GgaINT1020569 @ galGal4
Intron Retention
Gene
ENSGALG00000014450 | PABPC1
Description
polyadenylate-binding protein 1 [Source:RefSeq peptide;Acc:NP_001026768]
Coordinates
chr2:128380601-128382129:-
Coord C1 exon
chr2:128381990-128382129
Coord A exon
chr2:128380696-128381989
Coord C2 exon
chr2:128380601-128380695
Length
1294 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATG
5' ss Score
4.83
3' ss Seq
ATATTTCATTGACATTTTAGGTC
3' ss Score
7.28
Exon sequences
Seq C1 exon
ATTTGTTGGAAGGTTTAAATCCCGCAAGGAACGTGAGGCAGAGCTTGGAGCCAGAGCAAAGGAATTCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGAGACTTAAGGAACTCTTTGGCAAGTTTG
Seq A exon
GTAATGTCTTATGCTTTGAGTTTATATAAACACTGCTGAACTTCAACTTAGTTTGTGTCTGTACAGTGTTCCTATCTGCAATAGTGTTCCTATTACAAAGTAATAGGAACAATCACATGGCTATCTGCAGCTTTATTTAAGAAATTAGTACTTATTACACTTTGAATTTGAGAGTGTAATTAATACCCATTACAGAATTTTAAATAAGTGGAATAGAATATAATCCTCCTATCAGAACTTTCTGATGATCTGGAAATATTGTGTAAATAGTCTCTTTAATGGATTTTGCGAATCGTGAAGTTGCAAATAGAAATGTTTTCTGTTGTATGGATTGATGCTATGAGTTCACTACAGGATATGTGACAAATGAGTTTCCTGTTGCTTTTTCACGGATTTGCAGACAAACCTTTATTCAGAGTATCTGTGCTTTCCTTATTCAGTTGCACTGTCGTGGCTGACTTAAGGAATTGCAAGTAACTTCACTGTGAGCAAGCTGTTCAGTTCTGTCTTGACCCTTGGTTATGCACAGGGCAGAATTGCTGTGGGTATATATCTAGTAATATATCGGGTGTGTTATTGTTGAATTAGGAAGTGGCAAACTTCCTTTATCCAGTCACAGATCCTTATATTAGCCTTGTAGGCCATGTCTATTGTATCGTCATCCTCCTGGTTTTTATAGTGTTTTTTTTCCCTCTGTCTTGCTGGATTCCAGTGGATATCATGTAAACCGAGACAGAGCCTTGTATATGAGATCCTGTAGCAGCCCTAAGTAGCATTCACAGGAAATTACTTTTTATTACTGACATATCTGTGGATGAAATGGTAGCAAATTTAGCTAATAGCTCTTGCAACTGAATTTGAATAGCAATTTTACAAAGGTTCAGAACTGCTGAGCTGAGATCCTTTTGCCAAAGCAAGTAGGGCTAGTACAAGAGTCTCCTTTCCAGGCTTTAGTACCTATTTCAAAGAATGGAAGCACGAGCACTTCAAATGTTATTTTTTCCATTAAAAGTTACTCAGTTCACTTTGAAGTTAAATCCCTACCCCGTTTTGATTGAAAATGCAATACAAGAGATACTCAGCATGGCAGACATCAGCCATAAAAAGGCTATAGTTCAGCATCCATCCGGGCAGATCAGCAGTCTTATCCTAATGGGTGGCATTTCCTAGATACTGTCATTGATGCAGGAATCTTTTGTAGTAAAAATGAAGAGATGAGGTATTAAAATTTCTAAACAATGTTCAAGACATGAAGAGAATGTACACAACATAAAATATTTCATTGACATTTTAG
Seq C2 exon
GTCCTGCCTTAAGTGTGAAAGTTATGACTGATGAGAGTGGAAAATCCAAGGGCTTTGGCTTCGTTAGTTTTGAAAGACATGAAGATGCCCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014450:ENSGALT00000023333:3
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=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.4=45.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=100)
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:
TGTTGGAAGGTTTAAATCCCGCA
R:
TTTGGGCATCTTCATGTCTTTCA
Band lengths:
230-1524
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]