GgaINT0125970 @ galGal3
Intron Retention
Gene
ENSGALG00000001002 | RABEPK
Description
NA
Coordinates
chr17:10311435-10312096:+
Coord C1 exon
chr17:10311435-10311597
Coord A exon
chr17:10311598-10311946
Coord C2 exon
chr17:10311947-10312096
Length
349 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCT
5' ss Score
8.16
3' ss Seq
CACACGTTCCCATTTTTCAGTTG
3' ss Score
8.73
Exon sequences
Seq C1 exon
GAAATAGGAACCTGGGAGAGTCCCGAGGTGACGGGCATTCCGCCACTGCCCAGGACATTCCACACCTCCTCGGCAGCTATAGGGGACTGTCTGTATGTCTTCGGAGGGGGAGACAAAGGAGCGGAGCCGGTTAAAGACCAACAGCTTCATGTCTTTGACACAG
Seq A exon
GTACCTCTGGGTGTGTCACGGGCTGTGCCAGCAGTGGAAATAACCGCCCACTGTACTGGAGGTCTGCCTCCCAGATTTTGTCAACCTTGGCCGCAAGTTTAAATGGAGGGATGAAGGTTCCTGCTGATGAGTGCTCACCTCTGAATTGTAATGGGGAATTTGGGCCAAAGTGGCAGTGTAAAGATTTGTGATGGGAAATGCTGTGGGACTTCTCATGAACTGTTGATATTTTTCTGTTCATTCCTATGGCCCTGCATGCACCAGAAGGGAACCCCGGCGAGACTCAGGGGCCACTGGTTTGCAGAGCTGTCCGTTTTCCTCCTCATACACACACGTTCCCATTTTTCAG
Seq C2 exon
TTGCTTTGGCATGGACCCAGCCTGACACCCATGGTGATCCGCCTTCTCCTCGGCATGGACATGTTGTAGTTGCAGTTGGGACCAAGCTTTTCATACATGGAGGTTTAGCTGGTGATATTTTTTACAATGACCTGTTCTGCATTGATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001002:ENSGALT00000001479:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.182 A=NA C2=0.255
Domain overlap (PFAM):
C1:
PF134151=Kelch_3=PU(50.9=49.1)
A:
NA
C2:
PF134151=Kelch_3=PD(47.2=49.0),PF134151=Kelch_3=PU(48.0=47.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATAGGAACCTGGGAGAGTCC
R:
TGTATCAATGCAGAACAGGTCA
Band lengths:
310-659
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]