MmuINT0115699 @ mm9
Intron Retention
Gene
ENSMUSG00000027168 | Pax6
Description
paired box gene 6 [Source:MGI Symbol;Acc:MGI:97490]
Coordinates
chr2:105525044-105526100:+
Coord C1 exon
chr2:105525044-105525259
Coord A exon
chr2:105525260-105525934
Coord C2 exon
chr2:105525935-105526100
Length
675 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
CCATTTGGTTTGATTTGCAGGTG
3' ss Score
9.83
Exon sequences
Seq C1 exon
GTATCCAACGGTTGTGTGAGTAAAATTCTGGGCAGGTATTACGAGACTGGCTCCATCAGACCCAGGGCAATCGGAGGGAGTAAGCCAAGAGTGGCGACTCCAGAAGTTGTAAGCAAAATAGCCCAGTATAAACGGGAGTGCCCTTCCATCTTTGCTTGGGAAATCCGAGACAGATTATTATCCGAGGGGGTCTGTACCAACGATAACATACCCAGT
Seq A exon
GTAAGTTTATTGTGAACATCGTGTGTCTACCTTGCCCCAAGGCCCATCTCTGGCGCGTCTTTATCTCCTCCTGCTCTTTTCTCTCCCCAGGCCTTGCCATCTCTCTCCCTCTCTTCCCTGATTTGTCTCCAGGGTACCTGGGGGTATGGAGAGGTGGGCTTTGACTTTTTGACCATCTGGAAAATGGGGGTGAAGTGTGAGGAGTAGTTCCCTTCATTTGGATACCACAGACCAGGGGTCAAAGGAACTAGGGAAAGGCACTTGGAAATGAAAATGAAAACCAGATTCTAAATTCCCCTCAAAGCATTTTCCTGAAGCTTCTTTCAGGCAACATGCATCCATTTCTGCTCTCCGATAAAGTAGATCTCTAAAGTAAGTCTTTTATCACTGAGTCTTGGATCAAAGCGGAGCAGCCCAGTGAGCGGTTATTCGTGATATCTACAGAGGTGAAGGACTGCTCCCTCCTTTACACCCAACTTCATTTCCAGGAACAAAATGATAGCTGCCATTCTTTCCACAAAATAAGTTAAAAATCCACAGACTGTTCCAGGATGGCTGGGAGCTTTTGCATGTGTAGTGGGGTCATTCTTTAAAGCTTGGGAGAGCTGAGATGGGGACCTAAGATGGGGTGACTACGTGTCTTTCGGAGACACTACCATTTGGTTTGATTTGCAG
Seq C2 exon
GTGTCATCAATAAACAGAGTTCTTCGCAACCTGGCTAGCGAAAAGCAACAGATGGGCGCAGACGGCATGTATGATAAACTAAGGATGTTGAACGGGCAGACCGGAAGCTGGGGCACACGCCCTGGTTGGTATCCCGGGACTTCAGTACCAGGGCAACCCACGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027168-Pax6:NM_013627:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.005 A=NA C2=0.830
Domain overlap (PFAM):
C1:
PF0029213=PAX=FE(46.3=100)
A:
NA
C2:
PF0029213=PAX=PD(23.0=50.0)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
ENSMUSP00000016435, ENSMUSP00000087878, ENSMUSP00000097236, ENSMUSP00000106711, ENSMUSP00000106712, ENSMUSP00000106713, ENSMUSP00000106714, ENSMUSP00000106715, ENSMUSP00000106716, ENSMUSP00000114641, ENSMUSP00000115032, ENSMUSP00000118457, ENSMUSP00000119375, ENSMUSP00000121302, ENSMUSP00000122311, ENSMUSP00000129344, ENSMUSP00000133346
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAGGTATTACGAGACTGGC
R:
GTTGCCCTGGTACTGAAGTCC
Band lengths:
343-1018
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: