MmuINT0023085 @ mm9
Intron Retention
Gene
ENSMUSG00000033488 | BC026585
Description
cDNA sequence BC026585 [Source:MGI Symbol;Acc:MGI:2448516]
Coordinates
chr1:159400747-159402547:+
Coord C1 exon
chr1:159400747-159400928
Coord A exon
chr1:159400929-159402318
Coord C2 exon
chr1:159402319-159402547
Length
1390 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGG
5' ss Score
9.13
3' ss Seq
TGTCTCCTCCTTGCCGTCAGCCT
3' ss Score
5.29
Exon sequences
Seq C1 exon
GTCATAGCTGCCACTGGAAGTGACGAGAAGTGCAAGCTGGCGGTGCAGAGGGGAGCACAGTTCAGTGTGAACTACAGCCAGGGCAGCCTGAGGGATGCAGTGAAGAAGCTGGCAGGCAGCGGTGGGGTCAACGTAGCCATTGACATGGTGGGAGGAGATGTCTTCCTGGAGTCTCTCCGCAG
Seq A exon
GTGCGGGTATTGCTCTGTCCAGAATGGTTAGAGCTAGGGCTCCACACAAGCTCCATGCAGTTCTAACTCCCTGCATCTCTAACTCTCTCTGTCTTTGCTGCTCACATCTCCTGTAGGCATCAGCGTCAACGAGAATAGCTGAGTGGGCGGGTGACAAGGAACAGAAGCAGAGAAAATCAGGAAATGCTTAAATATAGTAAAAACAAAATACCCAACTGGAAAATATTCAAAAAATGACTCCAGACTCTCCAGTTGGCAACGCTGGAGACTTTAGAAATTATCCATGTGTTAAATCTAGCTCTCTGGTTCCCCACTAGGCTGCTTTAAATATGTGGGGGTGTGGGGTCCTGGGGCGATCATTGTTCAGATGCTAAGATTGCTGTGGTGGTAGTTTCTCCTTCCCAGGATGACTATGCACCAAGGTACAAGCTCTTTTGATGGCGCTGGTCCCGCAGTTGCTGTGTGCTTCCTTAGTTTGTCTGATTAACTATGTGTCACTAGAGACTTGGTAGGACTATTCTATCTTACAGTCTCTATATTTCACCCAGGGCTTCTGGTGATCTCTGAGAGCATTGTTCCTGTCTGCTCTTTCTCCATCCCCCTTTCCTTTCCTCCTTGGTTTCTTAAGACGAGGTATGTGCTGTGCTGTCCTTAAGCTCCCTCTGTAGCCAAGGCTGGCCTCGAACTTCTGATCCCAGTACCTCCTGAGTACTTAGTTTATAAGTATGCATGAGTCACCACACCAGGCCTGCTTTCATTTTTCACATCTGTGCTTTGTAATTTATCTCATTTTTGAAGTAGAAAAACCAGAGCAGCAAGAGCTGCCGGCCCGCAGAAGGAATGCAGTTAGTCTTGGATAGAACCCAGCAGGCATCCCTGAGCTGGGAGGCAGGTGTCTGGACACTGGTGTCACTTGCTGGTCCTACGCGCAGAGGAGAAACAGAGGAGGAAGCAGAGACCAAGTGGACCCACTCTTGTGCCTTCCATCTTGCATCCTGGATAACTGTGTTTTGTAAACAGCCTCTCACTTCCTTTCTGTGCAAAGCCCCGTGGGAAGCCATTGGTTACGACCCACGTGTGGTGTGCTCTCTGGCACTTTTCACAATGGGCTGCACAGAAACCTCAGGAGGCTTTGTAGATTATTCAGAATTCTCTAAAGAAGTCCCATGCCTTAAGGAGTCCTAAAGTGCCCTTGTTTAAAGTGACTCTTTATCCCTCATATCCCATCAGCTGCCTTATTCCCTACCGCCCGAGGTCCAAGCTGACTTGTCTTGACATACAACCCATGGAGTGCCATTGGTTGATACCCAATATCCTTCCACACTTGAAGTCAGCCTTGATTCTAAAGCACCCGGTCCGAAAACCTTTTCTGTCTCCTCCTTGCCGTCAG
Seq C2 exon
CCTGGCGTGGGAGGGCAGGATCGTGGTGTTGGGATTCGCTGGAGGAAACATTGCGTCCGTGCCCAGCAACCTGTTGCTCCTGAAGAACATCTCGGCCATGGGACTGTACTGGGGTCGCTACCAACACCAGGACTTTGCAGTGTTTTCCAAGAGCATGTCCACAGCCATGCAGTACTGCCAGCAAGGGCTCATCCACCCCCACACGGGTGCCGTGTTTAAGCTGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033488-BC026585:NM_001033284:8
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:
PF0010721=ADH_zinc_N=FE(44.4=100)
A:
NA
C2:
PF0010721=ADH_zinc_N=PD(42.2=74.0)
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:
CAGTGTGAACTACAGCCAGGG
R:
TCTCCAGCTTAAACACGGCAC
Band lengths:
347-1737
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: