GgaINT0123163 @ galGal4
Intron Retention
Gene
ENSGALG00000006706 | USP6NL
Description
USP6 N-terminal-like protein [Source:RefSeq peptide;Acc:NP_001026011]
Coordinates
chr1:5914174-5916032:-
Coord C1 exon
chr1:5915933-5916032
Coord A exon
chr1:5914327-5915932
Coord C2 exon
chr1:5914174-5914326
Length
1606 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGA
5' ss Score
3.22
3' ss Seq
AGTATTTTCTTCTTATGTAGAAC
3' ss Score
6.22
Exon sequences
Seq C1 exon
ACTCCCTTTATGTTAAGCCTCAGGATATGGGATATCTACATACTTGAAGGAGAGCGGGTTCTCACTGCTATGTCGTACACAATTCTGAAGATACACAGAA
Seq A exon
GTGAGAAATCTCTTGAGTGCTTGAATGCTAAATAGGCTTTCTGCTAGTTTTGTTCTTATTTTGTGTGAAAAATCTTAGTTTCTTCTTTGCCTTGTGCAATTCATGACAAGTGTTTTTCTCTCCTTATGAATAAGCAGAGCAAAATCTTTCCTTTATTAACGTAAGTGATTGTCAAAGAATAATTGTACCATCTTTGCAGTGGGCTTCCAGATGGTATTATGGTTGCCCCAAAATCGTACTTGATTTACTTAATCATAAATAATTAGACAAATATAGTCACACCATACAAATTTAAAAACTTATATTCTGCTGTATTTGTGTTTTAATGTAAGTTACTCAGAAAAGTAAGAAAGTTATTTAAACATCAACCTGGGTTGAGCTTTGTTGCTGGTTATAAAGTGGACAAAAAATGTCCTAGTTGCATGCTTTGTAAATGGCTTTCTAGCCACTATAAGTTTTAAAAAAAGTGTTAAAAGAATCCAGAGAGAAAAAGGCTGATATTTTGTGCCTGTAAATACCTGAAACTCTTATCAGCAAGCAATTCAGCAACAATGTACCACCAGTGTTACATATAATTTTATAGTGCCGTTTGTCCAAGAATGTCATTAAAATTCAGAATTTCAGTGGTCTGACCGAATGGTCTTTTCTTCCATCTTTTTCCAACAGGAAAAATAAGATTTGGAGTTTTGAACAAAAGCATTGTCCAAGGCATTTATGCCTGCCCATAGTGCCTGCCCATCTATGCCTGCTCCCATAGCACACAAAGTTCCAATTCTGAGAATGGATGTTAGCTTCTCAATATCTTTAGATGTTTCTCTGGGTGATACCTTGTAGTTCGATACCATTTACCTGTGGTACTTTTGCATTTTCTTAGTGAAATCATTTGACTCTATGTAAATTTAGAAGTCTACGTGGAACTCTTTGCAGAATTGACGTCTTCACTTGCTCACTAGCTTATCCTTATTAAACTGTATAAGCATGCAGTTACAGCCTTGAAAGCAAAACGTTTGTGTGGGAAACATGGCCTTACAGCTGTGTAAAATGGGAAGGAAAAATAATCTGATAACTATAAAATGGCTTTCAGAATATGACCTGAATTAATTGAAGTGGCAAATAATGCCTGAAGCAATGGTTCTGAACTGCCATAACCATTTCATTGGAAGTTAATTCAGTTGTGAATGAGAATACCTTAAATGTCAAACCTTAAACTGTTCTTCTGCTTCTGAAAGCTTTTAAATAAATGATGTATATTGTAAAGATCTATACCAGTGTTTTGTAAGTTGGGGATGCAGGCTGAAGAATGAAGATCAAAAACTGTTGGACATAACATAAGCAGACCAAAGGCAGGTGGCTTGTATTTAGCTTTTAGAAGATGCTCCTTTTTGGAAAACATTGTCCTATATAGAAAGCATTTCTGTATTAATTTGCAAGTGAATTTCTGATGCATTTTGTAGATTTTTAGTGTAGAATTCTATTTTCTGCTTAATAAATAGGCCTTTTTTGTTCTGTTTTAACAACAAAAGCATCTGATATTGTACATACATTTTTGAATGTTATGTTCATAATCAAGATATTTTATTTATAATAGTATTTTCTTCTTATGTAG
Seq C2 exon
AACATCTGATGAAATTACAAATGGAAGAACTTGTAGAATTTCTTCAGGAGACTCTAGCTAAGGATTTCTTCTATGAAGATGACTATGTAATAGAACAGCTCCAAAATTCTATATCAGAATTGAAACGAGCAAAGTTGGATTTACCAGTAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006706:ENSGALT00000010845:13
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(15.7=100)
A:
NA
C2:
PF0056613=RabGAP-TBC=PD(1.4=5.8)
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:
ACTCCCTTTATGTTAAGCCTCAGG
R:
ACTGGTAAATCCAACTTTGCTCGT
Band lengths:
248-1854
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]