GgaINT0123160 @ galGal4
Intron Retention
Gene
ENSGALG00000006706 | USP6NL
Description
USP6 N-terminal-like protein [Source:RefSeq peptide;Acc:NP_001026011]
Coordinates
chr1:5916404-5918087:-
Coord C1 exon
chr1:5917967-5918087
Coord A exon
chr1:5916499-5917966
Coord C2 exon
chr1:5916404-5916498
Length
1468 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGA
5' ss Score
6.56
3' ss Seq
TGGTTGGCTTCTTTTCTTAGGTT
3' ss Score
8.72
Exon sequences
Seq C1 exon
GAAGTTGGATACTGTCAGGGAATGAGCCAGATCACAGCTTTACTCCTAATGTACATGAATGAAGAAGATGCCTTCTGGGCCTTGGTGAAACTTCTCTCGGGTCCAAAGCATGCTATGCATG
Seq A exon
GTATGATGTGTCACATTACTTAGGATATATTAGATTTCAACCTGATTATTTAAGTTGTGAATTATTTGAAAATGGAACCATGCTGCTATGTGTTTATGTTCAATATAAAACATAATTGGAGCTTTATACTGGGATGCCATTGGATGTTACCAAAGTTCACATAGTTTTTAATAATTGTTTTTCTATGTGGTTTCAAATAGTTCTTAATGAAAATCAGATGTTGCTCTTCCACTTAAGCTCTAAAGGAATGTAACTAGTTGAATGCTGATTATGTAGATGTCTATATAGCGATAAAATACTAGTGGAAAACTAATACAGCATGTGTTAAATAACACTGCAGCTATTCTATCACATGGCAGGACAGGAATCCATAGTAAAAAATAAAAAAATAATTTAAAAAATTGCACTGTAAGCATTAACGTTGAGTTCCCTTGGTTTTCTCTTTCCCTCACACGGCATTTCCTGCACTCTCAGTCTTGTTACACTTATATTATTGGTTATCCTCTCTTTCCATGTAAAATTTAGTATGACCTATGCATATTGCATACCTACAGGGACAGAACAGCTCTGGGAGTTCCAGTATCTTGTGTTAATGTCACAGTGGTTCACAAAGCTGTAGTTCTTGGGCACCTGAAAAAGAGAACAGTATCTAGAAATTGGTTGTGGGTTTTAAATTTTTTTAATTTTCTTAAATTCCCAGCAGGCTCTGGGTTCCTTTTCCATTAAGACATTCTTATACCATGGTAGCTTCCTATCCTGTTCAGTGTTCTTAACCCAGTGTGCTGGGTCAAGAAAAAAAAAAAAAGTTATCTGAAACAGGGATCAATGTCATACAAGAAATGTGAATTTATAAGGAATCAAAGACTTGCTTGGAGCTTTACACAAAGATAACACGGACTAAGAAAATCTTATATAAGCCTGTATCTCTAGATCTAGTAGTAATCAAAAGCCATAAAAATACAGCTGTGTTGAACGTTGAGCTCCTCAGTGATCACAGAAAACTTTAGATGTCTTGGGGAATGAGTTTAAATCAATTCATTATATATTGAATCAGTGGATCTGATTTTGCTACCTGGGAGGGAGCTCTAAGTAGGCAACATTTTTAAGATGCCATAGTCAATTAAACAGGATATTTTTTTTTAGATTTGAAGACTTATAGTGAGACAAGCATAGGATTGATTCAGACTGATGTTATCTACCATTACTAACCTAATAATAGTCACTAGAGGAAGGTAGTGATGTTTTACTGTAGTTGCTTAAGCAGAAATATGTGCATATCCATACACGGACATGAGAATATTGCTATGAATGTCTGTTCAGATCCAGTGGTCTATACAAGATCAATATTCTCAGAGCTCTGTATTTCACCTCCCACCCCCTTGTTTATTTATTTATTTATTTATTTAACATGTTACTGTCTTTATAGTAAATAAACACATTTCATTTCATGGTTGGCTTCTTTTCTTAG
Seq C2 exon
GTTTTTTTATTCCTGGTTTTCCGAAACTTTTGAGGTTTCAAGAACATCATGACAAAATACTGAATAAGTTTTTGTCCAAACTTAAGCAGCATTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006706:ENSGALT00000010845:10
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:
PF0056613=RabGAP-TBC=FE(19.0=100)
A:
NA
C2:
PF0056613=RabGAP-TBC=FE(14.8=100)
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:
AGTTGGATACTGTCAGGGAATGA
R:
CAAATGCTGCTTAAGTTTGGACA
Band lengths:
214-1682
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]