MmuINT0039963 @ mm9
Intron Retention
Gene
ENSMUSG00000031503 | Col4a2
Description
collagen, type IV, alpha 2 [Source:MGI Symbol;Acc:MGI:88455]
Coordinates
chr8:11443831-11445122:+
Coord C1 exon
chr8:11443831-11443947
Coord A exon
chr8:11443948-11444930
Coord C2 exon
chr8:11444931-11445122
Length
983 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
CACTTTCTCTTGGTCCCTAGGGG
3' ss Score
10.48
Exon sequences
Seq C1 exon
GCTTCCGTGGGGCCCCAGGCAAGGCTGGGCCTCAGGGCAGAGGTGGCGTGTCTGCTGTTCCAGGGTTCCGGGGAGACCAAGGGCCCATGGGACACCAGGGTCCAGTTGGCCAGGAAG
Seq A exon
GTATGTGACAGACGGCTGATGGGACAGAAGCTCTGCTGAGGGTGGGAACACCCTGCGTGGTCTGCATGGGAGGAACAGACCTGGCAGAGTTGGGACACAAAAGCTCCCAAGCCCAGATGCAGGCTCAACCCAGGCCTGGCCTGGGCGCTGTAAAGACTGTATCGTCTCTTAAAATTATTGGTACATGTGCAAGAGGGAATGGGCCAGGAGCAACAGCAATTTGCACACCCCCAAAAGATTTGTTTTAATCAACCCAAGCTTAGCAGCAGCAGCAACCATACTAAGACAAAAACACCAGAGACTTCACCAGTGAGTCAAAGGACAGTGAACTGCTCTGTGGTGGCAGCTGTGGTCAGCCACGGAGACACACATTCTCCAGCAGGGACATATCAGACTTAGTCCTGGGCAGGCAGGGGACTGTCAAGGGGAAGGGAGTCCTAAGAGAAAGCAGATATACAGGGTGTGTCTCAGAGAGAATGGTGGGCAACGGGGCCAGGCAGCTGCTGATGGCCAGACTAGATGCTCTCGCGGCATCTTGGGTAGAACAGGGCCCTTAGTGACAGTTACAGGAGGCGGGTCTCACTCTTTCTGTGGAGCATTCTAACCCTGAATAATCTCGCTCGCCCTGAGATGCTGCTCTGAGAATAGCCATCCTTGGGGAAGAGGCCTAGCTGTAGGGGTGGTGGCATAGGTACTGGCTCTTCCCTGACACCTCTTACCCTAAGGGGCCCCAGTTCTGCTATGCAGCTGGCTCTCCCTGGAGAGTATTCCTGTAGCCACTGCGCTTTCCGGTCCTTCCTGTACATGTTTGATGCTGATGTTCTGTTGTCTTCTTGAACTGATTTGGGTCTAGAAAGCCTGAGGCCCAAGCCTCGGGGAGAAAAAAGAGGCAGAATCCTAAACTAACTGGGATGCTGTCCTCTGCCCTGGCTCCCGGGGGTTTCACAGCAGCTGAACAATATCCACTTTCTCTTGGTCCCTAG
Seq C2 exon
GGGAGCCAGGCCGTCCAGGGAGCCCAGGCCTGCCAGGGATGCCAGGCCGCAGTGTGAGCATCGGCTACCTCCTGGTGAAGCACAGCCAAACGGACCAGGAACCCATGTGCCCTGTGGGCATGAACAAGCTCTGGAGTGGGTACAGCCTGCTATATTTTGAGGGCCAGGAGAAAGCGCACAACCAGGACCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031503-Col4a2:NM_009932:45
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=0.262
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(40.7=55.0),PF0139113=Collagen=PU(59.6=85.0)
A:
NA
C2:
PF0139113=Collagen=PD(38.6=33.8),PF0141314=C4=PU(39.8=66.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGGTGGCGTGTCTGCT
R:
TAGGTCCTGGTTGTGCGCTTT
Band lengths:
270-1253
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: