GgaINT0018356 @ galGal4
Intron Retention
Gene
ENSGALG00000001045 | SLC4A9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:HGNC Symbol;Acc:HGNC:11035]
Coordinates
chr13:976973-977502:+
Coord C1 exon
chr13:976973-977060
Coord A exon
chr13:977061-977347
Coord C2 exon
chr13:977348-977502
Length
287 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TGTGGCTAATCTCACCACAGCTC
3' ss Score
6.48
Exon sequences
Seq C1 exon
GTTTCTTTTCATTCTACTGGGCCCCCAAGCCAAAGCGAAAGCCTACCATGAGATTGGAAGGGCTATGGCCACGTTGCTGACAGATGAG
Seq A exon
GTGAGCTTAACACAGCAAATGTCTTGAGCACACAGCAGCAGAATGGGGCCTGAGCTGAGGACACCAAGGTTCCTCTTCTCTTCAGGCTGCAGCAGAGGTGGCCAAGGACAGGGTGGGCTGGCAGCCTTCCTGGCCCAGGATAAGAAAACAAAGAATCTGGGTGGTTATAAGGTCTAAGCACAGACACTACAATGGGCTGGATGGGTGCCTTCCTCAGTGATGTCTACATACTGGGAGAAAGGCTCTGATTAGCCGAATGCAGGGGTTTGTGGCTAATCTCACCACAG
Seq C2 exon
CTCTTCCAAGGGATTGCCCGTCAGGCTAAGCACCAAGAAGACCTCATTGCAGGGATTGATGAGTTTCTGGATGAACTGACTGTGCTTCCTCCTGGAAAATGGGACCCCAGTGACCGAATTCCTCCACCACGCTGCCTGTCGTCCCCAAACAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001045:ENSGALT00000001559:8
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=0.135
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(12.0=100)
A:
NA
C2:
PF075658=Band_3_cyto=PD(14.9=69.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCATTCTACTGGGCCCCCAA
R:
CTCTTGTTTGGGGACGACAGG
Band lengths:
236-523
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]