GgaINT0126046 @ galGal3
Intron Retention
Gene
ENSGALG00000004548 | NUP188
Description
NA
Coordinates
chr17:5973487-5974058:+
Coord C1 exon
chr17:5973487-5973620
Coord A exon
chr17:5973621-5973951
Coord C2 exon
chr17:5973952-5974058
Length
331 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGT
5' ss Score
8.35
3' ss Seq
TTTGACTGTGTTCCCTTCAGGTG
3' ss Score
11.88
Exon sequences
Seq C1 exon
TGATGAGTCGCAAGGCCAAGGCCAGCTGCTGATACAAACTGTGAAGCTGGCGTTCTCAGTCACCAATAATGTCATACGATTGAAACCCCCCTCTAGTGTGGTATCTCCACTAGAACAGGCACTTACTCAGCATG
Seq A exon
GTATGTATTCCTCCATGGGGACAGCCTGGGAAGCTGTGTTTTTTTTGTTACTTAGAAACAGTCGTGTGTCTCACCACAGAGAGTATGTCAGTTATTGAAATGTCCAAAATATGCTTTCTAGTGATAGGAGAAGGCTAATTCTCCCTCCTGTAAGGCATTCTAGCAGGTGGTAACCCTGTTCATGGCAGAGGGGTTGGATCTAGGTGATCTTTAGGGTCCCATCATGCTTCATTTTTTTTGGAGGGCTTACCTAATTCTCACCTTCTGCTATGGAAGGCATTCTTTATGAAATAGCTGCTCTTATCTTTGATTTTGACTGTGTTCCCTTCAG
Seq C2 exon
GTGCTCATGGAAACAATCTTATTGCGGTCTTGGCCAAATACATCTACCACAAGCATGACCCTGCACTCCCACGCCTGGCCATCCAGCTGCTCAAGAGACTGGCTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004548:ENSGALT00000039668:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF104874=Nup188=FE(4.9=100)
A:
NA
C2:
PF104874=Nup188=FE(3.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAGGCCAGCTGCTGATACAA
R:
TAGCCAGTCTCTTGAGCAGCT
Band lengths:
223-554
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]