GgaINT0120022 @ galGal3
Intron Retention
Gene
ENSGALG00000016144 | F1NY88_CHICK
Description
NA
Coordinates
chr1:112393198-112394658:-
Coord C1 exon
chr1:112394483-112394658
Coord A exon
chr1:112393294-112394482
Coord C2 exon
chr1:112393198-112393293
Length
1189 bp
Sequences
Splice sites
5' ss Seq
CTAGTATGT
5' ss Score
4.69
3' ss Seq
TCACTGTATTTGTTTTGTAGATA
3' ss Score
9.34
Exon sequences
Seq C1 exon
GCTATTTTCTGACCCGTACATCTGGTCTGTTTATGCTGGGATTCTGAGTCAGAATGAGATGCACTCAAGGCCTGGATACAGAGTGCAAAAAATAATTTCCCATCCAAATTATGATACAGATTCTAAAGACAATGATGTCGCCCTTATGAAGTTAGAGACACCGCTGAGTTTTACTA
Seq A exon
GTATGTATTCTGCTCTTATTAAGGAAAAAAAATAAAATAAAAAGCAGGGGGCAGTGAGCATCTCTCTTAAAACTTCAGAAGTTGATGAAGAAATCCTTGTAGATACTTACTCATGGGAAGAACAAAAGAATATGAGATACTTTAATGTGCCCAACCAACAAAAAAACCCCAACCCCCTAAACCAACCCAAACCTCAGTTCCAAGTTCTTGATCAGATTCCTTGCTTTAAACTAAAAAGGGAGATTTAGGCTAGATGTTAGGAGGAAATTCTTTCCCCAGAGGGCGGTGAGGCGCTGGCACAGCTGCCCAGAGAAGCTGTGGTGCCCCATCCCTGGAGGCGCTCAAGGCCAGGTTGGATGGGGCCCTGGGCAGCCTGAGCTGGTGGGGGGCAGCCCTGCCCACGGTGGGGATTGGGGTGGCATGGGCTTTAAAGTCCCTTCCAGCCCACACTGTTCTATGATTCCTCATGTTAGCAGATTGGTAACAGTTTTTTAATACATAAAACTGAAAAGGGATTTTCTTAAAAGTGGGCATACTTCTTTGTAAGCAAGCTGTAGAAACTGGAATATAAAACATTAAAGTACTTCATATATATAGGTTCTGTGTATATATAGGTGCTATACTTACAAGTCCTGTATTTTGGTGCATCAGCTTAAACCTACTAGAGGTAATCTGGAGAGACTCTTCTGGTGCTGAGCACAGGGAGGTTGTCTGCTTGCTAGAATGTTTGTCTGGAATCTTTTATTTCACCTTTCTTGTATACAAGCATTGAATCCTACTTGCATTAGTGATTATTTTCAGCAGGGTTTTGCAAACAGGATGAAGCTAGTTGTTGGAAGAGTTTCTTCTCTTCTTTGTCCTTGTTTACACCTTGATCACAGGAACTGGTGTTAATTGTTGCAGGTAGCCGGGTTGCCAGGTGAATCGAGCTAGAAACACTAACTGTGCTCCTTCCTCACTTTGAGGTCAGAATGCAGTAGCCCTCTAGGAAGGAGCAACTGCATAGCTTTTCACTGCTGCCTGCATTGCACAGTATTGCTTATCTGCAGAGAGGGTAAAGTACAGAGAAAAAAGCAGAGTGTGTATGTATTTAAAACAAATGCTGGTCATGCTGAGTAATGTCGTATCCATTTGTTTTGCATTACACCTGGACATCTGGGTCTAGACTGTCACTGTATTTGTTTTGTAG
Seq C2 exon
ATACAATACGACCAGTTTGTCTGCCTAACCCGGGAATGATGTTCCAGCCTAATCAGCAGTGCTGGATATCTGGGTGGGGAGCAGAGTACCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016144:ENSGALT00000026003:9
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:
PF0008921=Trypsin=FE(25.8=100)
A:
NA
C2:
PF0008921=Trypsin=FE(14.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATTTTCTGACCCGTACATCTGGT
R:
CTCCTTGGTACTCTGCTCCCC
Band lengths:
270-1459
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]