GgaINT0010612 @ galGal3
Intron Retention
Gene
ENSGALG00000004123 | PABPC1L
Description
NA
Coordinates
chr20:5199137-5199974:-
Coord C1 exon
chr20:5199708-5199974
Coord A exon
chr20:5199228-5199707
Coord C2 exon
chr20:5199137-5199227
Length
480 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
AACTCATTCTCCTCCCATAGCCG
3' ss Score
7.7
Exon sequences
Seq C1 exon
GTGATGACAGAGGGTGGCCACAGCAAAGGGTTTGGCTTTGTATGTTTTTCCTCTCCAGAAGAGGCTACCAAGGCCGTGACCGAAATGAACGGACGGATTGTTAGCACTAAGCCTCTCTACGTTGCGCTCGCGCAAAGGAAAGAGGAAAGGAAAGCAATTCTCACCAACCAGTACATGCAGCGATTGGCCACCATGAGGGCACTGCCTGGCCCTTTCCTTGGCTCCTTCCAGCCTCCCCCGGGGTATTTCCTCCCCCCCATCCCTCAG
Seq A exon
GTGAGTCCCTCAGGGACAGCCTTGCGTGGGGACCTGAATTTGCTGTGTGTGGGGAGGAGCTGGGGTTGGTTGGTAGGACCTAGGAGCGCATCACTTGTGTCTGTGCAGAACAGAGCTGTTTGGTGTCAGTGCCTGGCCTCAAAGTCAGCGGCAGGATGTGCAGAAAAGCTGGCTTGAGGTGCTCCCACAATGGGCTGGGTGTTGGTAGCCCCAGGGTGCTCCTTGGATCACCAGGAAGTTTAGTGGAAGGGTTGGAGTGTGGAGATGGAATCTCCTGATGGAATGAGGGGAGACAGGAGGGTTGGGGAAATGTGGAAGACGCACGTGGGGAGGAGATGTGTGGGCTTGCTGGAGAAAACACAGGCAGTAGGATTGGAAGCAGATCTGTAGCTTGCCTGGTTGCTGAGATGCTCTTTGCCCTGCTGATCTGATATAGGTCAGCTCCCCAGTCACCTCAGATAACTCATTCTCCTCCCATAG
Seq C2 exon
CCGCAAACCAGAGCTGCTTTCTACAGCCCCAGCCCAGTTGTCCCTGTCCGTCCTGCCACTCGCTGGAGTGCGCAGCCCACCCGGCCTCCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004123:ENSGALT00000006565:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.090 A=NA C2=0.677
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=PD(56.5=43.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGACAGAGGGTGGCCACAG
R:
GAGTGGCAGGACGGACAGG
Band lengths:
326-806
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]