GgaINT0010608 @ galGal3
Intron Retention
Gene
ENSGALG00000004123 | PABPC1L
Description
NA
Coordinates
chr20:5201539-5202532:-
Coord C1 exon
chr20:5202393-5202532
Coord A exon
chr20:5201634-5202392
Coord C2 exon
chr20:5201539-5201633
Length
759 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGT
5' ss Score
9.27
3' ss Seq
GCTCTCCTTCCCTCTTACAGGAA
3' ss Score
12.57
Exon sequences
Seq C1 exon
GTTTGTTGGCCACTTTAAATCCCGCAAAGAGCGCGAGGCAGAGTTTGGGGCCAGGGCAATGGAGTTCACCAACGTCTACATCAAAAACTTCGGGGATGACATGGATGATAACAGACTGCGGGAAATATTCTCCAGGTTTG
Seq A exon
GTGAGTGTGGCTGCTGAGGCCAAATAACCAAATGTCTGGGAAGTGAGCTGGGGGCCCCAAAGAGAGGTGGGGAAACACACTTGGCTGAAACACAGAGCCCTTCTCTTGTTGTGACCTGCTTTGCTTAAAACACCACGTGGCCAAAGGGTTGCAGAGCCTTACACTGCTAGGATGCTGTGTGTGCTTTCCTGTAATGACAGAGGATGTTATTGGGTGACTCAAGAAAAGTGTTGGTTTCCTTAGATTTCTCACTAACAAATCTTTTGTATTTGAAATTGCCTTGAAATCAGCATGCTGTCTGCTTCCAGGAACCATGGGAATAGGAGATGTTGAGTTTGAATTTAAAGCAAAAGTGGCTTTCCCTGTTCAGTCCGTTACTGGAGGGTGCCTCTCACAGCAGGGCTTGGTGCCATGCCAGCTCATAGACCATGCTTGGCTAGTGCAAGCTCAGCTCATCTGTGAACGTCATTTGTACGAGCCTGATGTACGTGTTGATGCATCAAGGAGATGAGAACTCACAGCTAAAGAACCTGAAAAGCCAACAGCAGTGAAGCAGCATACTGGATGGGAGGGATCATCCTGGCCTCCCACAGCCTCCTTTTCCCACACCGCAGCAGGGATCCAGCAGTTCCTCCTGCTTGGCTCTTGCCACTGCCCCCCAGTCTTCTCTTTGGGCCACTGTCTTATGGTGGCTTTGTTTGCTCCCGTGCCCTGGCTGGGCAGCCTTCTTTACAGTGATGCTCTCCTTCCCTCTTACAG
Seq C2 exon
GAAAGACACTGAGTGTCAAAGTGATGATGGACCACACCGGCCGCTCCAAGGGCTTTGGGTTCGTGAACTTTGAGAAACACGAAGAAGCCCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004123:ENSGALT00000006565:4
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),PF073187=DUF1464=PU(9.0=18.8)
A:
NA
C2:
PF0007617=RRM_1=FE(44.3=100),PF073187=DUF1464=FE(31.0=100)
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:
TTGGCCACTTTAAATCCCGCA
R:
CTTCTGGGCTTCTTCGTGTTTCT
Band lengths:
230-989
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]