GgaINT0125869 @ galGal3
Intron Retention
Gene
ENSGALG00000001583 | TRAF1
Description
NA
Coordinates
chr17:9002442-9003343:-
Coord C1 exon
chr17:9003166-9003343
Coord A exon
chr17:9002591-9003165
Coord C2 exon
chr17:9002442-9002590
Length
575 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
TGAAGCATTCTGATTTTCAGCAT
3' ss Score
4.38
Exon sequences
Seq C1 exon
ATTGCAGAGCTGCACCACTGCCTGACTCAGAAGGATGCAGGCCTGAGCAGGCTTCATAAGAGCCTTGTGTTCTCCGAGCAAACTTCCTACGATGGGGTCTTTTTGTGGAAAATAACAGATGTTAACCAGAAGCTACAGGACTCAGTGACGGGGAGAGTAGTCAGTTTGTACTCACCAG
Seq A exon
GTAAACACAGCATACACATGTGTTAGCAGATCTCCATCCTCTAGAAAACGCACTGATTTCTCTAGAATTATGCTTCTTTTCTGCTCCTGGATGGGAGGTGCTTTAAAATACTTCCCTGAGCTACGGTGCCGTTTGAGTGAAGGCATTTTGCTCTCCTGCCCGTTACTCAGGGCAGCTGTGCTGTGCTCTGCCACAGAGCTACGTTCTCTTCTGGGCTTTTGTTTTGCAATTTGCCCTCTGCTGCAGCTACTTGCAGTGACATCTGCTGGATCTGCATTGTCTAACCCACAGCCTTGGTGCCTGGTGGTACTGAATGGTCTCCTGCTGCAGTTATCTCCTGTGTGAGAAGTGATTTAATTAGGGAAAATATCTTTATGTGGTTAATAACAGGTATTGTTTACCAAGGTATGAGGGATAAGAAGGATTCCAGCCACTGTATTCTCACTGTTTATTTGCTGTGTGTTCTCCTCATCTCTGTGGTACCAAATTTGGCACGTCTTTCTGAAATATGTCAGAGCACTCATTTTGCCTTATTTGCAGAGGAGGCTTTACTAATGAAGCATTCTGATTTTCAG
Seq C2 exon
CATTCTACACTGCAAAGTATGGCTACAAAGTTTGCCTGAGGATTTATCTGAATGGAGATGGGATGGGAAAAGGAACCCACGTATCACTCTTCTTTGTTGTCATGAAAGGAGACTACGATGCTCTGCTCCCGTGGCCTTTCAGGCACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001583:ENSGALT00000002404:12
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:
PF0091721=MATH=PU(15.5=36.7)
A:
NA
C2:
PF0091721=MATH=FE(34.5=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:
GCACCACTGCCTGACTCAGAA
R:
CCTGAAAGGCCACGGGAG
Band lengths:
310-885
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]