GgaINT0054595 @ galGal4
Intron Retention
Gene
ENSGALG00000009920 | Protein
Description
Cochlin [Source:UniProtKB/Swiss-Prot;Acc:O42163]
Coordinates
chr5:33533192-33534657:+
Coord C1 exon
chr5:33533192-33533708
Coord A exon
chr5:33533709-33534481
Coord C2 exon
chr5:33534482-33534657
Length
773 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAT
5' ss Score
8.76
3' ss Seq
GCTATATTCTTACGTTTTAGGAA
3' ss Score
8.93
Exon sequences
Seq C1 exon
GCTGTCTGTCGCAACAATGGCTTCTTCTCTTACCAAATGCCCAGCTGGTTTGGCACCACCAAATATGTAAAACCTCTTGTCCAGAAATTGTGTTCACATGAGCAAATGTTGTGTAGCAAGACATGCTATAACTCTGTCAACATAGGCTTCTTGATAGACGGTTCCAGCAGTGTTGGAGAGAGCAACTTCCGACTCATGCTTGAATTCATCAGCAATGTTGCAAAGGCTTTTGAGATCTCTGATATTGGTTCCAAGATTGCAACTGTGCAGTTCACATACGATCAGCGTACTGAGTTCAGCTTCACAGACTACACCACAAAGGAAAAGGTCCTCTCTGCTATCCGGAACATTCGTTACATGAGCGGCGGCACTGCTACTGGTGATGCCATTTCTTTCACAACCAGAAACGTATTTGGGCCGGTAAAGGACGGAGCAAACAAAAATTTCCTTGTAATTCTGACTGACGGTCAGTCTTACGACGATGTTAGAGGACCTGCTGTTGCTGCACAAAAAGCAG
Seq A exon
GTAAATGACCTTCACAGGCAGTGGAAGTTGATTCTTCCCATTTCTGCTGTATTGTCCACATCAAGATTTTAAATTTTAAATGATGCTGTAGAGAACAAATAAAGTATCATACTTGTCTTAAGTTTAGCAGAACAGGAGCTCTGAGGAGCTCTTCCATTAGGATGAGAAATGGGATTATCAAGCCAGGTGTAAGTAGACTCACTCATGGCAACTTTGTTTAAAATTTTTTAAAAAGTGCACTCAGTCTTTTCTTCCTAAATAAGAGAGAAATTAGTAGATGAAAAATAAAGAGATGTGTAGTGAAGCTCCAACCAGTGATAGCATCCAATATTGCATTATTTTTGTTCTCCATCATATATGGGGAAAAAAAATCAGTAATTTTAACCAAAAAGCCTCTTGGGCTTCTGATGCTTGAAAACACTAAGCATTATGTATGTGAAGGATCCAAATGTATTTCCAAAATTCTTCTAAACAGTAAGTCTTGAAACACAAGAATCACTGTGACACTGCTATGTTCGTACTGATTGCTGAAAAACATCTGTGATGCTTACTGGTAAGATATACTGGTATTCTATCTGGGTTCTTACTTAGACAGGAACTTAATTCCTGATGTTTAGTGGCACAGTCCAATAATTTTTGACAGACTACAGGTATTGAAGCACTATTTTCTCTTCTAATTTATTTAATGGATGTAGAAAATGCGTGTTTTCCTTGCAGCCAAAGACAAAATGGTTTTATGTATTTTCTTTCTTTGCTATATTCTTACGTTTTAG
Seq C2 exon
GAATAACGGTCTTCTCTGTTGGTGTTGCCTGGGCACCTCTGGATGATCTGAAAGACATGGCCTCTGAACCAAGGGAATCTCATACCTTCTTCACTAGGGAGTTCACTGGATTGGAGCAGATGGTTCCTGATGTTATTCGAGGCATCTGTAAAGATTTTTTGGACTCTAAGCAATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009920:ENSGALT00000016132:10
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:
PF0009223=VWA=PD(6.0=5.8),PF0009223=VWA=PU(73.7=72.8)
A:
NA
C2:
PF0009223=VWA=PD(25.7=74.6)
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:
TGGTTCCAAGATTGCAACTGTG
R:
CCTTGGTTCAGAGGCCATGTC
Band lengths:
346-1119
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]