MmuINT0023260 @ mm9
Intron Retention
Gene
ENSMUSG00000047228 | BC048546
Description
cDNA sequence BC048546 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128528752-128530497:-
Coord C1 exon
chr6:128530341-128530497
Coord A exon
chr6:128528805-128530340
Coord C2 exon
chr6:128528752-128528804
Length
1536 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
CAGTATCCCCTTTTCCTTAGTTC
3' ss Score
5.5
Exon sequences
Seq C1 exon
GTGTCTCAGATGTCCTCAGAGCAGTTGGCCTTTGTGGCATTACTTGTTCAGGGAAACACTCTTAAAATCTCTGAGAGAAGATCTGTGGCCATCGCTGCTGAGGAGAACGCCACTTTTGTGCAGACAGACACACCGGTCCATAAACCTGGAGACACAG
Seq A exon
GTAAGTTACTTTAAAAAAAAAAACACTTTCTCCAAGTTAATGTGTAAAATTGAGTAAAACTTGTCTTTATCATCACTGACTGCTGCATTTCCATAGTTCCTATAGCTATGAGACAGTGCTGTTAGAGCCGGGAGCTTGGGCATGGCTTCATAAGACTCTGTGTGTTCTTTGATTGTACACAAATCCTACTGACAAGGCTTCATAGTACAGTGGTTACCAGAATGCAGAGTTATAATTGTTTGATCTAAACCAAAGATCCATTACATACCCATTGGACAAGCTCATTAATTCTCCTTTTCAAGCCAATTATTCCATTCTTAAGGTAGAGATAATGAAAGTTTCTTTGAACTTTCAGGGAAGAAATGAGAGTCATTGTAAAAAAAAAAAAAAATAGTGCCAATAACAGCAAAGACCTCACCAGCAACATTTAGGAATTCTACTGTTCCATTTTTATGTCAATTGGTCTAGCAGGAGAAAGTCAGCCAGAGCCTTCCGCTTTCTTAACTATTGTTCTAAGCAGAATGTGCCATAAAGAATACCAAGCTAGAATTCAAAGCCTCTTGCTTCAAAGCTTAGCTCTGTTGACCAGTGATTGACTCTTGGCAAGTAAATTCTGGTCCTTGAGATATAATTTCTTCATCTGTAAAATGAAAGGGCTAGAGATGAAAAAGCCTGTGCATTGTATCCTGATTCATATTGTCTATGACTTAAAAAAAAAAAAAGAAAGAAACAAAAGACTGAAAGTAGAATTTATTTTGGCTTAAACAATAGACACATAGACACATACTTCTGGCAGCTGAAGAAACTGCCGATATGAAAGTGCCGGGGGTTGTTTCCTCCAAAGATTCTCTGCTGTACTCTGACTGATGTGACTGTGTCTGAGGCAGGGGAATTCCTCCAAGGAGTCTGTACTGTACTATAAACGGCCGGCTTATGAAGGCTTCTTTCCTTTTTCTTTTATAATTATTTTTAAGTCAGCTCACAAAGCAGTGCATTTCATTATGATATTTTCACATTTAATATTGCAAAGATAATTCTTAAAGGGAGATTTTTACTTCCTGATACTCCCTTTTCTGCTCTTGTTAAAATATTAGAATAAACTGTATATTTTAAAGAACCGACATCTTTTGTAGTTCTGCTAAAATAGCTTAATTTTGCTAGCATTGTTCTCAAGGAAAATTATACTTGTTCATTTCCATAAATGTCTGACATTTATGCTTCTATGGATAAGTCTGTCACTAATTCTGTTCCAGGCTATCTCAGTCTATGTCTGATAGGGTAAAAGCTTCTAAGGGCAGCATTGGGGACAACAAGAATCATTAAGAGAGGAATAATAAATACAAGTTGATATTTTCCCCCAATGAACTCCTAACCTGAAAAGGTGAAATCAGAGCTAGAGGGAAAGGAATGTGACGGGCAAGCTTGCCCATCTTGTGATGGGCAAGCAATTACTTATGTATATATCTTAAAGCAATCATCGCTATAAGGTGGGGATCACAAGAAATCCACTTTACAGCAGTATCCCCTTTTCCTTAG
Seq C2 exon
TTCACTTTCGCGTTGTGACACTGAACATCTGGCTGAAGCCTGTTGATGACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228-BC048546:NM_001001179:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0183514=A2M_N=PU(17.0=30.2)
A:
NA
C2:
PF0183514=A2M_N=FE(18.1=100)
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:
TGTCTCAGATGTCCTCAGAGCA
R:
CAAGTCATCAACAGGCTTCAGC
Band lengths:
209-1745
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: