GgaINT0080061 @ galGal3
Intron Retention
Gene
ENSGALG00000016565 | F1N9F1_CHICK
Description
NA
Coordinates
chr3:107878395-107879456:-
Coord C1 exon
chr3:107879277-107879456
Coord A exon
chr3:107878440-107879276
Coord C2 exon
chr3:107878395-107878439
Length
837 bp
Sequences
Splice sites
5' ss Seq
GTTTTAAGG
5' ss Score
-4.17
3' ss Seq
CTCTCCGCTTCCCACTGCAGGAT
3' ss Score
11.43
Exon sequences
Seq C1 exon
CTGCACCTGCTCCATGTCTCCACAGCCACCCGGGAGCAGAAACAGCCCCATGGCTTTGCTGAGGACCGTCTCTTCAAGCATCTCTTCACGGGCTACAACCGGTGGTCACGGCCGGTGCCCAACACCTCCGATGTGGTCATAGTGAAGTTTGGGCTGTCCATAGCCCAGCTGATCGATGTT
Seq A exon
TTAAGGAGCCCACGTAGGGATCTCATCCTAGGACCTCTGAGCCATTTCTTCTGCCCTCCATGCTGCTGACTGTCCCCGGTAGGGGACAAGCCACCCACCCGCCTCTACAAAACCTCCAACGAGCAGGGGACATTGCTCATCGCTCCTCCATCCCAAGCCTCCCCTTCCCCTGAAAGCAAGACAGCATCAAGGAAAACTGCACTGCTCTCCATCCCCGTTCTTATCTTCCCATCATCTATACCTATAGGGCTATGCCTGGGCTTGTTTTTACATCCATGTCTTGCTTGTTACTGTCATGCACACCCATCTGTCCATCCATCCATCCACCCACCCACCCATCCACCTACCACCACAGAACCCCCAGACCCCCAGGGTGCTTGGCACTGAAGGTAACCCTGGATCTCTCTGGTCTCCCCTCCCCACCCCGCTGCCCCAGAGGGGTCACCCAGCCACTCTTTACTACCTATAGCCTTTCTACTATCTGCTACATAGAGCCTAGATAAATCCATCATCTATCTACCCATCCATCTATCCATATATACTTCTATCCATCCGTCTGCCCATTTATCCGTGGCATTGTGCATTTGTCTACCCACCAGAACTTCTCCGAGCTTGCTGCCACAATATACTATTGTTTGCTGCCATCTAGTGAGCAAACATCCAATTTCTCCTGCACCTTGTTCTGGCATCAGTTACTTTAAGGAACTGAACCCCAGAGGCAGAATGGGAGTTCAGCAGCATGAGCCGGATAGGCAGAAGGGTGATATGGGGACTGATGCAGTGTTGGGATGAGCCTTCTCTGTCCTTCTTCTCTCATCTCTCCGCTTCCCACTGCAG
Seq C2 exon
GATGAGAAGAACCAAATGATGACCACAAATGTTTGGCTGAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016565:ENSGALT00000026738:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293118=Neur_chan_LBD=PU(18.8=65.0)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(6.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGCACCTGCTCCATGTCTC
R:
GCTTCAGCCAAACATTTGTGGT
Band lengths:
223-1060
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]