GgaINT0136942 @ galGal3
Intron Retention
Gene
ENSGALG00000003800 | PABPC4
Description
NA
Coordinates
chr23:5736333-5737149:-
Coord C1 exon
chr23:5737055-5737149
Coord A exon
chr23:5736471-5737054
Coord C2 exon
chr23:5736333-5736470
Length
584 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGA
5' ss Score
9.11
3' ss Seq
TCTTTGACCCCCCTGTACAGGCA
3' ss Score
7.98
Exon sequences
Seq C1 exon
GTAAGACTCTGAGTGTTAAAGTGATGACAGACCCCACTGGAAAATCCAAAGGCTTTGGCTTTGTAAGCTTTGAAAAGCATGAAGATGCTAACAAG
Seq A exon
GTATGACCAAGTGTTAATCCTGCTTGGGTGTCTTTGGAGAATAATTTACTTGGCTTACCGTAGAAGCAGGTTGAGGTAAAATTCTCCCTCAGATGTAACCTCTTCTGGATGTGGGGACTTGAAGCCATTTGCACGTCACTCCGATGTTACCTTATTTCAGGATTAAGCTGGCACTTCTCAGATTACTACACACAGAGTACAGTTGTAGAATCAGAACATTAATTGCTGAAGAAGTACTCTGATGGATGGCTCAGGGAGTGAATGTTCTTGGAGTAGTGTCTTTTGAGCATTATGTTTGTTATTATTTGATACTAAATCCAAGAAGGGTGGGGATAAATTAACAAGTTCCTGTTGTTAGTCCAGCACTAATGGTAAGGTTGTCAGCATGATCTCTCCTGATAACTTCAGTTTATTTTTAATTAGCTGGTGTTAAACAGGAGCAGTGTAGAGATACTGTGGCAGTTTTAGTTTATTGGCTAACAAGCAGGGAGATGCAAGGTGAGCTTTGGGCAGCCAAGTTCTTAACAGGATCGGCTGCTGTCTTGTTTCAGCAACTGATGGTTTTCTTTGACCCCCCTGTACAG
Seq C2 exon
GCAGTAGAAGAAATGAATGGGAAGGATATCAATGGGAAAATGGTGTTTGTAGGCCGAGCACAGAAGAAGGTGGAGCGCCAGGCAGAGCTGAAAAGGAGATTTGAACAGTTAAAACAAGAGAGAATCAGCCGGTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003800:ENSGALT00000006028:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.130
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=FE(44.9=100)
A:
NA
C2:
PF0007617=RRM_1=PD(20.3=30.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGACTCTGAGTGTTAAAGTGATGACA
R:
CTGGTACCGGCTGATTCTCTC
Band lengths:
230-814
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]