GgaINT0136943 @ galGal3
Intron Retention
Gene
ENSGALG00000003800 | PABPC4
Description
NA
Coordinates
chr23:5735637-5736470:-
Coord C1 exon
chr23:5736333-5736470
Coord A exon
chr23:5735733-5736332
Coord C2 exon
chr23:5735637-5735732
Length
600 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAT
5' ss Score
6.6
3' ss Seq
TACTGTTCTCTACCTTTTAGGGA
3' ss Score
9.82
Exon sequences
Seq C1 exon
GCAGTAGAAGAAATGAATGGGAAGGATATCAATGGGAAAATGGTGTTTGTAGGCCGAGCACAGAAGAAGGTGGAGCGCCAGGCAGAGCTGAAAAGGAGATTTGAACAGTTAAAACAAGAGAGAATCAGCCGGTACCAG
Seq A exon
GTGAATAGTCTGTCCCTTTTCTGAATTTAAGTACAGTTTTCCATCTATTGGTAGACTTATAAAGCATTGATGAAGCAATCGTTGTCCTGTGATGTATCCTGAGAGTTCAGACTTTGAGGTGACTCCATGGTATTTGGAGGCAAAGGAGACATCTGTGTATGATACTCACAATAAAGTGCTTAGGTGGATATGAGAAAAGTCATGCAGTCATCTTTAATTTCACATGAGCCTACCTAAAAGGATGAAAAGAGATGATATAGCTCTATAGTGTTTGTTTAGTTTTTAGCAAAATTGTGTCATGCCAGAGACTGCATCTGAATCTTTCCCACTCCTTGCGATGTAGTGCCGGACTGGGGACACATGATGCAACAGGAAAGCAGAGGAAATCCAGACAGGCTCTTTCACTGTATTGGGGTTTGTCTCTACACCTTTGCAACATTTATGGCCATCAGTCTTGGTGGCATGACAGTAATTTCCTGCTAAATTAAGAGGTTTTATACAAATGACAGCTTTGGTAGATGAATGCTGACAGTTGAAGTGCTGAAGATTCTCTTTATTACTGTAGATGTCTTAATTACCTTACTGTTCTCTACCTTTTAG
Seq C2 exon
GGAGTTAACCTATACATTAAAAACCTAGATGACACTATAGATGATGAAAAACTGAGGAAGGAATTCTCACCTTTTGGGTCAATAACAAGTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003800:ENSGALT00000006028:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.130 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(20.3=30.4)
A:
NA
C2:
PF0007617=RRM_1=PU(40.6=87.5)
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:
GCAGTAGAAGAAATGAATGGGAAGG
R:
TGCACTTGTTATTGACCCAAAAGG
Band lengths:
231-831
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]