GgaINT0136940 @ galGal3
Intron Retention
Gene
ENSGALG00000003800 | PABPC4
Description
NA
Coordinates
chr23:5737422-5738147:-
Coord C1 exon
chr23:5738032-5738147
Coord A exon
chr23:5737562-5738031
Coord C2 exon
chr23:5737422-5737561
Length
470 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
TGTAATTTTCTTTCATGCAGATT
3' ss Score
9.7
Exon sequences
Seq C1 exon
GTGGTGTGTGATGAGAATGGCTCTAAGGGCTACGCATTTGTGCACTTTGAGACCCAGGATGCTGCAGATAGAGCCATCGAGAAGATGAACGGCATGCTGCTAAACGACCGCAAAGT
Seq A exon
GTGAGTGTCACAGCCAGCAGCAGCAGCGATCGCATGAACCGTGATGCATCTCGGTATTAACAGGGACACACAAGGTTCTCCTGGCCCAAGCCTTGGCCTGCTACCTCTCCACTACAGGGCTGGTGAGTGACCCTGCCCAAGCCATGGCCTGCTCCCCTTCCATTGCAGGGCTGGTGGTTTCCCTAACCGAGCCTTGATTTACTCCCTCTCTGCAAGTGGGCTGGGTGGGTGTCTGGCCAGTACTCTTCACTGCAGAACTGGGTGGGCATTCTAGGCTGCTGCTTTTCGCCGTAGGACAGGTGACTTTTCTGGTTGGTCTGCGGCCTGTTTGTCCTTCTGTTCTCCTGGCACCCTTTCTTCTCCCTGTGTCTGGCTCCTACCACAAACTCATTTTTTTGCCTCACTGCAAATCACATGCTGTTTTTCCATTTTTGAAAACAAGTTCCTTACTGTAATTTTCTTTCATGCAG
Seq C2 exon
ATTTGTTGGGAGATTCAAGTCTCGTAAAGAGCGGGAGGCTGAGCTGGGAGCCAAGGCAAAGGAATTCACCAACGTTTATATTAAGAACTTTGGGGATGACATGGATGATGAAAGACTAAAGGAACTCTTCAGTAAATATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003800:ENSGALT00000006028:3
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=FE(55.1=100)
A:
NA
C2:
PF0007617=RRM_1=PD(1.4=2.1),PF0007617=RRM_1=PU(31.9=45.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTGTGTGATGAGAATGGCT
R:
ACTGAAGAGTTCCTTTAGTCTTTCA
Band lengths:
249-719
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]