MmuINT0110577 @ mm10
Intron Retention
Gene
ENSMUSG00000063972 | Nr6a1
Description
nuclear receptor subfamily 6, group A, member 1 [Source:MGI Symbol;Acc:MGI:1352459]
Coordinates
chr2:38723370-38729635:-
Coord C1 exon
chr2:38729483-38729635
Coord A exon
chr2:38727916-38729482
Coord C2 exon
chr2:38723370-38727915
Length
1567 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
TGTCTCTTCCCTTTACCTAGGCA
3' ss Score
9.26
Exon sequences
Seq C1 exon
ATATCAGGGGTCTGACCAGTGCCTCACAGCTGGAACAACTGAACAAGCGGTATTGGTACATTTGTCAGGATTTCACTGAATATAAATACACACATCAGCCAAACCGCTTTCCTGATCTTATGATGTGCTTGCCAGAGATCCGATACATCGCAG
Seq A exon
GTAATATTCTGGATCCAGGCTTCCAACCTTCCTAGCTTCTCCAAGCCTGTGAAGGGATTGAGATGAGCAGTGTTCATAGGGTATTTACTCTAGGCCATCACCAACTGCAGACAGTACCTTTGTCCTCAGATAAGTTCTATTCTAAGAGGAAGAGAAACTGGCATCTCCAGGCTCCTGTGCTGTGCAGGGGGTGTGGATGACGAGAGCAGCCTGTGTCTGTGTCTTGAACTACATATATTGCTCAGAAGTAATTTTATTCAAACAATTTTTTAAAGATTTATTTATTTATTTTAGGTATGTGAGTACACTGTCACTGTCTTCAGACACACCAGAAGAGGGCATTGGATCCCATTACCGTGTGGTTTCTAGAAATTGAACTCAGGACTTCTAGAAGAGCAGTCAGTGCTCTTAACCACTGAGTCATCTCTCTGACCCTCAGCTGTACACTTTTAACTTTTAGATAATGAATTTTATATGTGAATTATATGCCAATTTTCAAAGACTTTATTTCATAGGATTGTGCAAACTCTTTCCAGGGCCATATAAAGTGGCACCTTTAAGCTTATGTGTCTACAAAGAGATTTTGTGTGTTGCATTGTGTTGTGTTCATGGTCTTGCACCTTCTGCTAAGTTCCTGACAATCAGTAGGCCTGTTTCAGTGTATAACCTTGGCTCTTTGTTGTTGCTTTATGACATTTAACGAGGATTCTTGGTTTTGTTGTCCAGCACTCACTAGGATGATGTTTAGACTGGGTTGTTTTGTTTTGTTTTGTTTTTCTGTAAAATTTAGCAGCACAACTTTTCAAGGAAAAACATGTCAGTCTGACAGAATTTTTTTCTCTATTTCTTGAGCCCAGAGCAGTCTACAGATGTAGACTGGACCTGGCAGTATTTTCAATCACCCAGAAAGCTTTTGAAAAACAGCAGTGCTTAGTAGGTTGCATCTCCAGACGTTCTGACTACTGGTACGGGGTGAAGGCCAGGCATCAGTATATTTTAATGCCCTCAAGGTGACTCTAAGGTATTGTCAGGGAGAACTACAGCCTTGGGTATTTTGCTTGCAGAATTTGTGTACTTAAAGCTCTGAGAAGTTTATCAGTGAAAAAAGCTGTCAAACTTTATCTCCAGACATTTCAAATTTATTTTTCCCTGTAATTCTTCTCCTTACTTCCCTAGAACTTTTATTAATCATTACTTTGTTTTAAAGAGTAATTTTTTATAGAATGCTAGAGAGTTGGTGGGAAGCAAGTTTCCTATAGTCTTTCAGCTGTGAAAAGCTTAGTAGGACTCCTTCTCCATTTCAGCTCTAAAACAGGGGTAAGAGGCTATCACAGACAGAAATACGGAGTCTAATGAGACAATGCATTAAATTGGCTGGCACAGAGCAAGTGTAGCAGATGGGAGAGTGAGCAAAGACACCCTGATATTATCAAACCCTTGTGGCCGTCTCAGTACTTCTGATACACTTGCCCTCATCCTGGACCAAGGTGATCAGCAGCCTGAGTGGAGACAAAGCAGGCTTTCCTTCCCTCCTGGCCGCTGCTAACTGTCTCTTCCCTTTACCTAG
Seq C2 exon
