DreINT0150956 @ danRer10
Intron Retention
Gene
ENSDARG00000040257 | slc38a11
Description
solute carrier family 38, member 11 [Source:ZFIN;Acc:ZDB-GENE-050417-122]
Coordinates
chr9:50329065-50329382:+
Coord C1 exon
chr9:50329065-50329135
Coord A exon
chr9:50329136-50329220
Coord C2 exon
chr9:50329221-50329382
Length
85 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGG
5' ss Score
8.99
3' ss Seq
CTGCATTTGATCTTTTTCAGCTT
3' ss Score
8.3
Exon sequences
Seq C1 exon
ACCTGCGTCAGATGATGCATGGGTTTTTGCACGGTGGAATGCAATTCAGGCAGTCGCTGTAATGTCTTTCG
Seq A exon
GTGAGGGTTTTACATGCAGTATTTATGTTAATGCATTCTGAGATGTGATTTACCTTTTTTAATTGCTGCATTTGATCTTTTTCAG
Seq C2 exon
CTTTAATCTGCCACCATAACAGCTTCATGATCTACGGGTCGCTGCAGGAGCCCACCCTGAGCAGGTGGTCTCTCGTCACACACATATCCGTGGGCTCATCTGTACTGGTCAGTGCTGTCTTTGCTGCAGCAGGTTATGCCACTTTTACTGTTTACACACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000040257:ENSDART00000058892:9
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:
PF0149013=Aa_trans=FE(6.2=100)
A:
NA
C2:
PF0149013=Aa_trans=FE(13.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTTTTTGCACGGTGGAATG
R:
CAGCAAAGACAGCACTGACCA
Band lengths:
177-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]