GgaINT0054587 @ galGal4
Intron Retention
Gene
ENSGALG00000009920 | Protein
Description
Cochlin [Source:UniProtKB/Swiss-Prot;Acc:O42163]
Coordinates
chr5:33518242-33523525:+
Coord C1 exon
chr5:33518242-33518286
Coord A exon
chr5:33518287-33523368
Coord C2 exon
chr5:33523369-33523525
Length
5082 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GAGTTTTTCTTTTTCTTTAGCTT
3' ss Score
7.97
Exon sequences
Seq C1 exon
GCGTCTTTCTGCTCTGCGGCTCCGCGCGTGGGAGCGACAGCTCAG
Seq A exon
GTGAGTGTGCGGTCCTCTGTCCCGCACGGCGGCAGGACGCGGCTGCGGGGGCGGCTGCGAGAGCCGGTGTGTCCTTTGGGGTATGAGAGGCGCGGAGGCCGGGGGGGGTGTGAATGCGGAGGGGCACGGGGGGTGTCTGGAAGCGTTTCTGCGCTTGTCCCTCCTGGTCTGAGTGTTGACAGGCAGCGGTAACAAACGTGTCTGCCCGGGGGAGTGCCGAGTGAGTGTGGGTGTGCGTGTGCCGCGGGGTGCCCGAGCACCGACAGCGCGAGGATCCCCAGCGCATTTCTGCCTGTGAGATCGATACGACTTTTGTGCGCCCGCACCGCCGTCACTGAGACCTGGAAAGCAAAGAGCGAACTGAATGCACCTAGCGGTGCGGGAGCTGCTACGTGACTGCATCCCCGCCTCTGGACAACGGGTGCCCGAAACCTGTCAAAGCGAGGGAGCCGTGAGCCGCAGGAAACGCCGCAAGAAGTGTCCTAGGGGCGCGAGCCGCGTGGTCGGCCCTTCTAGCGCAGCCCGTCGCCGAGCGAGGGCGGGCAGGAGCCCCGGCAGCGCGCCCGCCCGGTCATCGCCCTGCCCGCGGCCGGTGAGTGACCCGCGGCCTCCGGGCCGTCGCTCGGGACCCTTTAGCGGGAAGCGGTTATTATCGAGATAACAGCCGTACGTCACAGGACTGCTGTGACTGAACAATAAAACAACAAAACAGCACCGGAAAACCTTCAGCAAGCAACCCCGGTTCCTTTTCTTGTTTTACAGGTGCATCACAGGTGAAATGTCAACGGGAAACAAATGGAAAGTTTTTTGTAATGCTTTCTCCCAAGGCTGGAGAAGAAACCTCTAATTAGAAGGTATCTGGGACCAACCGAAGTAATGTTAAGGGGACGCTGGCAAATGTTACTGAGCTTGAAGCATGCATAAGCTTTTACGGGAAAAAACAGATTACAATTCTGACATTCAAAGTAATGCAAGAACACGGAGCTTCCTTGAATAACTACCTTACTTAGGCTCGTAGCTACTCAGGGAGATCTTTTTTCATAGTCCCCTTTTAATAAATACACACCAATACAGCCAAGTACGACAACTGTCATACAGGAGATAGCTGCAGGGGTGGGTGCACACTGACATACGGTAATCAGTGAACTCAATTTGGACAGAAAAGTGCACACCTCAGACTGAAATAAGTAATACAGCCCTGATGCTTTTTAAAATTTCATTGCTCTTCATATCAAGATATACACTGATCTCTGTAATGTTCAGTACATAATGTATGAACGCGCTTTCCAAAATGTAAGCAGGTGTATTTCTACCAACATGGTTTTCTTCTGCTACGGACAAGGCTGGTAGGAATATTCATTGCCTGACGTATAAATCCAGGTTTGTCTGAAGCCTCAAGACAAAAAAAATGAAACAAACAAACCTCCAAACCTTCCTGTTCTGAAGAGAAATTAAGCACTGTATAAAACATACTGGGGAAAAAAAGCCCCTATTTTATGGCCTATAAAGCTATCTGGGTCTTAGCAGTCCCTGACACTTAGAATTACCTACACAGGTCCTTTTTTCTTCTCTTGCAAGAAGTCTAATTTTCCAAAACAATACATGGAAATGTCAAGGTTAGAGCTCAAATCTGAGCATTGATTTCACTTTTCTAGAGTCCGTGTGGCTCCTGCCAAAAACGAAGTGAGGGCTTCTTGTAGGTGGGCATAAGACACTGCTATTGAGAGCAAATCAGATTATGTGGGATGAGGCAACAAAAACATCAAACTGATGGAAAGATTGAAAGCGTGGTTACCAGACATGTGTCAGCACAGAAGTCAGCCTTCGCTTTTTTTTTCTTTTTTTTTAGGTCTACAATGAAGGAAGACATTCATCCCTGCCTTTAAAAATGGCTTGAAACAGGAAGAAATGCAGCTTTTGTTGGGTTTTGTGTGTGTGTGTACAGATTTCCCAGAGTACCCTCATGTAGTGTGTTTTCATAAGGCTTAAAGAGTGTGTCTTGACAGAGTGGGATTATGGTCGTTTTTTACAGACTAATGTGTTATTTTTGCATGTACAGAGGTCTCTGCTTTCCATCAAAGTCCAGAGTGGGTACAGGTCTAGGACTGAGTCCTTTCTTGTTAACTGCAAGCTTATCCCTCCTCTTTCTCAAAAACGCATGGATTTAGATCTGGAGGATTTAGATCTTAAGGATTCATGAAATTGATTAGAGTATTGGGTCACATAAGTATCCAGAGAAACATCTCAAGCACTGCTGCTCTTTCATTCTTAAATCACAGGGATTATAACACTTGGGTTTCATCTCAGTTACTGGTTTTGCAAAGATGAATTACCTTGGATATGCTAACAAAAATAACTACTTCCTTAAATTTGAGTAGCAATGCCTCACAAAACTTGGCAAGAATGATTACTGTGTAAGCTGGTAGAGAACTATTCTGTATGATCCAGTATTCAAGTATGATTAACCCATTTTAAGTTCATATTGGACTGCTTGTGATTTTACAGGATTCATTAAATAACAGGGAGGAACATAATCACTGCAAAGCTGGTACCATTAATTTTAACTTTGGTACCCAGTACTTACTATCTTGATAGTGTTCTTGATAGTGTTCCTGACATTGCTAATGTGAGTTCCAAAATTATAGCTCAGGAAGCCGTATCTACACAGCAAAACAAAATAAACTGCTTTTTAATTAACAGCGTAAGTACCCAAAGTCAAAGTGTGTGATACAAGACTTTCTTTGCTGATCCAACTGAGCTATGAGCTGTTAAAGGTCCTAGCTGCAGTATGTCAGCTGTTCATACAGCAGCAACTTGGTGTATTCCCTCTGGAGTGCCTCTTTCAAGGTACAGATGAGGATCTTTAGACAACCAGTACATAGAAAATGTATTGGGTTGCAGTGTATGACTGTGTTTTCGTGGCTAGAAAAACACAGTCAGATTTCTCCATGATCACCACCATCTTCACTGCTATCAAAAAGGTAAAATGTTAGTTTGACACGACTGTATTTAGTGAGTGTCTGCTAGTGAGAGACACACAGATCTCCAAGCAATAAGGCATGTATTAATTAGACATATCCAACTGTATTCATTTGTGCAGCCTGCCAAGGAACTCAGTCGGGGTAAGTACATTAGAAGTGGCAGGTATTATAAACTTCCTGTGGTGTTCAGCACTTTTGGAGGCTGGAAAAATGTTCCAGGGTACACAGCACAAGTTGTACTGCAAGACCAGATTACCTTTAGTGCCCATCGCAGTGATTCCTCTAAGGGTATCCAGCTTTCTGGCTGCTGTTGGATGGCCTCGCTAGTTGTCACTTGATGGATATTATTTTATTATGAAATTATCAGGGGACTCGAATGCAAGACTGTGTAAGTCTTAAAATATATATATTTATTTATTTTTAGAGAACTTGTTAATAAGACTAAAGCACTTTAGTGGTTCTTATTAAGTAGAAGGCTTCTATTATTCTAAAAGGAGGAAATGAAAAGCCATTTCCTGCTTTTTTTTTTTTTCCCCCTTCACCTGGACTATATAGACATATTCAGCACATTTAAGTAACATCTTAGTGCTGACAAATAGCTGCTAAGGTTTTTTAGGAAGATGTGATTAGATAGCTTATTGTAATTTACATGTAGTATTAATGAGGAGTAGGTATACTTAAGCAAAACTACACGTGTGTTCTGTAAACACATTTGTTAAATTCATGCAGCAGGAGTGAACAGACACGCTTCACTGTGCACTTCCAGCTGTAGATGTTCTGACTGTCAGCTTTAAAGTCAGTGAGATTAGCAGGAGGCACCACGGCAGCGTGATCTTTTCCATCTGCTGATTAGGAGCAGCATATGCTCCAAAAGCACTCTTTCAAATAACAGTAGCTTATTTTGGGGTCAGTAAACACTTTGGGTTAAGAATAGAAAGGGTGGGCAGGGAAGCAGGCATGGGGTGGAACACTAATCCATGAAACACACTTTCATGGTGCGCACACCTAATCGATAGCTAGGCTCTGTCAGCTCTAGATATCAGAAAAAGGCTACAGAAGAGGTTCATATCCAGTCATGAGTTAAACTTATGACGATGAATTGATGTTTATCTAAGCTAAAACGCTAATTTGCTATGCTACCAGACTGCACCATTTAGCAGTAAGGTGGTAGTTAAGCATATGAGATAGTGACCTCTAAGTTTTCAAAAGAAAAAGCTTCAATCCGACAGGCAAAAGTTAACACTGGTGTGCACCTGTCTGCATGTGTAGGTGCACGAACACGTAAGTACAATAAAAGCCAAAGGATAATAATTTGGGGAGTAACTTTCAAGATAAAAAGGCAAAATTCTTATGTGAAAAATTTATGTGCTGAAAATGAATAAATAACGTTAGTCTCACTGGCTGAATCTTAGAATTATCTGCACACCTGTGATGATTTAATATTATTGCAGTGAGCCAATATGAATGTCTGAGATGCAGCTAGTCTTGCTGGAACAGAAAGATTGGTACTCCCTTTTTGTTTTTACACTGGCTTCAGCAGGATCTATTGCAGAAGCTCAGGGAGATGCTGCTGTCAACCTGTTCCTTGAATGACACTGGGCAGAGCTTCCCAGGCAGTCTGCAGGTTGCCCATAGCTGAAGAGCACCGTGAGGATGTCTGTGTCCTTTGGTTCCTGTCCTGGAGACAGGTTCCTGTCCTGCCACTCCCTCCTGTGCCCACCAGCCCTCTAGGTTTTTTCCCTGGCCTTTATGTCTGCGGTAAACTTGCTTGTGTTGTGAACTGCTGCTGCTGTTTTCCTCTGTAATATTTCCCGGATGTTATTTTAATGTTTAGTGTTTCCTCTTTTTTTTTTTTTTTAAGGCTTTTCTGTACTTTTCTGCCTCTTCTTTTCCATAAATTAAGAACTGCGTTATAGTTGTTATAGCTGCACGCTTCTAAGTGCCAAAGAGACCTTTACAGACACACTGAAGCACAGGATGAGAGGCTGTACCTAATTTCAAATTCAAACAGTGCTTCATATTTGGCAACAGAGAGGCTTTCTTAAGAACAATAACAGCAAAAAATAAGATTTTCAGGTCACGAGTTTTTCTTTTTCTTTAG
Seq C2 exon
CTTCCAATGCTATCACATGCTTTACAAGAGGACTTGACCTTAGAAAGGAGACAGAAGATGTCCTTTGCCCAGCAAACTGTCCTCTATGGCAATTCTATGTCTTTGGGGATGGAATTTATGCCTCTCTTTCCAGTGTCTGTGGAGCTGCCATACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009920:ENSGALT00000016132:2
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:
NO
A:
NA
C2:
PF0381514=LCCL=PU(53.3=90.6)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]