Special

MmuINT0115667 @ mm9

Intron Retention

Gene
Description
paired box gene 3 [Source:MGI Symbol;Acc:MGI:97487]
Coordinates
chr1:78191826-78193711:-
Coord C1 exon
chr1:78193240-78193711
Coord A exon
chr1:78192062-78193239
Coord C2 exon
chr1:78191826-78192061
Length
1178 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
CTTTCGCCATCTCTTCCCAGTGT
3' ss Score
8.04
Exon sequences
Seq C1 exon
GCTCCCTAGTCCGGATCCCTGCACTCGGTGTCACGACGGGAGGAGACTTGGGACGTGTTCCTGCCTCGTCACCACCCTCCCTCACCCGATCTTCGCGGTGCAGTGAGCACCTTTGCCAGTAGCCCCAGCTGAGGGGCCGATCTGCTAGACTCGCACCAAACTCGTCCGCCCTGGGCTTGGGATCCTGCACTCAAGGGACTCCTCTGGAGCCTGTGGACTTGGATCTATTAGCGCCCCCCTCCCCGCGCCCCGCCTCCCTCTCTGGCCTTTTTTGGGGGAGGAGCTCTCCGAGATCCGGAGAGTTCCCGAGGGTCACCCGCCGCACTGTGCTCGCTTTTTCGTCTCGCCTTCACCTGGATATAATTTGCGAGCGAAGCTGCCCCCAGGATGACCACGCTGGCCGGCGCTGTGCCCAGGATGATGCGGCCCGGCCCGGGGCAGAATTACCCACGCAGCGGCTTCCCGCTGGAAG
Seq A exon
GTATGTTAGGGCCTCAGCTCGTCCGGATCCCCGGGCCTGGGATTGGCTGCCGCACCCCAATCCTGGTCTCCAGGGCCTCCACTCGTGCCTTACCGGGAGCCTCTTCCCGTGGTACTTCTCAACCCAAGAAGCAAAAGTGGGGAGGGGGTTCTCGTGGAGAGCGGGAGAAGCCCCATTTCACGTTCTGGCTGCAAACGGAGTGCTAAGCTCACTACAAGCTCTCGGAGCTTGCCTGGCCTGCTCCTGCCGGCTCCACTTTGCCCTGTTGTTTCGGAATTGCTGCCGTGAGAAAGGTGAACAAGCTTCGCAGCGCCGGAAGCAAGTTCTCTTTCTGTTCACCTAAAGTTGCTACGAAATTGTGCGGGCTGCGTTCACTTTTGAATAACTACTATTAGTTCGGCAAGAATTTTCCTGCTGTGAAAAATTCTGGTGGCCCTTCCTAGTTGAAAAGTTTTAGCATTGATTAGCAAATTCCACTCAACTCAAGTGGCATCTCGAAGTTTCTAAAATGGTTGGCAATGCCTTTCGGTTTGCTTAAAGGTGCTGGGAAATTTCGGGGAGGTAGAAATTACTGCAAACCCGAACCCGACCAAATAATTTGGGAAGTAAAAGCAGGAGACTGGGGTTCTGGAGGAGCCCTTCGACCTCGATCCAGAGTAAAACGTGACGTGCAAGGGCGGTCATTTCGGCAGTGGTGTCCACAGCTAGGCTCGCTGCCATTTTTATTTTTTAAGTGTAACAGGTGATACCTGCTGTCACCTGTGTCTCCTTTCGGGAGCCTCCCCAACCCTTGCCTACTATACCCTTATCGGGACCTCTGCCTTCTCAGGACTTTGAGGCAGTTATCGCAAGACATTTTAGACATCAGTCCTAGGTCTCCCTCCAACTTGCAGCACAGCCCCCCTCCCCCAAATAAAAGAGAAAATACAGTTTCTCTACAGCCAGTTACCTCATTCCGATCGCTCAATTTCCAAAAGATTATATGACCTTGCATCGGGTAATTATTTGAATAAATAGAACCTTAAGGGTCCGGGACTGGGAGCCCAGAGCTTGGTGGTTTGTGTTTTAACTGTCACAGGCAAATTGGCCAGAAGGATGCAGAATTAGGTTCTTTTTGCTGCTTTCTATTCTTCCTAAATGACTTTCTCGGGCTCTCTCCTTTCGCCATCTCTTCCCAG
Seq C2 exon
TGTCCACCCCTCTTGGCCAGGGCCGAGTCAACCAGCTCGGAGGAGTATTTATCAACGGCAGGCCTCTGCCCAACCATATCCGCCACAAGATAGTGGAGATGGCCCACCATGGCATTCGGCCTTGCGTCATTTCTCGCCAGCTTCGCGTGTCCCATGGTTGCGTCTCTAAGATCCTGTGCAGGTACCAGGAGACAGGCTCCATCCGACCTGGTGCCATCGGCGGCAGCAAACCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000004872-Pax3:NM_008781:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion (1st CDS intron)

No structure available
Features
Disorder rate (disopred):
  C1=1.000 A=NA C2=0.272
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
PF0029213=PAX=PU(57.9=92.4)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
ALTERNATIVE
Zebrafish
(danRer10)
ALTERNATIVE
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCACTCAAGGGACTCCTCT
R:
CAGAGGCCTGCCGTTGATAAA
Band lengths:
356-1534
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