MmuINT0040066 @ mm10
Intron Retention
Gene
ENSMUSG00000067158 | Col4a4
Description
collagen, type IV, alpha 4 [Source:MGI Symbol;Acc:MGI:104687]
Coordinates
chr1:82485581-82486664:-
Coord C1 exon
chr1:82486483-82486664
Coord A exon
chr1:82485645-82486482
Coord C2 exon
chr1:82485581-82485644
Length
838 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TTTGTTCCATTAATTGTCAGGGT
3' ss Score
6.08
Exon sequences
Seq C1 exon
GTGATAAAGGAAGCTCAGGGATGCGAGGGGGAAGAGGGGATCCCGGAAGAGATGGACTACCGGGACTCCACAGAGGGCAGCCTGGGATAGATGGGCCTCCTGGGCCTCCTGGGCCCCCTGGCCCTCCAGGATCACCTGGACTGAGAGGAGTCATTGGTTTCCCAGGATTTCCAGGTGACCAG
Seq A exon
GTGAGGAGATGCTCCTGCAAGGGAGAAGAAATAAACCCTGCTCTCAGGATCCCTTAAGACATCCCTTAGAATTAGCCAGTATGTGCCCTTGTCATTTATGGCTATTTGAAAGTAAGGTGACATGAAGGAAGAATAGAACCTTCTGGAAGGTTATGAGATTTCTGACCAGTGTTTAGAACTGGCTGTCCTGCTGCAGAGGAGCAAGTCAGGTGATTCACACATTCCAGCCCGCCCATGTTTAAATAACTCACAGAGCCTTTGCCTCGTGACTGATGCTTTATTGGAAAAGAAAAAAAAATCCTGAACACTGACCAGTTTCTGGTTTCTCAGCCTTCCCATCTGCTTGGGGATGTCATATTTTTTCCTTTAAAATACACTTGGCCTTTATAATCATGAGTAACATCCCCCTTGAGAAACCAGAAAACATAATGTAGCGACATGTATCAAACTTCTGGAAAATGTATAACATAGTTTTGGCTTTCCATCTTTTGGAATAAAATGGATCTTTAAAATTTATGATACAACACATCTTTCAGTATTTCATTTTATATCAAGTGGTTTGCTCAAAGCTTAAATTCAAGTTGTATGACAGTTACTCTTTGGTAATTGTGTATAACAAAGTCTATACTTCTTGCTGGGAAGAACATCTCTAATTCTGGAGGAGTTTTACCCGCTCATAAAACATAGACATAGTTAGTATTATGCTTACAAGACACTAACAGTTTCCTTCACCATTGCCAATTACAAACACTAACTTGGCTGCAGAAAACTGTAATGTCTTTGTGCCACAGCATGGAAAACCCAACGAGGGTCTTATTTTTGTTCCATTAATTGTCAG
Seq C2 exon
GGTGATCCAGGTTCTCCAGGACCCCCTGGATTCCCAGGAGATGATGGAGCAAGAGGACCTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000067158:ENSMUST00000087050:33
Average complexity
IR
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(64.6=68.9),PF0139113=Collagen=PU(53.0=57.4)
A:
NA
C2:
PF0139113=Collagen=FE(31.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGATAAAGGAAGCTCAGGGATGC
R:
CTTTAGGTCCTCTTGCTCCATCA
Band lengths:
246-1084
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types