GgaINT0093868 @ galGal3
Intron Retention
Gene
ENSGALG00000014450 | PABPC1
Description
NA
Coordinates
chr2:133703199-133704724:-
Coord C1 exon
chr2:133704585-133704724
Coord A exon
chr2:133703294-133704584
Coord C2 exon
chr2:133703199-133703293
Length
1291 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
GTAATGTCTTATGCTTTGAGTTTATATAAACACTGCTGAACTTCAACTTAGTTTGTGTCTGTACAGTGTTCCTATCTGCAATAGCGTTCCTATTACAAAGTAATAGGAACAATCACATGGCTGTCTGCAGCTTTATTTAAGAAATTAGTACTTATTACACTTTGAATTTGAGAGTGTAATTAATACCCATTACAGAATTTTAAATAAGTGGAATAGAATATAATCCTCCTATCAGAACTTTCTGATGATCTGGAAATATTGTGTAAATAGTCTCTTTAATGGATTTTGCGAATCGTGAAGTTGCAAATAGAAATGTTTTCTGTTGTATGGATTGATGCTATGAGTTCACTACAGGATATGTGACAAATGAGTTTCCTGTTGCTTTTTCACGGATTTGCAGATGAACCTTTATTCAGAGTATCTGTGCTTTCCTTATTCAGTTGCACTGTCGTGGCTGACTTAAGGAATTGCAAGTAACTTCACTGTGAGAGAGCTGTTCAGTTCTGTCTTGACCCTTGGTTATGCACAGGGCAGAATTGTTGTGGGTATATATCTAGTAATATATCGGGTGTGTTATTGTTGAATTAGGAAGTGGCAAACTTCCTTTATCCAGTCACAGATCCTTATATTAGCCTTGTAGGCCATGTCTATTGTATCGTCATCCTCCTGGTTTTTGTAGTGTTTTTTTTCCCCTCTGTCTTGCTGGATTCCAGTGGATATCATGTAAACAGAGACAGAGCCTTGTATATGAGATCCTGTAGCAGCCCTAAGTAGCATTCACAGGAAATTACTTTTTACAATTGACATATCTGTGGATGAAATGGTAGCAAATTTAGCTAATAGCTCTTGCAACTGAATTTGGACGGCAGTTTTACAAAGGCTCAGAACTGCTGAGCTGAGATCCTTTTGCCAAAGCAAGTAGAGCTAGTACAAGAGTCTCCTTTCCAGGCTTTAGTACCTATTTCAAAGAATGGAAGCACGAGCACTTCAAATGTTATTTTTTCCATTAAAAGTTACTCAATTCACTTTGAAGTTAAATCCCTACCCCGTTTTGATTGAAAATGCAATACAAGAGATACTCAGCATGGCAGACATCAGCCATAAAAAGGCTATAGTTCAGCATCCAGGCAGATCAGCAGTCTTATCCTAATGGGTGGCATTTCCTAGATACTGTCATTGATGCAGGAATCTTTTGTAGTAAAAATGAAGAAATGAGGTATTAAAATTTCTAAACAATGTTCAAGACATGAAGAGAATGTACACAACATAAAATATTTCATTGACATTTTAG
Seq C2 exon
GTCCTGCCTTAAGTGTGAAAGTTATGACTGATGAGAGTGGAAAATCCAAGGGCTTTGGCTTCGTTAGTTTTGAAAGACATGAAGATGCCCAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014450:ENSGALT00000023333:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
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
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTGGAAGGTTTAAATCCCGCA
R:
TTTGGGCATCTTCATGTCTTTCA
Band lengths:
230-1521
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]