GgaINT0125166 @ galGal4
Intron Retention
Gene
ENSGALG00000003830 | NUP214
Description
nucleoporin 214kDa [Source:HGNC Symbol;Acc:HGNC:8064]
Coordinates
chr17:6098362-6100016:+
Coord C1 exon
chr17:6098362-6098488
Coord A exon
chr17:6098489-6099854
Coord C2 exon
chr17:6099855-6100016
Length
1366 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
ATGTATGTGGTCTCTGGCAGGTG
3' ss Score
9.29
Exon sequences
Seq C1 exon
CAGAACTGGGAATCATGGATTTTGGAGGACTCCAGCAGAGCAGAACTTCCTGTGACAGATAAAAGTGATGATACTTTGCCTGTTGGTGTTGCTGTAGACTACACCAATAACATGCCTATCCCGATCA
Seq A exon
GTAAGTCTTGTTAGTCTCGTGAAATAGCCCAATAGTAGCAATATGTGAGATATTCTTGAGAAGCAATCCAGTGCTTTAGGGACCCGGCAGATTCATCTGAAAGTGGGGCTGACACACTACCAGTCCTACATTTTTATAGGAAGCCCACAGCACATGCACAACTACATCTCTGTAAGGATTCAACTATTAGATGCAGTTCTTCCTGAAAGCTTGCAGCAGATTGGGATGCTGCAGTAACAGGCATGGAAGGGAAAGCACCTCAGTTAGGTTTGTGTTTCACAGAACTGGGGTAATAATGAGTTTTAAAGAGCCATATTCTGTTAGGGATTTCACACTGCCGATGTGGTTTTCATGATGCTTGTAGCTTCTGTCATTTTGCAGAACTTTTTATTAAGTATGTTTGCAGTGGTCTAAAGGGGAAATAAAGGGTTGGTTACAAAGCCAGAAAAAGCAAGAATCGTTGAGGTGAATGTGTAGGTTTTAATTCTGCATTAAAGCACAGGGCCTGTACTAACTGAACCCTGCTGTGCTTTGCATCTACCCAGTTACATTACTGGTGTACCTTCTGTGCTGCCTGAAGGCTCTTCAAAGCACATTGTCAGAGGCTGAAGCGGAAAATACATCTGAGCTATTGTGCTCTACCTCAGTGAATTCTGAAAGCTCTCTCTTGCAACCCAGAGACATTAAAATAGACATGCGTTCAGGCAGAGTGTAAGGTAGTGCAGTTGTGTTCCTGAAGAGCACAGGAGGGTGCCGATTAACTGGGAACTGCAGCAGCCTTTACCTGAATGACAACCTACAGCAGGGAATTGAGGTCAAACTTTAATGCAAAATTGAATTTGAAGCATTTTCTGTTAACCTGTACGTTTATTAGCTTAAGGAATCTGTCCGAGCAGCCTCGTTAAACCCAGATTGTGCTGCCTTGGAGTTTTTAGAAAGGTTTTTGGAGAAGCTTTTTGATAACTGTGTTCTCATTTAGTGTAGTCAGTTCCTTTTTGACTGCACATTATTTGATTTTACAGTTTTGCAACAAGTTTGGATCGAAAAGGAAGTATATTTGTCCTGGAACACACTTCCATGTGGAGTTTTCCCTTCCCCAACTAGAGCCAGTATTAGAGGCGTGTGGCCCTTCACTGCACCAACCAATAAAAAAGAAATGCTAATATTTAAATGAATTTCTTTTCATTCTATATTTACTTTTTTATATTAAGTAAAGTTTATAGAAAATGCTTTAGGAATAGTTTGGGGCCTTTAACTGTGCTGAGAATACTTGAACTGAAGCAGACTAGCTCAAGATGGTGCCGATGAGAGTAGGAACGGGAGGGGAAACCTTGGTTGCTGTGCTTATGTATGTGGTCTCTGGCAG
Seq C2 exon
GTGATGAGAAGACCCTTCCTCCAGCACCAGTTCTCATCTTGCTCTCTACGGATGGTGTGCTCTGCCCATTTTACATGATCAATCAAAATCCAGGGGTCAGATCGCTTCTTGTGACCCCAGAGCCATTGCCAGCAGCAGGGGAGAGAGCACCAAAATCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003830:ENSGALT00000006070:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.353 A=NA C2=0.345
Domain overlap (PFAM):
C1:
NO
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:
AGAACTGGGAATCATGGATTTTGGA
R:
GGTGATTTTGGTGCTCTCTCCC
Band lengths:
286-1652
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]