MmuINT0138108 @ mm9
Intron Retention
Gene
ENSMUSG00000039656 | Rxrb
Description
retinoid X receptor beta [Source:MGI Symbol;Acc:MGI:98215]
Coordinates
chr17:34170967-34172771:+
Coord C1 exon
chr17:34170967-34171146
Coord A exon
chr17:34171147-34172598
Coord C2 exon
chr17:34172599-34172771
Length
1452 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
TCTCTTTCCCCACCCCACAGCGG
3' ss Score
10.03
Exon sequences
Seq C1 exon
GCAAGCACTATGGGGTTTACAGCTGCGAGGGCTGCAAGGGTTTCTTCAAGCGCACCATTCGGAAGGACCTGACCTACTCGTGTCGTGATAACAAAGACTGTACAGTGGACAAGCGCCAGCGGAATCGCTGTCAGTACTGTCGCTATCAGAAGTGCCTGGCCACTGGCATGAAAAGGGAGG
Seq A exon
GTAAGGGCCTGCCCCGGCCAGGCCTCAGTCACAGGCCCTTCTCCAACCCTGTGGGAGAGCCCTGAGGAGGAACAGGGGAGACTGCTGAGGGCCCCATGGCCTCCATATCTTGGGACTTTGCTCACTTTCTCCTCCAGGGGGCGCAGTTGGGTTTCTCTTTCCTGTCCTCCACAGCTTGGTACCTCTCAGTGTCTCTGTCTCTGTCTCTGTCTTCATGGTTGCATCTCAGGGTTCATCCACCTCCCAGCAGAGTTTGGCCCTAGGGCGAGGTGACCTCTTTCCTCATGGGTCTTTGTTTCCTCTCCTCCACTGCACACAGCCCTTCCCTCTTTTGATGCCATGTTCTTTCCCTAGTCTCCCAGTCTTTCCTTGGACCTGGTTAAACTACAGAATCACTGAAGAGGTCGGGACTTGGTGTCTCTCCTTCTGTCTCTAAGCAAAGCTGACTCCTGGAATTCTAAGAGATATTTTAGAGCTCATTTTGGTCCAATTCCTGCTTTAAAAAAGATGAAAGTCAGCCCTCCCGGGGTTACCCCAGCAGAGTGATAGGACCAGCATCAGAACACACACCGTCCAGACCAGACCAGGCTCTTTCTGCTGCTGCTCTTTAGTTAGCAGAGCTTAGAGTTTGCCATCAGGAGTGTCTGCAGTCAATGTATAGCCCTGGCTATCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCACCACCCGGCTCATCGTTTTTTGTTTTTTGGTTTTTTTTAAAGGTTTATTTATTATATATGAGTACACCTTAGCTGTTTTTAGACACACCAGAAGAGGGCATCAGATCCCATTACAGATGGTTGTGAACCACCATGTGGTTGCTGGGATTTGAACTCCAGACCTCAGAAAGAGCAGTCAGTGCTAGAGCTTTATTATAGAAAGGCAGGGGGGAAGAGAGAAGGTAAAAGAGAGGCCGGCCATAGCCAAGAGGAGACAAAGGGGGAAAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAAAGGCTAGAGAGAATAAGAGGGGGAGAGTGAGAGGAGAGGAGAGTAAGAGCAAGAGAACAAAGGAGTGAGAGCAGTCAGTGCTCTTAACCACTGAGCATCTCTCCAGCCCTCATCCTTGATTCTTGTACCCTTCTCTTTTTATCTGCCTATTCGTTTACTTTTTGTGTGTTTATAATTTGTGGCGGTGGGGCCAGAGCTCAGGGTCTGGTGTGTGCTGGACAGATTTGCTTTTGGACTCTTCTACCCTTCTGATCCTAATTACCTCCCTGGTCGCTTTATCTCAAGGGACATTGGCCCTGAGAAGGCCCCAAATGAGTTTCAGACAACCCCATAGTTGGCTTCTAATTTTGCACTTCTCTTTCCCCACCCCACAG
Seq C2 exon
CGGTTCAGGAGGAGCGTCAACGGGGGAAGGACAAAGACGGGGATGGAGATGGGGCTGGGGGAGCCCCTGAGGAGATGCCTGTGGACAGGATCCTGGAGGCAGAGCTTGCTGTGGAGCAGAAGAGTGACCAAGGCGTTGAGGGTCCTGGGGCCACCGGGGGTGGTGGCAGCAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039656-Rxrb:NM_011306:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.033 A=NA C2=0.828
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(82.9=95.1)
A:
PF0010513=zf-C4=PD(82.9=95.1)
C2:
PF0010425=Hormone_recep=PU(0.1=0.0)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGCACTATGGGGTTTACAGCT
R:
CAGGACCCTCAACGCCTTG
Band lengths:
326-1778
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: