GgaINT0142996 @ galGal3
Intron Retention
Gene
ENSGALG00000000505 | KCNH6
Description
NA
Coordinates
chr27:2603654-2605718:+
Coord C1 exon
chr27:2603654-2603853
Coord A exon
chr27:2603854-2605465
Coord C2 exon
chr27:2605466-2605718
Length
1612 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGT
5' ss Score
10.49
3' ss Seq
CCCTCCCTTGCTTTCCGCAGGTG
3' ss Score
12.48
Exon sequences
Seq C1 exon
CTCTGATGTACGCCAGCATCTTTGGCAACGTCTCTGCCATCATCCAGCGCCTCTACTCGGGCACAGCTCGCTACCACACACAGATGCTGCGAGTGAAGGAGTTCATCCGCTTCCATCAGATCCCAAACCCGCTGCGCCAGCGCCTGGAGGAGTATTTCCAGCATGCCTGGTCCTACACCAACGGCATCGACATGAACGCG
Seq A exon
GTGAGTGCCATGCAGGGAGGCCTCACATTTATGCAGAGCCTTGTCCTAAAGTTATAGAGTCCACCTTTGTGTCCACCCAAATGTGTCCACCCTTTTGACCAGGATGGAGAGGTTGGAGGAGGATAGAGATTTGGGAAGCTGATGAGTCTGTCAGCCTGTTCTCCCCTATTTTCCCCTTTTCTCCTTCTCCCTCCATCTTTCCATCCCTCCAGCTGTTTCCTGGGACCATGAGGGTATTTCTTGGCTGCAGAGCAGTGTTGGTGCCAGCGAGGAGCTCAGAGCCCCATCGGCACCAAGCTCTTTTGGGACAGTGTCTGCTGGTGCCGCAGAGCCACGGAGCCGGGATCGATCCAGCTCCTCTCCACGCTGCCGGTTGCTAAGCAAAGTGCATCCTGCTCTCAGCATCAGGGAAAGAAGGGCATTTAAATAAACCTCGATCCATTTTAATTAGAGCCTGGAGAGGCAGCTGTTCGTTAGCAAAGAGGGGATCAATGGGGGAGCAGCACTGGAGAGGCACAGTGGCTCTGAGCCTAGCGGGGAGGGTTGGACAGAGCTGGGGCACCACCACGGGGTCTGGAACCCGGAGTGGCACTGGGGAAACAGGACTCCGCTCATGGCCTTGGGGTTCCAGGCACAACTGTGCTGCCTTGGCCAGCTGCAAGGCAGGGAGGGGTGAGGGGGTGAGCACTTGTTTTAAGTGAATTCAGCCCCTGCTGCCTCAATAAACTGGGCAGCACTGGGGGTATTGCTGCTGGAAGAGCTTGGGGCCACCCTTTGCCCACAGAGGAGACACCCTGGGCTGGACATCAGTTGCAACAACAGGAAGCAAAGCCACGGCACTCTGCCAAGCACAGGTTCTGGCTCAGTGCAAACCCAGGTCACAAATCCCCTGTGCTGAGCTAAGCCTGCGGCTTGGACGTGCCGCCGCTCACACCAGTTCCTGCTGGATGCTGCTAAGACACAACACAGCCTGATCAATCATGCCACATCCCAATCGATGCACTCGCCCCCGATTTCCCAGCAGGGAAATGAAGGGGGCCGTGCAGCACTACCAGTGCATGCAATTGTGATGGAAGGGAGAGCAAGCTGTGCTCATCAGCCCCTGCTTGGCTGTCCCATGTTGTGAATTTTACCTTGATCTCACCTTCAGGTGCAGCATTTGTTCAAGGAGAGGTATTTGCCATGGGTATATTTAGCTGTTGCTGCGCACAACTGGCCTGTGCTGCTTCTTGGCATTCAGGCAGGTGCTGTTTAATTAGGACAGCACCTCGTTACCGGTTTGCGCTCTCATTCAGCTGAGATTAGTGGGTGGAAAGATGAAAGGGGATATGCCACCAGTGGGTATAAATAGATTGATCTGGTTATCATTATTATTTATTGCTCAGGAGTGCTCTCATCCCTGGTCACATGTGGTGACAAGCCAGGGACAGGCAAGCAGCAATCCACCATGGGAAGATCAGCTTTTGGATTCAGCTTCTTGGGCTTTGGGCTCTCTATTTGGCTGCAACACGCTGCCCCGCATGCCACCCATCCTGTGTGTGCCTCGAGGTAGCCAGAACTGTGGCATCCTGGGGACAGTAGTGTGACCACATCCCTCCCTTGCTTTCCGCAG
Seq C2 exon
GTGCTGAAGGGCTTCCCTGACTGCCTGCAGGCAGACATCTGCCTCCACCTCAACCGCACACTGCTGCAGAACTGCAAGGCTTTCCGAGGAGCCAGCAAAGGCTGCCTGCGTGCCCTGGCCATGAAGTTCAAGACGACCCATGCACCGCCTGGAGACACCCTGGTGCACTACGGGGATGTCCTCACCACCCTCTACTTCATCTCCCGGGGCTCCATTGAGATCCTCAAGGAAGACATTGTGGTTGCCATCTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000505:ENSGALT00000031464:5
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:
PF0052026=Ion_trans=PD(4.8=14.9)
A:
NA
C2:
PF0002724=cNMP_binding=PU(63.5=47.1)
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:
ACACAGATGCTGCGAGTGAAG
R:
TGAGGATCTCAATGGAGCCCC
Band lengths:
349-1961
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]