GgaINT0010611 @ galGal3
Intron Retention
Gene
ENSGALG00000004123 | PABPC1L
Description
NA
Coordinates
chr20:5199708-5200680:-
Coord C1 exon
chr20:5200585-5200680
Coord A exon
chr20:5199975-5200584
Coord C2 exon
chr20:5199708-5199974
Length
610 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TTGTTCTAATCCAATTTTAGGTG
3' ss Score
9.74
Exon sequences
Seq C1 exon
GGCGTCAACCTGTATGTGAAGAACCTGGATGACGGGATAGATGATGAGCGGCTGAGGAAGGAATTCTCTCCTTATGGCACCATCACCAGTGCCAAG
Seq A exon
GTGAGGGCTTGAGGGTCCTTGGGCTTTGCTGGCTGGCTGCTCCAGCCCTCTGTGAGGGGTTGAGATGATTGCCCTTTTGAACGACAGTTCCCTACTGATGGCTTGTATCCCAAGCCAAGCACGAAGGATGTGTCACTTGTATCCAATTCTGATTCAGCAGGTCTTGGTAACTTTTCGGAGTTATCCCAGCCCCACTGAAGTGCAGGATGTGGCCCCTTAAAGCCAAATCACTCTGAATATTGTGCAGCTGCTAATGTTGTTCAGGGCCAGTGTGACACTGCAACCCTGCTTGCTTCTGAGCAAGCATCAGATGCTGCAGCATTACAGAGTCCTGCAGGGCTGAGGGAGATCACAGTTCTTGAGCTGGTCTGGGCTCTGACCTCTGCACTTAGCAAACCTGTGGTTTTCACCCAGGTATATCCTCTCCTTCCTTGGGAAAGGCTGGGGCAGGTGGGAGCATCCTTTGCCAACCTGTCCAACCCTGGGTGTGGGTGCCATGGGGTGCCCCTGTCCCGCTGTCCTCATGCAGGGGAGGCCCTGACTGCGCCGTGCTTTGTGGGTGGCTGTGCTGATCTGTGGACTTAGCTGTGTTGTTCTAATCCAATTTTAG
Seq C2 exon
GTGATGACAGAGGGTGGCCACAGCAAAGGGTTTGGCTTTGTATGTTTTTCCTCTCCAGAAGAGGCTACCAAGGCCGTGACCGAAATGAACGGACGGATTGTTAGCACTAAGCCTCTCTACGTTGCGCTCGCGCAAAGGAAAGAGGAAAGGAAAGCAATTCTCACCAACCAGTACATGCAGCGATTGGCCACCATGAGGGCACTGCCTGGCCCTTTCCTTGGCTCCTTCCAGCCTCCCCCGGGGTATTTCCTCCCCCCCATCCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004123:ENSGALT00000006565:7
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=0.090
Domain overlap (PFAM):
C1:
PF073187=DUF1464=PD(12.0=37.5),PF0007617=RRM_1=PU(40.6=87.5)
A:
NA
C2:
PF0007617=RRM_1=PD(56.5=43.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCGTCAACCTGTATGTGAAGA
R:
GGGAGGAAATACCCCGGGG
Band lengths:
350-960
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]