GgaINT0125868 @ galGal3
Intron Retention
Gene
ENSGALG00000001583 | TRAF1
Description
NA
Coordinates
chr17:9003166-9003847:-
Coord C1 exon
chr17:9003710-9003847
Coord A exon
chr17:9003344-9003709
Coord C2 exon
chr17:9003166-9003343
Length
366 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TGTTTTCTTTTTCCTCCTAGATT
3' ss Score
10.42
Exon sequences
Seq C1 exon
CTTGAAAATAAGCTACATGTGTTTGAGAATATTGTGGCAGTGCTCAATAAAGAAGTGGAGACCTCCAACTTGGAAATCACAGCCTTTCGGAGACAGAGTGAACTCGATCAAAATGTAATACGAGGCCTTGAACTTAAG
Seq A exon
GTAAGTATTTATGGCCAGCATTGGATTTGTGCTTGCTGTATAGATAACAAGTACTTACCCATATCAGAGAGGAGTGCTGTAGAGATGGGGATGGAGATGAGCACAAGCACTGAGGCTGTGCAGGGTTGTGTTCTGGACACACCAGTAGGATCCTTTTCTTGTTTTGAATGTCCTTTCAAATGGGCATCTCTAATATTTGTTCTCTAAACCCACCTTTAGGCACATGAGTGCCCCCTTGAGTGTTAAGAAGTTGCCAAAAGAAATCAGAGGAGACCCCCCAGGATGTGAGGACCTCGGAATGACTCTGCTACTTCTGCAGTGCATGGGGCTGGAGTTGACTGAGAACTGTTTTCTTTTTCCTCCTAG
Seq C2 exon
ATTGCAGAGCTGCACCACTGCCTGACTCAGAAGGATGCAGGCCTGAGCAGGCTTCATAAGAGCCTTGTGTTCTCCGAGCAAACTTCCTACGATGGGGTCTTTTTGTGGAAAATAACAGATGTTAACCAGAAGCTACAGGACTCAGTGACGGGGAGAGTAGTCAGTTTGTACTCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001583:ENSGALT00000002404:11
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:
NO
A:
NA
C2:
PF0091721=MATH=PU(15.5=36.7)
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:
TGAAAATAAGCTACATGTGTTTGAGA
R:
TGAGTACAAACTGACTACTCTCCCC
Band lengths:
310-676
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]