MmuINT0110576 @ mm10
Intron Retention
Gene
ENSMUSG00000063972 | Nr6a1
Description
nuclear receptor subfamily 6, group A, member 1 [Source:MGI Symbol;Acc:MGI:1352459]
Coordinates
chr2:38729483-38731167:-
Coord C1 exon
chr2:38731046-38731167
Coord A exon
chr2:38729636-38731045
Coord C2 exon
chr2:38729483-38729635
Length
1410 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
ATTTTTGTTTTTGTTTTCAGATA
3' ss Score
11.49
Exon sequences
Seq C1 exon
ATTTAGTGATGAAGGGATGGAGGTGATTGAACGACTCATCTACCTATATCACAAGTTCCATCAGCTGAAGGTCAGCAACGAGGAGTACGCATGCATGAAAGCAATTAACTTCCTGAATCAAG
Seq A exon
GTGAGTAGGTGGTGGCAAGAGCCCTTGCCCTTCTGTATCACAAACACAACTCCCCATCCCCCACCCCCACCTCCCGCCCCCAGGACTGTCACAGAATCTGTCACACCATGTGACCATAAGTCTTGGAAGACCTGTACTCCCCCTAGTCATCACCCTGGTACTCTACGGTGCAAGGAATGCTTAGATTTTTTTTCTTGAAGTCTAAATGCCACAATCTCTATAACTCACAGAGGAAGGAAGAGGATTCACTTTGTTTAGTCAGTTTTCATGCATTTAAACACAGACATCAAGGACAGAACGTGCGTCATTTAAAATATGTACAAGTTTACCAGCAACTGAAGAGAGGGTGACTTATGAAACTGTTGGAGATAAGGCTGGTTGACAGGCTGGCCATGGCTCTGATGTCAGGGATGAGTGGTGGTACGCAACCCTCCATGTGCACGTGAAGCTCGCTCTTCATCAGAGTAATCCAGTTGATTTATAGGCATAGTGCCAGCAAGTAGCATGTGGTACTTGCTGGAAACTGGCCTGTGAAAGAAAAAGTAGCATATGAATGCCCCAATCCCAGAGTGGACCTGAGTGATTCTGTTGCTGTAGCCTCAAAAGTGCTCAGTTTTCTAATCCGGAGACTTGATCAGCCCTTCCTTTCTACCACTATTCCCTACTCAACTTTCCAGTGCAGTATAAACATACTACTCCAGTCTGTATACCATCATGCATTTATCAGGTGACCTACATGCCTTCTCTAGTCAAGCCCTATACTATGTATTAAGGATATTGGCAGGGTTTGGGGAAAGGAGAAAAAAAACCAGGCCAGCCCCCAAGTCCCTGGAGAATTCACATTCCAGTAACACTCTACACAGTAATTGTACTGTATACGGGGGAAGATTGGTAGCAACTTCTTAGAGGAGGAAAATGTGTACTGGACCTCAAACGCTTGGTAGACTTTACATGCTGAATGCTTTATTCATCTCCTATCCATTGTACATAAGGATAGATATACATATGTATGTACATGCATGCATACGTGTGTACAGTAAGACAGAATAGTAAGAACACAGGGACAATGGAGATGATAGGTGTCAGGCTCCTGACAACCTCTGCTTCAAAGATGCTCTGAAGGGTTATTGAATAAGCTGTTAGCCACCACACTCGTTGGTTCCTGTTTTGTGCCACCATATATATCCTTTATTAAGAGCTTAGCACTCTTAAGGTCCAGGCAAAGGGCTAGCCTTTGCATACTTTCCCTTTTCTATCTTACTTTCCCTTATCCAGATCTTAGTTTCTCCACATTAGAAAAAGAAAAATCTTTGTTATAACTATATTTAACAATGTCTCATTTTTTATAAATCTGATGCCACCGCCGCACCCCCCCCCCATTCCCTGGGTGATTTTTGTTTTTGTTTTCAG
Seq C2 exon
ATATCAGGGGTCTGACCAGTGCCTCACAGCTGGAACAACTGAACAAGCGGTATTGGTACATTTGTCAGGATTTCACTGAATATAAATACACACATCAGCCAAACCGCTTTCCTGATCTTATGATGTGCTTGCCAGAGATCCGATACATCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000063972:ENSMUST00000112877:10
Average complexity
IR
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:
PF0010425=Hormone_recep=FE(21.2=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(26.4=100)
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:
TTAGTGATGAAGGGATGGAGGTGA
R:
CGATGTATCGGATCTCTGGCA
Band lengths:
270-1680
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types