DreINT0013218 @ danRer10
Intron Retention
Gene
ENSDARG00000104868 | KCNT1 (2 of 2)
Description
potassium channel, sodium activated subfamily T, member 1 [Source:HGNC Symbol;Acc:HGNC:18865]
Coordinates
chr5:64855689-64857226:+
Coord C1 exon
chr5:64855689-64855797
Coord A exon
chr5:64855798-64857076
Coord C2 exon
chr5:64857077-64857226
Length
1279 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
CTTTGTGTTTGTGTTTTCAGAGA
3' ss Score
10.41
Exon sequences
Seq C1 exon
ATCACGTGGTGTGTGAAGAGGAGTTCAAGTACGCCATGCTGGCCCTGAACTGTGTGTGTCCCGCCACCTCCACACTGGTCACCTTGTTGGTGCACACGTCTCGAGGACA
Seq A exon
GTGAGTACTGACGTTTTCCCTCTTACTCCCGACACTGATGTATGACGCGTGTTTCCTGAAATTCTCTTTAATTCACTCAATGTTTAACAGTGAATGATGACTCCTCGCGCAACCTTTCCAGCTCTGTGATCCCTAAACAAATAACGGTGTCACTAATAATTACTCTGAGCAGATTAGCGAGAAGGGCTGATCAATGTCATTAAACTTGCCATGATCAATCATCAGATGGACACCTAACAGTAAATTGTTTCACGTTTGCTCACACAATCAGCCAAACAGGAGTCTATGCGAAGCAAACCTAGAGTCATTTTCTGTTGCGTTCACACAAAATGAACACATTTTTCAAAACTTCCCAAACCCTTTTTGTCATTTATACTCTACAAACTGCAAAAACAATACATTTTTAGGACGTTTTTTTTACTAACAAACTCATTTCTGAATAGACTGATGATAAATTACATGCTTTTTTTTAAATATAGAAGGTCTTTTTAAAAAAATATGAAAACAATAGAATTTTTTTGTTAAAATTGTAGTAAAAAAAGTTTTGTTGGTACTAATTATGTTAGAAAATAGGAAAATATAGCTTTATTTTTCCGTCAACTATTATTATTATTTTATTTATTAATTTATTTTATTTTTGGGGGGTGGGGGGGGGGGGGGGGTAGGAACCTCCACAATGTAATGAACATTGTGTAAACAATTTTGAAAATGTGGCCGAAGTATTGCACAATGCTTGTTAGCGGTTGAAAAACACATTACACATCTGCCACTCTAATAAACTACAACTCCCATCATGCACCTTATACACACCAGTTTCTGATTCCCACTGATTACACACACACAGTTGGAAGCTCATGATGGAATGATAACCAGGGATTTAAAGACTGCACACAGACTTCTTTGCTGAGTCTTCAGCTGTCTGTGCAATCAGGTAGAGAACTGGAACAGAAACCAGAACCAAACTGGAACCGGAACTTGTACTTGTGCTTGTGCTTGTGTTTGTGTCTGTGTCTGTTGCACGATGGGATTTGTAGTTCATATAAGTGGTTCTGTGGAATTGTAGTTCTCCAGCGATCTGCAACAGCCGAACCAGTGACCTTCTTGCTGTTTGGTGATTGTGCTACCCACTGCGCCAACGTACTGCCACCAACATTGTAATATATGTCCTATATTTCATTTAAAATGGTGATTAAATAATCTTAACCTTTTACTTGGTGAAACCTGATTCCACAGTAATATCGTGAAGTTAGCAGTGTGATCTTTGTGTTTGTGTTTTCAG
Seq C2 exon
AGAAGGTCAGACGTCTCCAGAACAGTGGCAGAGGACTTACGGTCGCTGCTCGGGGAATGAAGTTTATCACATCCGTTTGATGGACAGCAAGTTTTTTGGAGAATATGATGGGAAGAGTTTCACTTATGCCTCCTTCCACGCACACAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104868:ENSDART00000161567:13
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=0.197
Domain overlap (PFAM):
C1:
PF0349313=BK_channel_a=FE(34.0=100)
A:
NA
C2:
PF0349313=BK_channel_a=FE(47.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACGTGGTGTGTGAAGAGGAG
R:
TTCTTGTGTGCGTGGAAGGAG
Band lengths:
257-1536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]