGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031273-Col4a6:NM_053185:40
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=FE(54.1=100)
A:
NA
C2:
PF0139113=Collagen=PD(19.7=24.0),PF0139113=Collagen=PU(54.2=64.0)
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:
GAACCTGGCCTCATGGGGA
R:
CAGACCCACAGAGCCTTGAGA
Band lengths:
231-2034
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: