GgaINT0050388 @ galGal3
Intron Retention
Gene
ENSGALG00000011052 | SLC38A11
Description
NA
Coordinates
chr7:21482897-21483495:+
Coord C1 exon
chr7:21482897-21483014
Coord A exon
chr7:21483015-21483420
Coord C2 exon
chr7:21483421-21483495
Length
406 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
ATCTCCTGTATTTTTTAAAGGAC
3' ss Score
8.32
Exon sequences
Seq C1 exon
ATAGAAACAGATGACCATACAGCCCTGGTTAGTAAGCCCAGGAATAAAGGAGGAAATGGTGATCTGGCATCAGCTGGATTTAACATTATCAACTCCATTATAGGATCAGGTATTATAG
Seq A exon
GTAAGTGTACTTCACTATTGTGTGTTCAGCCCTGTTTATGCACACAAGACTATCCAGTGTTGATTAATGTGCTGTCTTCTTACTTTTTGCTGTTACTGCTGAAGATTTTTTTTTTCTACTTTTATTCTCTTTTTAGATGAAAATCCAATTTTGTCAGCTGAGACCAGGTCTGACTGTGATAAATATCCTACAGTCTTTTTTGCTGTAATGACCAGAAAGTACTGGTTGGGCAGGTGCTTGCTTCTCAGACAGAGGCAGCCCTTCGTCTTAACCTTTTCTGAAGTTATTAATTCTTTCTGGTCCAATCTGGGAGATCAAAAGCAGCGTATTTGTTTATTTTTTTTAATCCAAATATTTCTTTATTTTGTTCATCATAAATATTTGTAATCTCCTGTATTTTTTAAAG
Seq C2 exon
GACTGCCCTATTCAATGAAAGAAGCTGGTTTTCCTTTAGGAGTACTGCTTCTGTTTGGGGTTGCCTATATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011052:ENSGALT00000018002:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0149013=Aa_trans=PU(5.7=55.0)
A:
NA
C2:
PF0149013=Aa_trans=FE(6.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
AGAAACAGATGACCATACAGCCC
R:
TGTGATATAGGCAACCCCAAACA
Band lengths:
190-596
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]