MmuINT0023243 @ mm9
Intron Retention
Gene
ENSMUSG00000047228 | BC048546
Description
cDNA sequence BC048546 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128516262-128517078:-
Coord C1 exon
chr6:128516933-128517078
Coord A exon
chr6:128516412-128516932
Coord C2 exon
chr6:128516262-128516411
Length
521 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATG
5' ss Score
5.22
3' ss Seq
CTACCCTTCTTCCACCTCAGGTT
3' ss Score
10.35
Exon sequences
Seq C1 exon
CCTGGAATGGGAACTTCTCTTTCCCAATCAGCATCAATGCTGATCTGGCGCCATCGGCTGACCTGTTCGTCTACACCCTCCACCCTAGCGGGGAAATCGTTGCGGATAATGTCAGGCTCCAGATCGAGAAGTGCTTTAAAAACAAG
Seq A exon
GTGATGTTTCCCTTATCAGCAGGGTGGGCGTTTTGCTTCCTGCTTCCTCCTTTTAAAGTTTCGTTCTTTATTTGGTGCATATGTGTGTGCGCATGCGCACATGCAACCATGCCTGCGAAGTGAGTGCGTGAAGATCAGAGGACAGTTTGCAGGATTCCATTCTCTCCTGCCACTGTTCTGGCTGGATAGACCTCAAGCTGTCAACCTTGATAACAAGCATTCTCACCCACTGTGCCATCACTCCAGCCCTGTCTCTGTCTGGGCCCCTCATGATCCTTACATAGTAATCTTACAGTTAAATTACCAACAAATGAGTCACGAAGAGTTATCTTGCTGACGCCTGGTCACAGCAAGCTGGGGGAGTTGGGGAGACTGAAAGATATCCCCACAGGGAACTGAGAATGGGCAGGAAAATGTATGTACAGAAATCGGTCGGGATTTGTTTGGGAAGACAGAATTTATTCAAGTTTTCTTCACATGTAATTGTCTCTACCCTCATTACTACCCTTCTTCCACCTCAG
Seq C2 exon
GTTAGCATAAACTTCTCACGGGATAAGGATCTACCGGGCTCTAACACCAGTGTTCATCTTCAAGCGGCCCCTGACTCCTTCTGTGCCCTGCGAGCAGTGGACAAAAGTGCCCTTCTACTGAACCACGGACAAGAAATGACACCTGAGAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228-BC048546:NM_001001179:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF077039=A2M_N_2=FE(32.7=100)
A:
NA
C2:
PF077039=A2M_N_2=PD(26.5=78.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGAATGGGAACTTCTCTT
R:
TCTCAGGTGTCATTTCTTGTCCG
Band lengths:
294-815
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: