MmuINT0039964 @ mm9
Intron Retention
Gene
ENSMUSG00000031503 | Col4a2
Description
collagen, type IV, alpha 2 [Source:MGI Symbol;Acc:MGI:88455]
Coordinates
chr8:11444931-11446246:+
Coord C1 exon
chr8:11444931-11445122
Coord A exon
chr8:11445123-11445959
Coord C2 exon
chr8:11445960-11446246
Length
837 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGC
5' ss Score
7.72
3' ss Seq
CTCATGTGCTCCTCACACAGGAC
3' ss Score
7.98
Exon sequences
Seq C1 exon
GGGAGCCAGGCCGTCCAGGGAGCCCAGGCCTGCCAGGGATGCCAGGCCGCAGTGTGAGCATCGGCTACCTCCTGGTGAAGCACAGCCAAACGGACCAGGAACCCATGTGCCCTGTGGGCATGAACAAGCTCTGGAGTGGGTACAGCCTGCTATATTTTGAGGGCCAGGAGAAAGCGCACAACCAGGACCTAG
Seq A exon
GTAGGCACTGCTGTCAAGCCCCAACTCCGTTCCCAGGTTCGGTGGTGCTGACTGTGAGATTGTGAGCCCCAGTGACAAGCGCCTCTCAGCTGCATGGCCCACCACCTTCTCCAGGGTAGGAGAGGCTGAGGTGGCCATGGAGACAGAAATCTTACTATACCCTCAGCCTCAGGACCCCACACAGGGCTTTTAACTTAAGATAGCATCCATGTCTCATTAGTTAGTCTAGCCAAGCACTGCCCTCCCCGTTGCTTTTGGACTCAAACCTAGGATCATGGATTTAAATCAATTCTTCACACAGATGCAAAACAAACAAACAAACAAACAAAAATACCAGTCATGTGTGTGTGTGTGTGCATGTGTGTGCCTTCAAAGGACATGAGCATGATGTCAAAGAATTTTTAAAAACTACGAAACACACAAGTGGGTGGGTATCTCTGCCTACCATCCCTCAGAGGGCCAAAGTGCACATGGAAGCCTGGAGTATTCTGTATGTCAGTGTTAGTGACACCAAGGCCATCAGCTCCTAGATGTATACCAACAAGATGCTACCACTGTGGGCATTCCTGACTGTGGCCCCTTTCCAACAGTAAGTTTTACAATGCATTGGAAAAAGGGCAAACAAGAATAGGACCCAAAACAGCCATAGGAACAGGGGGATGAGAGCAGGCCTCAGCCCCTGCTGGTTTGCTGAGGGTGGACCCTGTCTGAAAGCTTTGCAGCATGAGAAGTAACACATGCCCCTGGCCAGGCACAGTCAGAGTCCAGTTCTGTGCCTCATGGCCGCACAGCTGAGGTGGAGGCAGGGCTATATGTCCTCATGTGCTCCTCACACAG
Seq C2 exon
GACTGGCAGGCTCCTGCCTGGCACGCTTCAGCACCATGCCTTTCCTGTACTGCAATCCGGGTGACGTCTGCTACTATGCCAGCCGCAACGACAAGTCCTACTGGCTCTCCACCACGGCCCCTCTGCCCATGATGCCCGTGGCTGAGGAGGAAATCAAGCCCTACATCAGCCGCTGCTCTGTGTGCGAGGCTCCGGCCGTGGCCATTGCCGTGCACAGCCAGGATACCTCTATACCCCACTGCCCGGCTGGGTGGCGGAGTTTGTGGATCGGATATTCATTCCTCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031503-Col4a2:NM_009932:46
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.262 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(38.6=33.8),PF0141314=C4=PU(39.8=66.2)
A:
NA
C2:
PF0141314=C4=PD(59.3=66.7),PF0141314=C4=PU(26.1=31.2)
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:
CTGTGGGCATGAACAAGCTCT
R:
TATCCGATCCACAAACTCCGC
Band lengths:
355-1192
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: