GgaINT0125167 @ galGal4
Intron Retention
Gene
ENSGALG00000003830 | NUP214
Description
nucleoporin 214kDa [Source:HGNC Symbol;Acc:HGNC:8064]
Coordinates
chr17:6099855-6101538:+
Coord C1 exon
chr17:6099855-6100016
Coord A exon
chr17:6100017-6101090
Coord C2 exon
chr17:6101091-6101538
Length
1074 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
ACCTATTTATGTTTCTGCAGGAA
3' ss Score
10.49
Exon sequences
Seq C1 exon
GTGATGAGAAGACCCTTCCTCCAGCACCAGTTCTCATCTTGCTCTCTACGGATGGTGTGCTCTGCCCATTTTACATGATCAATCAAAATCCAGGGGTCAGATCGCTTCTTGTGACCCCAGAGCCATTGCCAGCAGCAGGGGAGAGAGCACCAAAATCACCAG
Seq A exon
GTGAGTGCTGCAGTGGGTTAAGGAAAGATTTGTGGATCTTTGTCGTCTTCATCTGTGAGTTTGTTATTCAGATAGACACGCAGTCACAGAAAATGTTGTATGTTTTGATTTATAATGATAATGGGATCAGCTCTTGGGTGTTTTATGTTCACCAGTCAGTTCTCCATCTCTTGTACATCCAGATGAAATAATATAGTCCTGTTCATCCTAGGGGATCTCAGACAGTTTTCAGACAGTGCATTTAAACCCCTCCATGCAATGAACCTTTGGGGAACAGGGCCAAAGCAATTCTAGGAGGCCTTTTGCCCACTGGAACTGCAGCAGTGACTGCAGGCTCCACTTGGGGGCAAGGATCAAATGCTGTGCAGACCTAGAGCAGGGTCCATATGCACCCAGGAGATGATGGTTTTCCTCTCTGTGTTCTTATCATGGCCTCCCATGGCAAAACAAACGTGTTTGACTGCAGAAACAGCTTACTTAAGTTATAGCTTTCTTCAGCACTGTGAAAAGTGTCAGGAGGTGAAAAGCAATAGTTGGACTGTATGTTGGGTACCATATATAGTGTGAAGTAGACAGTTCCCTATTCTAGGGTAGACAGGTCAGTTGGTTTTTACTGCATGCATGCAGAGAAGCAGAACAATTGCAAGCCCACCATTTTCTTTCCTAAGCCTGCATTTGCTTCTCCTTCTCCAAACAGAATGCATCTGTTTGGCATCCTGCCTCTCTGCAGTGCTGGCTGACTTGTGTGCTGACAGCCTTTTTTATGTGAGATGGCAGGAACCTCATCAAAAGCAGTGGAGAAATGTGAAAGCTTTTCACTGGGAATTCCAGGTGATGTTAATCTAGTTAGATGCGAGTAAACTGCAGTATTGATCACAGCTTGGACTTTGTGCACTCATTTGCTGGATGTGAGGACTGGAAGCCCTCTTCCCTCCTCACTTTTCTTCACTGTGCTGTCTGCCTAGTGAATGAGGTTGTACCTAACTGTCCCATCAAATAGCGTTTGGCCTTGCAGTACCTTCTGCCATTAGTCAGTGCAACCAAATGAGTCTCTACCTATTTATGTTTCTGCAG
Seq C2 exon
GAAGTACTGTCACAGCTCCGACCACTCCGCCAACTTCTTTAAAGCCTGATGCAGTACCAGCTGTTGCTCCTGCCCCAAGTCAGCCTCCTGCAGGAGATGGAGCAGCTGCTTTTTCCTTTACACCTTCAACTGCAAAGGTGCCTAGCTCTACAGGCAGTGAACTTCCACCCTACCCCTTTGCCACCGATACCTCCAAGCAAGTCCTGGCTCCAAGTCTTACAGGAGCGGCAACATTCTCTTTCTCCTCTGCTTCTCCTAAGGCATCCATAACACCAGCTCCTTCTGTGGGCACTACTGCAGCCACTGCCACATCCTTCTCCTTTGGATCCATTAACTTGAAACCATCTGCAGAAAGTTCACCTGGACTGCCACACTCCACAGCTCCTGCTGCACAGAAGTCATCTTTTGCCCCTTCGGCTTCTTCAGTTAAAGTGAATCTCAATGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003830:ENSGALT00000006070:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.345 A=NA C2=0.711
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATCGCTTCTTGTGACCCCAG
R:
GGAGCTGGTGTTATGGATGCC
Band lengths:
343-1417
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]