GgaINT0018360 @ galGal4
Intron Retention
Gene
ENSGALG00000001045 | SLC4A9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:HGNC Symbol;Acc:HGNC:11035]
Coordinates
chr13:979464-979994:+
Coord C1 exon
chr13:979464-979597
Coord A exon
chr13:979598-979722
Coord C2 exon
chr13:979723-979994
Length
125 bp
Sequences
Splice sites
5' ss Seq
CGAGTAAGA
5' ss Score
6.87
3' ss Seq
TGGGCCACTCTCCCTACTAGGGA
3' ss Score
6.27
Exon sequences
Seq C1 exon
GGTGTACTGGAGAGCTTCCTGGGCACTGCCTTCACTGGCTTCATCTTCTGCCTCTTCTCTGGCCAGCCCCTGACCATCTTGAGCAGCACTGGCCCAGTTCTGGTCTTTGAGCGTCTCCTCTTCTCCTTCAGCGA
Seq A exon
GTAAGAACTGTGTGAGGGCATCTCCCCATGTGGCAGCCCCCAGCTGCACCATCCCTGGACTGAGCACAGGCTGCTTTCACATGGCTGAGTGCCATAGTGAGGGTCTGGGCCACTCTCCCTACTAG
Seq C2 exon
GGACTACGGTCTGGACTACCTGGAGTTTCGTCTTTGGATTGGGCTCTGGGTGGCCTTTTTTGGCTTGGTTTTGGTGGCCACTGAAGCGAGTCACCTGGTGCAGTACTTCACCCGCTTCACTGAGGAAGGCTTCTGTGCCCTCATCAGCCTGATCTTCATCTATGACTCTCTAAAGAAGATGCTGAGCCTAGCAGAAGCCTTCCCCATCAACTGGCACTACCGGGCTGATGATGTGACCTTGTACAGCTGCACTTGCAACTTGTCTGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001045:ENSGALT00000001559:12
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:
PF0095516=HCO3_cotransp=FE(9.5=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(19.6=100)
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:
GGCCCAGTTCTGGTCTTTGAG
R:
CCAGTTGATGGGGAAGGCTTC
Band lengths:
258-383
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]