Special

MmuINT0115701 @ mm9

Intron Retention

Gene
Description
paired box gene 6 [Source:MGI Symbol;Acc:MGI:97490]
Coordinates
chr2:105531722-105532433:+
Coord C1 exon
chr2:105531722-105531880
Coord A exon
chr2:105531881-105532350
Coord C2 exon
chr2:105532351-105532433
Length
470 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACT
5' ss Score
6.64
3' ss Seq
AAATCAACTTACTCTTTCAGAGT
3' ss Score
7.31
Exon sequences
Seq C1 exon
ATGGCTGCCAGCAACAGGAAGGAGGGGGAGAGAACACCAACTCCATCAGTTCTAACGGAGAAGACTCGGATGAAGCTCAGATGCGACTTCAGCTGAAGCGGAAGCTGCAAAGAAATAGAACATCTTTTACCCAAGAGCAGATTGAGGCTCTGGAGAAAG
Seq A exon
GTGACTGGGAAATTTCCAAAGCAGAGAAACCTTAAATCAAAGGAAATGCCACAGCAAAAGCACAAAGGGCTAAATTTAGCTAGGGCTCTTTGCATAAAGGATGAAAAGCCCCCCCCCCCCACTTTTCAGTGTGTGTGTGTTTTTTTTTTTTTTGTGTGTGTGTGTGTGCGCGCATATGCATTTTCTCTCTTCTTTTCACACACCAGCAAACTGAAATATTACAATTCTGACAGACAAAGGAAATGATGACCTATCTGACTGTCTTAGGCCACAGATAAGGACAAACACTAAATGTCATTCCAAAGAAAACTTGCTCCTGGTGGGAAAGTTCTTGCTAGTACAGTCAGCACACTGTCAAGCTGTCTGATTGGCTGGATGAGATGGGAGTTGGGTGTTAAAAGCTAGGTTGATCCAGTGTCTGAACTATCTTGTGTTCTGGTATAATATATAAAATCAACTTACTCTTTCAG
Seq C2 exon
AGTTTGAGAGGACCCATTATCCAGATGTGTTTGCCCGGGAAAGACTAGCAGCCAAAATAGATCTACCTGAAGCAAGAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027168-Pax6:NM_013627:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (disopred):
  C1=0.926 A=NA C2=0.584
Domain overlap (PFAM):

C1:
PF0004624=Homeobox=PU(29.8=31.5)
A:
NA
C2:
PF0004624=Homeobox=PD(40.0=85.7)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
LOW PSI
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCCAGCAACAGGAAGGAG
R:
CTGTATTCTTGCTTCAGGTAGATCT
Band lengths:
238-708
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