GgaINT0054594 @ galGal4
Intron Retention
Gene
ENSGALG00000009920 | Protein
Description
Cochlin [Source:UniProtKB/Swiss-Prot;Acc:O42163]
Coordinates
chr5:33531672-33533708:+
Coord C1 exon
chr5:33531672-33531898
Coord A exon
chr5:33531899-33533191
Coord C2 exon
chr5:33533192-33533708
Length
1293 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
GACTTTTTGTTTTCAAATAGGCT
3' ss Score
9.3
Exon sequences
Seq C1 exon
GGAAAGCTCTGAAACACGCAGCTCAGAAATTCTTCTCTATGGAAAATGGAGCACGCAAAGGAATACCCAAAATCATTGTAGTGTTTCTAGATGGCTGGCCCTCAGATGATTTAGAAGAAGCTGGTATAGTGGCCAGAGAATTTGGAGTCAATGTGTTCATTGTATCTGTAGCAAAACCCACAACAGAGGAACTGGGAATGGTACAGGACATTGGTTTTATTGACAAA
Seq A exon
GTAAGAGAATATAATTATTCATTTTTCATTCATGGGTATGAATAGATAATGTACGTCATGCTAGAGTTCTAATGAGCTAAGTCTTACACATATAATAAAAGATATTCTTTCAAGAAAATACGAGAGGAAAAAAACCAAAGAAATCACCAGGAAGCCTAAAGTAATCAGTAGTAGAGATTTGAATAAGCCTGTTAGTTTCTTCTTACTAAATTATATGCAACTGCTGGGTTATTTTCTTGCTAATGGGGCTGCACAAAGGTACCAAAATGCTGTTGCCATCCTCCCAGTTCAGAGCCTTGGCCAAGCTGTAGCTCTTGGACTTTGCATTGCATGAAGATTCTCACAGCAAGGGATTCTCCTTTCTCAACCATAACAAAACATGTTGAAGCAAAGAAGTACAGCTGTATCTCCTATCTCAAAATGACAGACAGGGAGACCTATCTTTCAGTATGTGATCTGAGGAATTGTTTACTTACTTTTGCTACAAGGTCAGAAAAGATTGACAAATGCAATCCTACCAAGTTTGTATGCAAGACATTCATCTTGGATGAACGGTTTTCAATCTAGCTCTCAGAACTCAAACTCAGTTCTCACAAGAGCTTTCTAAGCACTAGTTCACTACTTCATGTTCCTTAGGGAGGTTTTAGATATTTTATTTCAGCAGAAAGTTCATAACTTAACATGAAAGAACAAAGCACTATTGTGGCTCTGCAGCTTCCATGCACAAGACAGCTTGCTTCCGATCCCAGACAGGTCCAATGTATGTGGACTTACAGACACACAAAGGAATGACCTTAAGTGAAAGAGGCTTGTCTCCTTCCCTTCTGCATTTTGATTTGAGCAAGATTAGTTATCACATTTGGAGAGCTGATTTTAAATTTAATCCCTTTCTCAATTACCTTGCACTTCACATGTATGCTATAGAAACCAAAGGAAAAACAGATTTTACTTAAAAATAACCTAGACATATATTTCTACTCAACTGTGTGTCTGTATTTATGATGTGTCATAGATTTTTTTTAAAGTGCTTATGATGTTAAAATGGAAAATATAGAAACCTAATTTTCAGTGGGTAAGGAAAAAGGCAAAACTTCTACTCCTTTGGATAGTTAGCAGCCAGAGCTTAGTTCACTTCCCAAGAACATAATTAAAATTTCAAGTTTTTAAGGTTCTCATTAATAAAATGAAATTTTCTAAAATTTCTGGAGGGAAGAGGGGGCAAGCTTGATTGTCTGTTTACTACCTACAGAACCTATTTTGGTATTTGCCTTTTGACTTTTTGTTTTCAAATAG
Seq C2 exon
GCTGTCTGTCGCAACAATGGCTTCTTCTCTTACCAAATGCCCAGCTGGTTTGGCACCACCAAATATGTAAAACCTCTTGTCCAGAAATTGTGTTCACATGAGCAAATGTTGTGTAGCAAGACATGCTATAACTCTGTCAACATAGGCTTCTTGATAGACGGTTCCAGCAGTGTTGGAGAGAGCAACTTCCGACTCATGCTTGAATTCATCAGCAATGTTGCAAAGGCTTTTGAGATCTCTGATATTGGTTCCAAGATTGCAACTGTGCAGTTCACATACGATCAGCGTACTGAGTTCAGCTTCACAGACTACACCACAAAGGAAAAGGTCCTCTCTGCTATCCGGAACATTCGTTACATGAGCGGCGGCACTGCTACTGGTGATGCCATTTCTTTCACAACCAGAAACGTATTTGGGCCGGTAAAGGACGGAGCAAACAAAAATTTCCTTGTAATTCTGACTGACGGTCAGTCTTACGACGATGTTAGAGGACCTGCTGTTGCTGCACAAAAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009920:ENSGALT00000016132:9
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:
PF0009223=VWA=FE(44.9=100)
A:
NA
C2:
PF0009223=VWA=PD(6.0=5.8),PF0009223=VWA=PU(73.7=72.8)
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:
GTGTTTCTAGATGGCTGGCCC
R:
GCATGAGTCGGAAGTTGCTCT
Band lengths:
346-1639
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]