GgaINT0018361 @ galGal4
Intron Retention
Gene
ENSGALG00000001045 | SLC4A9
Description
solute carrier family 4, sodium bicarbonate cotransporter, member 9 [Source:HGNC Symbol;Acc:HGNC:11035]
Coordinates
chr13:979723-981738:+
Coord C1 exon
chr13:979723-979994
Coord A exon
chr13:979995-981645
Coord C2 exon
chr13:981646-981738
Length
1651 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CTCCCTCCATTGCCTTGCAGGCC
3' ss Score
10.72
Exon sequences
Seq C1 exon
GGACTACGGTCTGGACTACCTGGAGTTTCGTCTTTGGATTGGGCTCTGGGTGGCCTTTTTTGGCTTGGTTTTGGTGGCCACTGAAGCGAGTCACCTGGTGCAGTACTTCACCCGCTTCACTGAGGAAGGCTTCTGTGCCCTCATCAGCCTGATCTTCATCTATGACTCTCTAAAGAAGATGCTGAGCCTAGCAGAAGCCTTCCCCATCAACTGGCACTACCGGGCTGATGATGTGACCTTGTACAGCTGCACTTGCAACTTGTCTGGCCCAG
Seq A exon
GTGAGTGCAAGCTGTCTGCCACAGCTCCTGCCCACACACTCAGTGTGTCCCTGGGCCGAGTCCCTGCACAATGCTGGTGGGCAGAGTGCTGGGCTGTGCTCACATGGTTATGCCTTCACAGGGACAGAGTCCCAGCATGGCAGCCTCAGTAATATCTGCTGTGCATTGGCCTCCACACCTCACTCAGAGTTGCACAGGGGAGATGAAGGATACGGGCATGGCAGGAGGTGGTGGTCCCAGGCACCACAGGAGCTAACTGTGGCCCCAAGGAGCACCACAGTTCCCAAGAAGGATGAGAGATGTCTAGCTTAAGGATGCCTCACAGCCAAAGACAAAGGAGGCTGCTCAATCCTAGCCTTGCCTGCCCAGCCATATTGGCACCTGGTTCTCCCCCATGGCCCTGGGCATCCCCACACCTTGCTTAGGTGCAGGCATAAGAGTGAGCAGTCAGCTGCATGGAAACATCACCTCGTCCTGCCCCTGTACTGGTTGGAGCCAGACCTTTTCCAGTGGGATACAGGAACTACCTTCCTGCCACAACCTGCCATGCACCAGGGACTCCTGATGAGCCTCTTTATGCTGCAGGGCTCGTGTCAGGACAGGGTTGCCATCTATATCCCTGGTCACCTGGGATGGAGCACCCTGACAAGCACAGTCCAGCTCCCAGTGCCAGGAGCAGGCATCCAGTCTGTCACTCGTGTCCCCAGATGTACCCTGTCCCCTGCCTGTAACCCCAGGTCAGACTGCTCCCAAAGGCTTATCCCTTCTTTTGGAGTGGCACTGCCTGTCCCCCTCTGCTCCCCTCCCTCTGCCTCCTGGCTCATGCAGGGACAGAGACCTGAAGAAGCCTGGGGCTGTGCTCCTGGAGCCTTGGCAGTGCTGGGAGTGGGGTGAGCTGCAGCTCAGCTCCTGCAGCTTGGGGCCAGAGGATGTGGGGCACTGGGGAGTTCAGCAGACCATGCAGCACCTCAACAGACTTTCTCTGTAGTCTATAATCTGGTCTATAATTCAGAGGGTGTTTCATGGGGTCTGAACAAGATGTGTCTCTGCTTCCATGGTGATTACTATGTCTGCAGGACCACTGTGGCAGTGGAGCCATGGCACTGTGCACCTGAAGCACCAGTGCTAGGCAGAGCTTGGTGCTGCTGTTGACTGTTAGTGTGCTGATGCTTCAGCCAAGCCCTTTCCAAGCCTTTACAACCCCAGAAGCACAGCTTTGGGCTGGAAAATATCACCCTGAAGGACTGAAGTTTGGTCAACTTCAGGACCGCTGGAAATGGGCTGTAGGAATTGCTGAAGGACTATTTTAGCATGGCAGCAAGGAGACAGCAGTGAAGAACTGTGAAGGATGTGAGGATGCCTTGTAAGGTCTGCGAGGGGCTGGGCCAGGGATGCATCCTGGAAACCTTGACTTTGGTGCTCCCAGGCATCGGCCCTGGCCTGGTGCTACCCAGAGCATCCAGCTGCAGGCCAGGCTCTCCCACTGCCCAGTGTCATTCCCATGCCTCAGGAGTCCCACATGGCCCCATCTGGGTAGCCAAGCCAGCTCAGGAGTCCTGGGAATATTTTGGGGAGAGAGTACTGGCTGCTTGGTGCCCAGCTCTGCAGCCCCATGGCTCCTGGGGCACTGACTCCCTCCATTGCCTTGCAG
Seq C2 exon
GCCATGTCTCAGCAGGCAACAACACGCTGTCTCCTCCACCTACAGCCCTGCAGCAGGTACAGACCCTTCTCCTGGGAGGGGACACACAGTACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001045:ENSGALT00000001559:13
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(19.6=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(6.7=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:
CGGTCTGGACTACCTGGAGTT
R:
CCCAGGAGAAGGGTCTGTACC
Band lengths:
342-1993
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]