GgaINT0054594 @ galGal3
Intron Retention
Gene
ENSGALG00000009920 | COCH_CHICK
Description
NA
Coordinates
chr5:36617779-36619821:+
Coord C1 exon
chr5:36617779-36618011
Coord A exon
chr5:36618012-36619304
Coord C2 exon
chr5:36619305-36619821
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
AACTAGGGAAAGCTCTGAAACACGCAGCTCAGAAATTCTTCTCTATGGAAAATGGAGCACGCAAAGGAATACCCAAAATCATTGTAGTGTTTCTAGATGGCTGGCCCTCAGATGATTTAGAAGAAGCTGGTATAGTGGCCAGAGAATTTGGAGTCAATGTGTTCATTGTATCTGTAGCAAAACCCACAACAGAGGAACTGGGAATGGTACAGGACATTGGTTTTATTGACAAA
Seq A exon
GTAAGAGAATATAATTATTCATTTTTCATTCATGGGTATGAATAGATAATGTACGTCATGCTAGAGTTCTAATGAGCTAAGTCTTACACATATAATAAAAGATATTCTTTCAAGAAAATACGAGAGGAAAAAAACCAAAGAAATCACCAGGAAGCCTAAAGTAATCAGTAGTAGAGATTTGAATAAGCCTGTTAGTTTCTTCTTACTAAATTATATGCAACTGCTGGGTTATTTTCTTGCTAATGGGGCTGCACAAAGGTACCAAAATGCTGTTGCCATCCTCCCAGTTCAGAGCCTTGGCCAAGCTGTAGCTCTTGGACTTTGCATTGCATGAAGATTCTCACAGCAAGGGATTCTCCTTTCTCAACCATAACAAAACATGTTGAAGCAAAGAAGTACAGCTGTATCTCCTATCTCAAAATGACAGACAGGGAGACCTATCTTTCAGTATGTGATCTGAGGAATTGTTTACTTACTTTTGCTACAAGGTCAGAAAAGATTGACAAATGCAATCCTACCAAGTTTGTATGCAAGACATTCATCTTGGATGAACGGTTTTCAATCTAGCTCTCAGAACTCAAACTCAGTTCTCACAAGAGCTTTCTAAGCACTAGTTCACTACTTCATGTTCCTTAGGGAGGTTTTAGATATTTTATTTCAGCAGAAAGTTCATAACTTAACATGAAAGAACAAAGCACTATTGTGGCTCTGCAGCTTCCATGCACAAGACAGCTTGCTTCCGATCCCAGACAGGTCCAATGTATGTGGACTTACAGACACACAAAGGAATGACCTTAAGTGAAAGAGGCTTGTCTCCTTCCCTTCTGCATTTTGATTTGAGCAAGATTAGTTATCACATTTGGAGAGCTGATTTTAAATTTAATCCCTTTCTCAATTACCTTGCACTTCACATGTATGCTATAGAAACCAAAGGAAAAACAGATTTTACTTAAAAATAACCTAGACATATATTTCTACTCAACTGTGTGTCTGTATTTATGATGTGTCATAGATTTTTTTTAAAGTGCTTATGATGTTAAAATGGAAAATATAGAAACCTAATTTTCAGTGGGTAAGGAAAAAGGCAAAACTTCTACTCCTTTGGATAGTTAGCAGCCAGAGCTTAGTTCACTTCCCAAGAACATAATTAAAATTTCAAGTTTTTAAGGTTCTCATTAATAAAATGAAATTTTCTAAAATTTCTGGAGGGAAGAGGGGGCAAGCTTGATTGTCTGTTTACTACCTACAGAACCTATTTTGGTATTTGCCTTTTGACTTTTTGTTTTCAAATAG
Seq C2 exon
GCTGTCTGTCGCAACAATGGCTTCTTCTCTTACCAAATGCCCAGCTGGTTTGGCACCACCAAATATGTAAAACCTCTTGTCCAGAAATTGTGTTCACATGAGCAAATGTTGTGTAGCAAGACATGCTATAACTCTGTCAACATAGGCTTCTTGATAGACGGTTCCAGCAGTGTTGGAGAGAGCAACTTCCGACTCATGCTTGAATTCATCAGCAATGTTGCAAAGGCTTTTGAGATCTCTGATATTGGTTCCAAGATTGCAACTGTGCAGTTCACATACGATCAGCGTACTGAGTTCAGCTTCACAGACTACACCACAAAGGAAAAGGTCCTCTCTGCTATCCGGAACATTCGTTACATGAGCGGCGGCACTGCTACTGGTGATGCCATTTCTTTCACAACCAGAAACGTATTTGGGCCGGTAAAGGACGGAGCAAACAAAAATTTCCTTGTAATTCTGACTGACGGTCAGTCTTACGACGATGTTAGAGGACCTGCTGTTGCTGCACAAAAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009920:ENSGALT00000037860:9
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(45.6=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
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]