GCAAGATGGTGAATGTGCCCCTGGAGCAGCTGCCCCTCCTCTTTAAGGTGGTGCTGCACTCCTGCAAGACAAGTACGGTGAAGGAGTGACCTGTGCCCTGCACCTCCTTGGGCCACCCACAGTGCCTTGGGTAGGCAGCACAGGCTCCAGAGGAAAGAGCCAGAGACCAAGATGGAGACTGTGGAGCAGCTACCTCCATCACAAGAAGAATTTGTTTGTTTGTCTGTTTTTAACCTCATTTTTCTATATATTTATTTCACGACAGAGTTGAATGTATGGCCTTCAACATGATGCACATGCTTTTGTGTGAATGCAGCAGATGCATTTCCTTGCAGTTTACAGAATGTGAAGATGTTTAATGTTACCGTGTTGTCATTGTTTAGAGATAGGTTTTTTTGTATTTTGAGGGAGAGGGTAGGATGGACTAGATGAGTATTTCCATAATGTTGACAAAGACAACTACCTCAATGGAAACAGGTGTATGACCATCCCTACCTTTTCCACATTTTCTCAGCAGATACACACTTGTCTGTTAGAGAGCAAACTGCCTTTTTTATAGCCACAGACTTCTAAGTAAAAGAAGCAAACAAAGGAGCGAAGTGGTATAGGGAGATTTACTAATGGCCAGTGGGACATCTGAGAGGCAATTTGATTTTGATCATCTCATCCCACAAGCCTGAAGGGCAGAAACTCTGCCTTACCTTCTGCTGCACCCCTCCCCCACACGCTGTTGTCTGTTGATGCTGCTGTCAAGTTTTCATCCAGGTAGAGTCCTAACAATAAGCCAGTATGTAGGACTTGCCTCCCAGCGCCCTTGTAGCTCATAGCTGCCTAGTTTGCTGTTCTAGATCTACCAAGGCCTACCTTCTTCAGACCCCATCCCTACCTCTTATGAATTTGACTTCCTGTCAGTCCTTTAGAAAGGGACAGGAAAATGCCATGTTCTGAATTCTGATGCCATTTCTGATTTGTTTTTTACATTGTTTCCCTCAAAAGGTAGAGGGGCAAAGACCAGGCTGCTGAAAGAATAAAGACTTCTTTGGAAGTCGCTGTTCTCACCCAACCTTATCCTCTGAACCAAATCCAAAATCCAAAACTGCCACTTTTAAACAGTAGAAAGGACCAGAAACTTTGCTGCAAATTTTTGTTGTAAGTTCTCCCATTAGTCCCAAAATGAGATTTGTTTGCCAGGGTCTAGAACAGAAAGTCAAGACCCAGAGAAGCCCAGCTCTTCCTTCAAGTATTATCAGGGATCTAACCTACCAAGGTTTGGAGGGATGGAGCCAGAAAGACCTAGAAAGGAAAGGGGCATTAAACTACCTCATGTTTCTAAGGGCTAGGCTGCTGCTCTGCAGCTGCAGCCTGGGCCCCTGTGCTTTACTGCCTACCCCATCTAGTTCTAGGAAGAGTTTTTACCCTCCAGACTTTGGCCAGACCAACTAGGTTTGTCTTAGAGCTGTTTCAGCTGCTTTTCCCTTTCTTTGTACCAGGCTCTCCTACCACTAGTACCCCAGACACATGCTCCACTGGCTGGTATCTCGTGCTGGGTCTGCCTCACCCACAGTATCTTTTTTAGCCTGTTTTGTCAGGAACTGTTTACACTTCCCCAGTGAAGCCTATTAACTTACCCTGGAGACAACAGCATCCTGTGCCTCCTAGGTAGTGCCTCCATTTGTCAGTTTTTCTCTTTAGTGAAATGATACAGGTACCAGCAAAGTGACAATATGTCCTTTGATGTCCAAAGTTCAGAACATTATTTCTTCTCATTCTTATTCCCCAGCCACTTGAGAGAGAAAAAGTTCCAGATAGAATGTTTTTCACGTTTGTGGGAAGATATATGTATTGATGTGTCTGTTTCTGAGCTCACAATATTTTCATGTTTGCCTGAATTTTTATATTTAACCAACCAGATCATGTTATTTGGCTCTGGGTCAGATTCTCAGCTGCTTTCCTCAAGCTAGAAATCAGAGACACAGTTCAGAGACAGCACCTCTGTGCACACAGCAGCCTTCTTTGCTTAGACTTCCATTTATCAAATTGGTACTTTTTTAAATTGCTTTTCAAATTAGCATTTTACCTGTTGTGTTGAATGTCAAAGCTCTGATGAGACAAGAACATATCTTTCCAATAATGTAGTATTAAACAGAGCAAGTTGTTAATTTGTAGAGTGGGGGAAAGGTTCTGCAAGTTGCCATTGTACAAATCCATTTTTACAAATGTTTGCAGCAGATTCCACAGAACAAAGAGCCCATTCATTGCCAAGAGCCCTGCAGAATCTCTGAGCCAAGTGGCTGTGTGTTCCGAGCTGGAGCCTGACCTGTGGACCGCCTTTAATGTCTTCTGCACCCAGTCCTTTTATGACATGGGCTTCTTTTAAACAGGGTAAAGTAAATGGGCTGCTTTGCAAACTCAGGTATTATGAGGAGAAGGTAGGAGTGTAGCTAGCAGCGTGGAGACATTAGGTCAGCCACTAGATGTATTTGTGATTTTGGTTTGAAGGACACAGAGAAAGGTTGGAGGAGGAGGTTTGGTATGCTTGTTTTTTGCCTTTTTTCCTATAATGTTTGATTAACAGGCAGCCTTTTAGCTAGTGGAAGAAGGAAAAACTTGTGCATGCTATATCTCATTCCCCCCTCTCTCTCTCCTGTCCTCTCTGATCCAGACCACCAAAAATACTCACTTTGAGTGAGAATTTTTCAACCATAAAAACATATAGCCCCCAAAGCCATGTGGAGAAGGAGAGCCCACCTCCTTGCACTGTGCTGAAACATAGAGGTTTCCCCCTGCCTTTTCTTATGTATGCTTTCTTGACCCAAGGCAGAAGTGTGGAGTCTTAGAGCTTTGTAATTCCTGTTCTCTGGCTCCCTTTAAAGGCCATTTTTGTCCTTTGCAAGGTTTGGTAGTCTCACCCTTAGTTCGATGAAATTCCCTACAACTCCTCTCAAAGCACTCTACCTGGGTCCGGACACCCAGTCCCCAGGGCCAACCTACAAGTGAAGGAGACAGGTCTCTAGGGTAGAGGGAAGCAGGCAGGAACCTCCCTGTCCTGATCTTAGAACAGTGGAAGTGAAGAACACCCCACACTCTCTAGCTTTAGAATACTGGGGTTTTGGTTTTGGTTTTTTAAATTGCAGTTGTTTTAAGAAATTCAACCTTTCAGACCAGCCCTTCCACTAAACTTTGATTCTTTTTCTTTACTGCTTTTTTAAACCTAAAAAAAAAAAAAAAAGAAAAAAAAAGGAAAGAAAGCAAGCGCACTCAGTGACTCCCCCACCTTGGTCTGTGGGAATGCCCGCCCGCACTCTGCCGTCCATCCTCCTCCCTTCTCCTCATGCAGTGTCTGTGAAGTAGTTTTATCTGTTTCTTAGGATGAAAAACGGCAATCATCCCACCAGGTGCTGGAAACTGGTCAGCCTTGAAGCAGGCACTTCTGGGACCACAGCTCAGGGATGTGTATTTAATTACAGGGTCCCCAGAAAGCCTCTCTTGGCTGCCACAAGTAGCATCTTTCCTGGACTTGGAGTCAGACCCTGACAACTTCCTCTGAGTGAGCAGCCCCAGGCCACTGAACTGAACGCAAGCTTGCCTATGGGTCTGGGCTTCCTCAAGACTTTTGACCGTCTTACACGTGAGCTTCTCTAGTGCTCATGAGAAGCCTAGACCCTTTGCCCAGGGTCTTATCTGGCAGTCCTAAGTACACCCAGCTCGCTTGGGTATCAGCTGTAGGCTCAAATGGAAGCTGTGGGAAAGGCTAAGGCCTGCTCCAAACCCAAGAAAAATGTGCTACTGGTGGAAGCTAGTCTTCTAACCTGGAAGCCAGCCAAAGGGTTCTCTTGCTCTTTGCTGACCTTTTTCTTAGCCGAAATATAATAGGTGATAATGTTTTTTACTCAAATTTCCATGGGGGAAAAAAGACTACCTCTTGAGTGACATCCTGGTCGATTCCTCTCTGAGGAGTCCTGTGGGAAAAGAATACTGTAGCTCCCGTGCTGTTTACATGTTTCTGTCGGGAATGAAACCCTGGACTGTTGTGTTTTTGTCTGTGTTGCCATCCCAGGCCTGTGATAGGAGCTTGTGGCTGTATTGTAATGTCTGGGCAGTGTCTGGGGAGTCCTTTTCACCTGCCCAAATAGGGACAAGCCATCGCTAGAAGAGGCCTCCACCCCCTTCCTATGCTCCATAGCTTGGATTTCAGGGACTCTGATGGCAAGTGCATCATGAACCTACCTCAGGCTACCTCCCAGTCCTCCCACAGTCCTATGTAGGAATCGAATGAATGGATGTCTCTGAGCCCTTGTTCCCAAAGGGCCGGCCAAGGGCTGCCTGCCAGCCTGGCTCCATCAACCCTGCATGACCAAATGATAGTTGGCGGGCTCTGCAGGCTGCTCAGGCCCTCTGCTACCTCCCACACTTGCCTGCTGGCAAGGGGTGGGCCCTGTTCTGTGAATTGACTACCTGTGGAAATGTGACCAATTAGTATGAAATGCATGTTTAGCAAGTATTAGGTACTGTATTTGAACCAATAAATGTGAATCCTCTGCACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000063972:ENSMUST00000112877:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(26.4=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(8.8=56.7)
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:
GCCAAACCGCTTTCCTGATCT
R:
TGTGCATCATGTTGAAGGCCA
Band lengths:
353-1920
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