GgaINT0077109 @ galGal4
Intron Retention
Gene
ENSGALG00000011604 | SLC4A4
Description
solute carrier family 4 (sodium bicarbonate cotransporter), member 4 [Source:HGNC Symbol;Acc:HGNC:11030]
Coordinates
chr4:49770262-49771905:+
Coord C1 exon
chr4:49770262-49770440
Coord A exon
chr4:49770441-49771832
Coord C2 exon
chr4:49771833-49771905
Length
1392 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
ACCTAGTGCTTTTCTTCCAGGGA
3' ss Score
7.88
Exon sequences
Seq C1 exon
AAAGGTGCTGGATATCACCTGGATTTGTTCTGGGTGGCCATTCTGATGATTGTCTGCTCCTTTATGGGTCTGCCCTGGTATGTTGCTGCTACTGTGATCTCCATTGCTCATATTGACAGCTTGAAGATGGAGACTGAGACTTCAGCCCCCGGAGAACAGCCCAAGTTTTTGGGAGTGAG
Seq A exon
GTATGTCAAACCAAATAGGTCTTTATTACCTTGTTTGCCTGCAGAGATCAGTTTGTACTATAAATGGTCGTGCTTTGAATAGAACACGTGTAGATGTTCAAGGGGGAATAGCTCTTAGGTTTGCAGTAAATCTTCAGATCAGCTGTGCTTCCTTCCAGCTTTTTTTCCCCATCTTCAGAGGATATATCCAGTTAAAAGTTTGTCTGGCATAGTCCTTCTGCAGATACTCTTTCTTGAAAAGGAAGAAAACCATTCTACCACGTGTGTCTGTGTGCAGGGTGAGGGCAAGCGAAGGGAGGAAGAAAAGGGAACTTAATTTCAGAATTGAGATAATTTTTATCTGCTTTGGGCACACGCATTGAAGCCACCTCTAACTACACAAGGCTTTACATTGTACGGTCTGGTGCCATCGGGGCACTGTGGAGTTCTCATGAAGAATCTTTTACATCCTTCTTCGTATTTCCCAACCTGACTATGAGATTCAGCAGTGCAGTTCTTCATTTTCTAAAGTTTATTCAAGCAGATCAGATAAAGTTTTCCAGTGTTTGAGAAAGAAGATGTATTTACTTCACATTTCTTTATCCATGGAAACTAGGCAGGCGTTTGCTAGCAAACGTAGTGGTAAAAGACCTAAACTTGTTGTGGCTAAAGCATTCGATTCTATTAAATCAAACCACTTGTTCTGTCTTTGGTAATTAAGTGGCCTGAAGTGCTTTCAACAGGAGCAGCAGCACTCCTGGAAATCAGTTAGGCAAATAATAGAAACTTAATGGCCTAACTTTAAGTACTCAGAAATAGTATTTGCAAAAGCATTTTCATATGCAGGGAGCAGTTGTGGGTGCCTCTTAAGTCAATGTCCAGCACCCCATGAAGTCCTGGACCAGGGGATTGTGAACTCCCTTTGTACCTGGTGTGCAGAGCAGTGTACAGTACGGTGAGAAACAGCATTTATCTGTCGGAATACTGTGACCAAGCTTTAAAATATGTTGCTAATTTAAGAGTGGAGAGCTAATGATTTATTACCTATTTGCATGTTGTGAAAGCTGCCGTGCAGAGAATCTGGTTTGCTGGTTAACAGTTTCTAATGTTTAACATTTAAACGCACTCCTCATTACTTGGTAGCAGTACTCTGCTGATTCACAAACAATGGAGCTAGGGGAACAAGCAAACATACAAAAACTGATCTGGTGTTTGAAAATAGATCTGTATGAAGCTTGGTCGTGATAAAGATGTCTGCCTGAAGGTGTTGGCTTGTTATTGTCAGTCAGCTTTGGAAATGTGGCTGCAAAAAATGAGTTGCAAGACTTTACATAGGTTTTGAATGCTCTGAGAAGGGAATAAAATTGGAATTAAAGCTGAAACTATACTGCTAACCTAGTGCTTTTCTTCCAG
Seq C2 exon
GGAGCAGAGAGTCACTGGAGTCATTGTTTTCATTCTGACTGGTGTGTCTGTCTTTATGGCTCCTATCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011604:ENSGALT00000018948:19
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(11.3=100)
A:
NA
C2:
PF0095516=HCO3_cotransp=FE(4.6=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:
GGTGCTGGATATCACCTGGAT
R:
CAAGATAGGAGCCATAAAGACAGACA
Band lengths:
246-1638
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]