GgaINT1020579 @ galGal4
Intron Retention
Gene
ENSGALG00000003800 | PABPC4
Description
poly(A) binding protein, cytoplasmic 4 (inducible form) [Source:HGNC Symbol;Acc:HGNC:8557]
Coordinates
chr23:5422612-5423470:-
Coord C1 exon
chr23:5423375-5423470
Coord A exon
chr23:5422885-5423374
Coord C2 exon
chr23:5422612-5422884
Length
490 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTG
5' ss Score
7.76
3' ss Seq
GCAATTGGTCTTTACTGCAGGTG
3' ss Score
7.59
Exon sequences
Seq C1 exon
GGAGTTAACCTATACATTAAAAACCTAGATGACACTATAGATGATGAAAAACTGAGGAAGGAATTCTCACCTTTTGGGTCAATAACAAGTGCAAAG
Seq A exon
GTATTGTGGGGCTTGGGGATTTTTGGATTTTAAGGCCTGAAGAAGGAACTGTTACTTGACAAAGGACTGAAGGGCAGTTTGTATATCCTCTGACTGGTGCAGTCATGAGAACTTTGGACTAGTATATAGGCAGATTTCCTTGGGTCTCATTGCGATTTTACTGATAAATTGTTTGATTCCTCATCAGAAGTGGAGGGGGCAAGAGGTGGGGAACATGCCATGTCATACTTATTGGCAAGCAAGCATTTCTCCACATGTGATTAGAGGCACCTAATCTTTCCCATTCCTTGCTGTGCAGTGTGAGCCTGGGGACGCATGGTGCTGACAGAAAAGCAGAGTAAATCCAGACAAGTGGTTCTTCATTGACTAATTGTCTCTACACCTCTGCAACAGTTCTTTCCTGAAGTCTGATATTTCTCTGCAGTCAAAAATAGAGATTCTTAAACTGTTCTTGAAATGTTGCTCCACTAGCAATTGGTCTTTACTGCAG
Seq C2 exon
GTGATGCTAGAAGATGGACGGAGCAAAGGGTTTGGCTTTGTCTGCTTTTCCTCTCCAGAGGAAGCTACGAAGGCTGTGACAGAGATGAATGGTCGAATAGTGGGCTCTAAGCCACTCTATGTTGCACTTGCACAAAGGAAAGAAGAGCGAAAGGCTCATCTAACTAATCAGTACATGCAGCGCATTGCTGGGATGAGAGCCTTGCCAGCCAACACAATCATTAATCAGTTCCAGCCTGCTGCTGGCGGTTATTTCATGCCTGCTGTGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003800:ENSGALT00000006028:7
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=0.176
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PU(40.6=87.5)
A:
NA
C2:
PF0007617=RRM_1=PD(56.5=42.9)
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:
ACACTATAGATGATGAAAAACTGAGG
R:
GGGCACAGCAGGCATGAAATA
Band lengths:
335-825
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]