MmuINT0115691 @ mm9
Intron Retention
Gene
ENSMUSG00000027168 | Pax6
Description
paired box gene 6 [Source:MGI Symbol;Acc:MGI:97490]
Coordinates
chr2:105516602-105520046:+
Coord C1 exon
chr2:105516602-105516995
Coord A exon
chr2:105516996-105519966
Coord C2 exon
chr2:105519967-105520046
Length
2971 bp
Sequences
Splice sites
5' ss Seq
TTGGTGGGT
5' ss Score
4.3
3' ss Seq
CTTTCTCTGTTTTGTCTTAGGCA
3' ss Score
10.78
Exon sequences
Seq C1 exon
CGCCAGCCCGCGCTCCGGCTTTGTGCAAGATTCTCCCGGCACAGAACTGCCCGCAGCACTCGAGCACCAAAGGGTCATCGCGCCCTCCGCCAGCCGGAGCCGTCTGGATGGGCACCACGGCCGTGCGCCGGAGGCCACGAGGGACCCAGAGCGAGAGCGGGCGGTGAAAGAAGCCACTAGGCCGAGGCGGTCGGATGCGCTCTGCGAGGGAGCTCCGAGCCGATCGCAAGGACTGCCAGCTTCCATCCACCCCCCAGGGCCCTCGCCTCCAGCCTCAGCCGAGCGCTGAGCTCAGATTTGGAAACAAACGCCCTAGCTCTCCCGGCTTCCCACAACTCTATCTTGCGAAAGTTGGTGTGTTCCCTGTCCTGTGGACTCCCACCTCCAGCTCTTG
Seq A exon
GTGGGTATTTTCCCGTGTCTCCATTGACCAAGCTGTACCCCGTGTTGCCATTTCAACAAGTTTCGAGCTGGAAAGGCGGTTTGCTCCCCCTTTTCGAGTGTACTGATATTTTTCTTTGTGTGGCCTAAAGGGGGAAAAAAAAAACTACAAGAAAGCACTGGCTTTCCCTCTCCTCGGATCGCGTCCTCTCCCTGCTAATTAGTCTGAGTAATTCGAGAGCTTTTGGATTCTAAGACCCCAGGAGGAAAAGTGGCTTTTCAAAGTTCAGAAAGTTGTTGCCTCTTTCCCGGGGCAGATCTCCTCAGTCTCCCTGAGCCATAATAGCCTCGAATTTTAGCAAGTGTAATTGAGGGAAATGGAGTTGAATTTCAAGTGGAAATGCTTTCTTTTTCGAGTGCTAAAAAACCTGGCCTTTCATTAATGAGCTTTCTGAAAAGTTTAAAAACAAAGTGAATGCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCGCCATTTTGGATGTTAAACTCGAACTTGGGAAGGGCTGAGGAGATAGGATCAGAAAAACAACTGACAAGCTAAAATCCTTGAAAGCCTAGCAGGTTTACCCAAGAGCACGAATAGTTAGTTGTTGCCGCTGACGGGGAGGAGGTTGCCGCTAACCGGGAGCAGGGCTGCTGGGGATCTTTGCATATGTTTGAAGGCAATTGATGAGTTGTAATCATTTGGCCCTGGAGGGTAAACTTTGTCGCCCTAATTGCTAATTTCCAGGAAGGGCATCTGGAAGAGAGAACCCAAGCTTCTCTGAACACTTCAGCTCTGGAATGCGGGAGTAGGTTTTGAAATTTAAATAATTGAAACAATAGCATAGTGTGAGAGTTCTGGCTTGGGTTTGGGTCAGGGAGTGAGGAGGACAGAGGTCCAATGGACCTTGGAGACTCAGACCTTGTGGCCTTGGAGATTTCTGAATACTCCTTCATTCCTGATGCAGGACTATGACCCCCTCCAAGGCAATACAAAGACCTAGCCTAGGCTAGGGGTTTGGGCTGAGGCAGAGGGGTCTAGCTTCTTTAAGAATAGGTCTGCTTCCGGGTGCAGGGTGTGCCCTGCTTCCCAGGGTGCTTTCTGCACTGAGTGTTAACGACTACTTAGGTAATTAGATAGCTTCTTAGAGGAGAGGAGGGTGGGAACCGAGCAAAACCGGAACCTGAAGTGCTATCACCTTCCCACTTGCTTGGGAAACTAATCAGCTAGCTTTTGGGGGATCAGCTAGACAATTTTCTAAAATGGTATTACGGAGGTCCGAGCCGGCTTGGAGACATGAGGCTGTGTAAAAAATGTGGTTCGAGAAGAGCTTAGGAAGTTTTCTGTCGCAAACAGAATTCTCCACACACACACACACACACACCCTCCACACACACACACACACACACACACACACACACACACACACCCTCCATACACACACCCTCCACATACACCTGCTATCCTTTGCAGCTTGAGTCATATATATATATATATATATATATATATATATATATATATATGATGGACATTTTGTTCTAGGTGAGGTATCTGTTCGCGACATGATATAGATTCAGGAACTGGCCTAGAGACAGGAAGGAGACTGTAGGAGTTAACCGCAATGATGGTATCTAGTCCTTGGCTATGTTCAGTCATTAAACAGACACTGAGAAAGTCCTCATCCTAGACTTAGGTCTTATGGATTTAAGTTGCCTCTCAGTTACTTAAAAGTTAAATCATAAAAGGCCTTAAAGAGAAAACTATTCCCTGGAATTCTTTGCAGGGTGGCAAAATTAATCATCATCACAGCTAAAACAAAACAAAACGGGGGGGGGGAATGATTTCTTAAAAATAAAACTAAATGAGATGCTGTGACTATTTCATTATTTTAACCCTCCCCCTTTTTCCTGGGCAATCCTCTTGAATGGGCTCTTTATTGTAACTCCCCCTTTCCAATTGAGCTCCCCACGGTGCCCTTGTATCTTTTTACAGCCCCTAACAACTCACACCAGTAACACAATTACCTCCAGATATTTATAACAAGAAATTACTTTACTATTTTCTCCACCTCACTCCCAAGAACCCTCTTTTTGAGGGAAAGCCCGGAGGACTGGACGCCTTGAGGGGCGCTGTGGCAAGTCAGTACTTCAGTGAGTGGAGTCCTCATTTTTTCCTTTGGGAGTTGCAGAGTTGTTGGTTTCTTTGCTTGGACCTGATGTAGCTGGGTTGAGAGCCTGGGCTTTACTGTCTGGGTTTGGGGAGAGCCACAGAATAAAAGCCATTGTTTGGTGTCTGTAGACTTTGTCTACACCCCCTTCCCGTTTGTACTTTTTAAAACAGCGAGGCGAGGTGGACAGCTTGTGTCACGGTACAGGAAAAGAGGAAGATGTAAACACCAAAAGCAAAGTTAGCTACAATAAATGAGATCTAGGGTAAAAGGCTCACCACTTGCTCAGTCAGGAAGGAGCTGAGAGATGGACTGTGGGGGTCTGACTGGAAAGCGTTTTTGGGGGGTGGGGGGGTGGTTAAGTATAAAGGAGTGCCCAGAGAGCTTAGCTCCTCAGGAAAGTTGGGAGCTTGGTCTGAGGTTCACCCAGACTTCCTAACCTGAGGCCCAAGGCACCACCAGGTCCTTCCCTTCTTCCTCTGCACACTCCCTTCCCCAGCGCTGTCTCTCCTCCCCTCTCTAATGTTTTAGTTTAAACCTTCTCCTTTCCCTGGTACTTGGTAGTTTTGCAAAGTGAGACCCACAACTCAATTTTCCCCATTTTCCCAAGCCTAGCCAATACAGCCTTTTCCTGAGCATTTAAATTTCAGTGGGAGAGGCCACTGGAAGCTTGGGGTGGGTTTGGTGTTTCTAGGCAGAAGGATCTAGCCTCAGATTTACTTTAAGTGGACTGCAGACAGACAGCCAACTATGTGCTGGGCCAGTTTGACACACCTTTCTCTGTTTTGTCTTAG
Seq C2 exon
GCAGAAGACTTTAACCAAGGGCGGTGAGCAGATGTGTGAGATCTTCTATTCTAGAAGTGGACGTATATCCCAGTTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027168-Pax6:NM_013627:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (disopred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: