MmuINT0039940 @ mm10
Intron Retention
Gene
ENSMUSG00000031503 | Col4a2
Description
collagen, type IV, alpha 2 [Source:MGI Symbol;Acc:MGI:88455]
Coordinates
chr8:11423717-11425540:+
Coord C1 exon
chr8:11423717-11423823
Coord A exon
chr8:11423824-11425338
Coord C2 exon
chr8:11425339-11425540
Length
1515 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGC
5' ss Score
8.8
3' ss Seq
TAACTGGGATTCTCTTGCAGGGC
3' ss Score
8.42
Exon sequences
Seq C1 exon
GGGAGCGAGGACAGCCAGGTATCCCTGGTGTACACGGAATGAAAGGTGATGACGGCGTCCCAGGACGGGATGGGCTGGATGGATTCCCTGGCCTGCCTGGCCCCCCG
Seq A exon
GTAAGCTGTCGCCTCGCTCCAGCCAACCCGGCCCCACTCCTCAATTGCTTCCTGTTCTTTGGACATCTCGGGAGTCATGGACTTGCCCTTGGCTCTCACCCAGTGCCCAGGACAAGTCCATTCTGTTTTAGTCCGCGGACATCATGTCTTTAAAGACTAGTGAGTGAACTGGGAAGCACAGGGTGAACGCTTCAAACAGTGGAGGGACGTCCATTATGGTCTCTGTGGAATAGGCCCTGGGTGTTGTCAGGAGAGGGTCTTCCCTGTTCCCAGGCAGATCTTAGAGAGTTAGTGTCCCTCCATTTTCACAAATCTTGTGGGCTCTAGCAAGCTAGAGAGAATGACGTCATAAGGTAAGAACAAAATGGTGGGGCTGGAGAGATGGCTCAGCGGTTCAGAGCACTGACTGCTCTTCCAGAGGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTTTAATGGGGTCTGATGCCCTCTTATGGTGTGTCAGAAGATAGCGACAATGTTTGTATATATATATATATATATATTGTGTATATATGTGTGCATTGTATATATGTGTGTACATTGTGTGTGTGTATATATATATATATGCATATGTGTGTGTATATATATATATATATATATATATAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGCAAAATGGCTTGCCCAGATGCCATCCTGTGCTGTCCACTCTATGGTCTCAGGTGACCCTATGAAATGGGAAAATGGGAAAATGGGAAGTCCTGCTTTGTTGACCCCGCCTACACTAGAAAGGCTAAATATGGATGCACATGTGCTTTGAGGGTCCTACAAACAAAGAGAGACTTGGCCCAATGACTTGCCATAGTACTCTCTTATCTTTGAATCCAAAGGAGAAAGTAATGTCAGGGCAGGCTGGCTTCTCCACTCCTGCCTATCAGAAGCCCACACCCTTACCCATGACTCTGTAGGCAGGCTAGGACACTCAGCATCTCATTAGCCATACAGAGCACTGACATTGGGGCCACACTGGGCACAACCCTGTGAGCCCTGCCCCTGCCCACTCACCACTCCTACCATTATCCCTCCAAGTGTCCCCACCTGGCTGAAATCATCACTACATGGCATGCCACTGGACAGGACACCTAGCCTGTCCCCTGTAGATGCCCCTCATTCTAAGAGCGCATGGCTCCTTCTTGTCTAACTCCCTTTCCTCTAATGATTGATGTCCCTCATGAATAGCAGGCATGTCACACATGTGACAGAAGGACACGAGTTCCTGTGTCCATGGTCCTGAGTATAAATGTGTCTCCCAGGCTGACCCTCCACTGTGCTGAAAGTCAGTGCTTTAAGCTCTAACTTCGACTCAGTCACTCGCTTAGATGCTTTCCTTCCAGCTGACCTGTTCTTGACCTGCAGCCCAGAATTCCAGAGAAACGGGGAAGGGCAAAGGGGAAGGCATGGCTGGCTCAAATGTCTGTATGTGTTTGAAGGTAACTGGGATTCTCTTGCAG
Seq C2 exon
GGCGATGGCATCAAAGGCCCTCCAGGGGATGCAGGTCTCCCTGGTGTACCCGGAACCAAGGGCTTTCCAGGAGACATCGGTCCTCCAGGACAGGGCTTACCAGGTCCGAAAGGCGAGCGTGGTTTCCCTGGAGACGCTGGGTTGCCTGGACCTCCGGGCTTCCCTGGTCCTCCAGGTCCCCCAGGAACCCCAGGACAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031503:ENSMUST00000033899:24
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=FE(50.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(42.9=44.1),PF0139113=Collagen=WD(100=97.1)
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:
GAGCGAGGACAGCCAGGTATC
R:
CTCTCTGTCCTGGGGTTCCTG
Band lengths:
307-1822
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