GgaINT0059794 @ galGal3
Intron Retention
Gene
ENSGALG00000008332 | F1NXV6_CHICK
Description
NA
Coordinates
chr5:25592017-25592771:-
Coord C1 exon
chr5:25592645-25592771
Coord A exon
chr5:25592185-25592644
Coord C2 exon
chr5:25592017-25592184
Length
460 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
CCTCTTTCCTTGTGTCTAAGGCA
3' ss Score
6.33
Exon sequences
Seq C1 exon
ACTGTGGAACTCGCCCTTTATTCGAAAAGAAACAGATAACAGACCAAAGTGAGAAGGAGCTGATGGACTCCTACATGGGAGGCAGAGTTGTACACGGGAACGATGCAGAAGTTGGAAGCGCCCCCTG
Seq A exon
GTAAGTATTATCTCCCTTCTCTTCCCTTCCCACCCCCTTCACGCAGGGGGAAATAAAAGGGCAGTATGCCAGTTAGTATGTAGACGGTATCATTTCTAATCACAGATTCTCCAAGTGGTTGACAAGGCAGTAGAAGAATAGCTGGAAATAAACTTCTCTTGAGCTAAGTATACAAGCATCAGGGAAAGCAGGAGTGCTGGTGTGGCTCACGGTTCCAGCTTTGCTGGAACAGAGAGGATAAGAAATCTTTGCAAGTGAAGGAAATAAGGCAAATTGTCGTGTAACTTATGTAATAATCTCCAAGGTAGAAATATTTTCAATAAAGCCACCTGTCTTTTTAGCAATACAGCACAGTGTGTTTCCATGCTTACTGCAGATCCCGCTCTCCTTGCACAACACCAAGACACATGCATCCAGCCAAGACTTCAATCCTAAGCATTCCTCTTTCCTTGTGTCTAAG
Seq C2 exon
GCAGGTGATGCTCTACAAAAAGAGTCCTCAAGAGCTGCTGTGTGGTGCCAGCCTCATCAGTAACAGCTGGATCCTGACTGCTGCTCATTGCCTTCTTTATCCACCCTGGGACAAGAACTTAACTACAAATGACATCTTGGTGCGGATTGGCAAGCATTTCAGGGCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000008332:ENSGALT00000013559:9
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:
PF093965=Thrombin_light=PD(57.1=65.1),PF0008921=Trypsin=PU(5.2=30.2)
A:
NA
C2:
PF0008921=Trypsin=FE(22.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGTGGAACTCGCCCTTTAT
R:
TTGCCCTGAAATGCTTGCCAA
Band lengths:
294-754
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]