GgaINT0001717 @ galGal3
Intron Retention
Gene
ENSGALG00000013419 | PBX4
Description
NA
Coordinates
chrUn_random:30305639-30306577:-
Coord C1 exon
chrUn_random:30306442-30306577
Coord A exon
chrUn_random:30305796-30306441
Coord C2 exon
chrUn_random:30305639-30305795
Length
646 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
ACAGGGCTCTGAATCTCCAGGTT
3' ss Score
5.84
Exon sequences
Seq C1 exon
GCGTAAACGGCGTAACTTCAGCAAGCAGGCAACAGAAGTGCTGAATGAGTATTTCTATTCGCACCTGAGCAACCCTTACCCCAGCGAAGAGGCCAAAGAGGAGCTCGCAAAGAAGGGTGGCATCACCGTTTCGCAG
Seq A exon
GTATGAAGTGGTTGGTCTGGAGTTGTTGTTTCTTTCCTTGAGTCGTAGAGTCGTTAAGGGTGGAGAAGACCATTGAGGTGGACAGAGTGACTGTTAAGGGTCCCCATCCAACTCCAATGCTTCAGTGGTCCCATGAAAACTAGCCTTGATTCGACTAAGAAATGCCATTTGAGCAAAATGGTCGCCCAGTCGTGACCAAATGGAGCTTTAGGGGCACAAAAACAAGTGGGCTAAGGGGAAGCCGAGGCGATGTTCCGTGAGTTCCATGGATTCCACGTTCCATGGGGCTGATGGATGGAAATCTCTTCTCAGTCAGATGAAGGTGCAAAGAAATGCAAGGGAAAATGGGAATAACCTTCAGACAACATCACGGACAGCTGGGAAGGGAACAACAATGGCTTTGTAGCAGAATGAACACGAGAGTCGACCTCAGGCCATATAAACACATCTGAGTTCTGTTGGGTTGTCCCCTCCGGGCAGCGATGGGTTTCAGTTGGCGGTACTAAAAGAAAACAAAGAACATTTATGTTGTTCCAGAGGGGTTTTTCTGCTCGAACCCTACTATAAAACATTATTTTTGCTGCTAAGCTGTTCACGTAACAGAGAATGGAATGGTTTGAATGGTAACAGGGCTCTGAATCTCCAG
Seq C2 exon
GTTTCCAACTGGTTCGGTAACAAAAGAATTCGGTACAAGAAGAACATGGGGAAGTTCCAAGAAGAAGCCAACATTTACGCTGCGAAAACAGCGGTGGATGCGACCAACGTTGTGGCTCAGGGCAACCGGGCAAACTCCCCATCAACACCAAATTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013419:ENSGALT00000021886:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.196 A=NA C2=0.321
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(75.0=97.8)
A:
NA
C2:
PF0004624=Homeobox=PD(21.7=24.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGTAAACGGCGTAACTTCAG
R:
TGGTGTTGATGGGGAGTTTGC
Band lengths:
286-932
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]