MmuINT0110566 @ mm9
Intron Retention
Gene
ENSMUSG00000026398 | Nr5a2
Description
nuclear receptor subfamily 5, group A, member 2 [Source:MGI Symbol;Acc:MGI:1346834]
Coordinates
chr1:138839864-138841654:-
Coord C1 exon
chr1:138841536-138841654
Coord A exon
chr1:138840006-138841535
Coord C2 exon
chr1:138839864-138840005
Length
1530 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGC
5' ss Score
5.42
3' ss Seq
CTATTTTCTCTGTCTTACAGGGT
3' ss Score
11.84
Exon sequences
Seq C1 exon
TGTCTCAATTTAAAATGGTGAATTACTCCTATGATGAAGATCTGGAAGAGCTATGTCCTGTGTGTGGCGATAAAGTGTCTGGGTACCATTACGGTCTCCTCACGTGCGAAAGCTGCAAG
Seq A exon
GTTTGCCTTTTCTGTGCTACCTAAAAAAGATAGAACGGTTTGACCAAACCCATGGAAACTCTTCAAAGTTAAACCTGTTTGTTTCTTTCTTTCTTTTTTCAACTGGAAAGAGTGGGGTGGGGTGAGGTGGGGGAAGTGTCATAGAGCGACTAGGACTTACAGTATGTCTGATTTAGTTCCAAAGGCAGGTAGGTGCCTATGCTGTAGAAAACTGTCAGACTGGTGGCTTTAAAGTAGTTTATTGTGGTGCGGTGCTGTATCTATAGGGGGACATTCTAACAGTCCTAAATATTGATTTTGCTTGACTTATATATATTTAAAGCATCCTTGTTAAAAGGAAACAGGACAGAGTACAACCCAAGTGTGTTTTAATTTGAGAGGAATCTGTGCTGCAAGTTGGAACATTTTTCTTTAGTCCAGAAGACATGAAGGTCTGATTTCCCAACTGCATGATTTCATCCTGATGGATTCTGAAAATAATTTTAAAAGATTTTTTTTTAATCAAGGTATCAAGAAACCAGATTTTAGTTTCTAATTGAACAATTTTTATTAGTGTATCATATGACTTATTTAAAAGCAGGAGGAATTTGAGTATGTTTAATGTCTCTTATTGTTAATAATCTTGTCAAGACCATAAGCATTTGTCAGAGGTTTTATATTTTTTTAAATAGTCCCCATGAATTCAATTTCCTCTAATCTTTCCCCAACATCTTCTTTAAAGTAGAGACTCAATGCATTTATTTAAACCTTTGCTAGGAAATCCCGCTTTGTTTTCCATAACAAATTAAGGTTGTTTTTGTGTGCTCGCTCAAATAAGCAAGGATACCATCTTAGTAGAGAGTAGAGGAGTTCCTCATTCAAAAGCCAGACACCAGGCCTGACCAGCCCCTTAAGTGTAAACAGGCACAGGCTATGCTGCGGTCCAGCTTCGTGGCTTATGCTCACACACACATCCCTGCCTATGTGTGTGTCTTTTCCATTAGTTGGATTTTCAAACACAGCTACAACCCTTGAATGGGTTCCAGTGGCCTTAGGAACATTTCCCCATTTTGTTCTTGAAGTCCTTTTCCTTTTAACTGTCAAGTGTTGACATTTGTAAAAGATCTGAGGTACTTGCTATTCAGCTCTTACAATGGTTTGCGACTGAAATTGTATGAGACTACCTAAAAACAATGGCAGGGTTCTTCTGTGAGTTACCTCTGCTTGGAACATGGATGTTAATAGGAAACCAGATTTAAGAAAAAAAAAAAATTGGTCAATATAGAGTGTATTTTTTTTTCTGACTGTTGGAACGAAATGGTACAAAATTGATGTAATTCTTCAGGAATATAATTCTGAGGCCAGAAAAATCTTCACTGAGGCCTTGCACTGATGCTGAGGGTTGGTCTTGCTGAAATGTGAAATTAAACCTCAGGACCACATAAGGGCTCAGTGGCACAATAAAAAGACCTACTGGTGATTTCCTGAGAGTACAACAAAAGAAGAAAAGCGAGTTAGACTCTACATCTCACTATTTTCTCTGTCTTACAG
Seq C2 exon
GGTTTTTTTAAGCGAACTGTCCAAAACCAAAAAAGGTACACGTGCATAGAGAACCAGAATTGCCAAATTGACAAAACGCAGAGAAAACGATGTCCCTACTGTCGATTCAAAAAATGTATCGATGTTGGGATGAAGCTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026398-Nr5a2:NM_030676:4
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:
PF0010513=zf-C4=PU(32.9=57.5)
A:
NA
C2:
PF0010513=zf-C4=PD(64.3=93.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGGTGAATTACTCCTATGATGAAGA
R:
TTCCAGCTTCATCCCAACATCG
Band lengths:
246-1776
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: