GgaINT0111133 @ galGal3
Intron Retention
Gene
ENSGALG00000010342 | OTOGL
Description
NA
Coordinates
chr1:41731317-41733260:+
Coord C1 exon
chr1:41731317-41731396
Coord A exon
chr1:41731397-41733059
Coord C2 exon
chr1:41733060-41733260
Length
1663 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGA
5' ss Score
10.1
3' ss Seq
AATTCTTTATTTATTCATAGATA
3' ss Score
6.51
Exon sequences
Seq C1 exon
GCAAAAGGGAAGAAAGGATTTGCCAGAAAATGACAATCAGGACAACTATAAGAAAAAATGACTGCATAAGTCAAAGCCCG
Seq A exon
GTAAGAATAAAAAAACCATTTTTCATGCTGGTCCAATGGTATGATCAAGTATCAAGAAGTAGGCTATAGCTATGTACAAGCAAGAAAAAATGTTGCTGTCTTCTCAAAAGCAGGCCTTTGACCTGATGGGTGTTATTCTACTCGTAAAAGGAATTAAGTTAGCTGTTCCTGTGGCTGAAAGAGTGACCCCTCCTACCTAGCTTCAAATGAAAAGTACACAGAGTATTTGCACAAACACACTAAACTCCTCACCATGAAATAACATCCCATTCTAAAAGAGAAGTAGAAATGTGTCCAATTAGAATGTGATGGAAAATGTGCTACACTCCTCCTTAAAGAACTTTACTCTCAGGGTGTCATCTCCTCCAAATAGCACGTCTCCGTATCATAAATTCACAATTCCCTTTATTTTGTCATCTATTTAAGGCATCTTATTTCTCATCTTTGATTTATTCCCATCTATAAAACTGGTCTGATAAGAACCTAGCACTTAAAAGAGAAGCAGTTGACATAATATCTTGAGACTTCTGAAAGGTCTCCAATAAGATTTTGCTGAAGAACCTTAATAGTCCAAAGGGACAGCACATCATCACAGATTGAAAGCTGGGCAGGTTAATTTTCAGCCTGATAGAAAGAAAACAGTGACATATATATAAGGCTTCACTACAGTACTAAGAGTGTGCACTGTATTTATTTAGTTTTAGAAGAGTAAATATTGAGGGAGTATAACGAGGGAGATTGTTCATGATTAAGATAAGATCTAAAGAAGTTATTTTTCCACTCTCAAATTTGATGAAAGATGTAAGACTAACCTATTGACCTAATTTCTTTGGATATGGCCCTCCTGTTGAAGTGCTGCTTGAAGGAAGTGCATCAGAGAACACATTTCATAGGCTTCATTTGCATAAGAAATCAAATTAAAACAATATCACAAACAAACAAACAAACAAAAAAACCTAGGTCTAATATAGTCACTTCTGATTTCCTAGCATATCAACGTTTGTTGAAGTTCTAATTAAAACTACCGATCTACCAATTTCTGTTACAGTATTGGCTAGGAAGATTTCACATAATGTCGTACAAGAGAAACCTTGGCCCTGCTTTAGTCTAGTGCACAAATAATTTTATAGCCAACCTCTTCCCTTGCTGGACTGTTATACCTACTTTGTGGATGTATTTGTTACGGTGATGACACAACTAATGTTGCACCCTTAGTTGCAAGCATTGTGAGTACAAAAGGAAAATGCTTTTGGACTGATACATTCTTCCTCTTGAACCTTCAAAGAGAATGACAGACTATGCTTTGCTTTCCTTAGAAGAATGTAAGTTTTCAGCAGTGAACATGGAAAGGACATTAATTTAGCTATGATGTTTTGACGTTATTCATCAGTAAAGTAAGGATTCGATTTTGTTATCCGCAGCACAAAGATGAGCTTGCTCAAAGTTAAGAAAGAGTACATGATTAAACAAGTAAAAACATATGATTTCGCATAAACTTTACTTAAAAAATGTATCTCCATTTGAATGAATTTTAAAAGATAACTTTTAAGACCAGAGTTCTTTTCAAATGTAAAAATGGATTTTAATCAGAAAGAAGTTTGAAATGTTACATCCGGAAAACAAATTCTAAGATGTCTAATTGCAATTCTTTATTTATTCATAG
Seq C2 exon
ATAAATGTGGCTTCTTGTGATGGAAAATGCCCATCTGCAACAATTTTCAATGTCAATATTGATAGCCATTTAAGATTCTGTAAATGTTGTCGAGAACATGGAACGCGCAATCTGACTGTGCCTCTACACTGCTCAGGAAACGGCACTGAAATTATGTATGTCATTCAAGAGCCTGTAGACTGCTCATGCCAATGGAACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010342:ENSGALT00000017091:59
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AAAGGGAAGAAAGGATTTGCCAGA
R:
TCAGTTCCATTGGCATGAGCA
Band lengths:
278-1941
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]