MmuINT0023242 @ mm9
Intron Retention
Gene
ENSMUSG00000047228 | BC048546
Description
cDNA sequence BC048546 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128516933-128517881:-
Coord C1 exon
chr6:128517827-128517881
Coord A exon
chr6:128517079-128517826
Coord C2 exon
chr6:128516933-128517078
Length
748 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGAC
5' ss Score
2.93
3' ss Seq
GGAACTGCCTGTTTCCACAGCCT
3' ss Score
6.16
Exon sequences
Seq C1 exon
GTGATGGTGAGAGGAGGTATCTCCCGCAGCGGACAGAAGCAAGTCAGAGTTCAAG
Seq A exon
GTGGACACTATGCCCTTGCTTTGGAATGCGTTCCCTACCTCCATACTTCCTACAAGTTAGGATGAGCACTTATTACCACGAGCAGTTGGAGGGCAGTAGGTAGCATGACCTGAGGTAGCACTGAATAGTTAGAAAAAGGCGATTGTTGCCTTTCTATCATTACTCTAGTTTGTTTTCGATTGCTGTAATAAACCCTAGCCAAAAGCAACTTCAGGGGGAAAAGGGTGTATTTCATTTTAGACTGCAGGTAACAGTCCATCATGGAGGGAAGTTGGAGCAGGAATTCAAGACAGGAACCTAGAGGCAGGAACTGGAGCAGGAACCATGAAGGAGCACTGTTGACTGGCTTGCTCTTGATGGCTTGCCCAGCCTGCTTTCTTACATGCCCTAAGTCTGCCTGTCCAACCCACAGGTTAGGCCCTCCATATCTATCATTAGTCAAGAAAAGGCCCACAGGCCAATCAGACAGAGGCACTTCCCTAATTGAAGTTTCCTCTTCCCAGCTGACTCTAGTTTATGTCAAGTTGACAAAACTTGGCTGCACCCATTAGTCAGTAAATGTGTACACTGTAGAATAGTGATGTCTAAGGCAGTCCTACCACAGTATCTTCATCTGTGAATATGTCCCCTTTTTACTTGCATCTGAGCAAGGCCCAGGTCATTTCTCTATCCACACGCCATTCCCCTTCATCTAAGCAAACCCAGGAGCGCTAGCACACTGTCATCTGGGAACTGCCTGTTTCCACAG
Seq C2 exon
CCTGGAATGGGAACTTCTCTTTCCCAATCAGCATCAATGCTGATCTGGCGCCATCGGCTGACCTGTTCGTCTACACCCTCCACCCTAGCGGGGAAATCGTTGCGGATAATGTCAGGCTCCAGATCGAGAAGTGCTTTAAAAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228-BC048546:NM_001001179:13
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=0.000
Domain overlap (PFAM):
C1:
PF077039=A2M_N_2=FE(12.2=100)
A:
NA
C2:
PF077039=A2M_N_2=FE(32.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGATGGTGAGAGGAGGTATCT
R:
TGTTTTTAAAGCACTTCTCGATCTGG
Band lengths:
199-947
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: