BtaINT0136204 @ bosTau6
Intron Retention
Gene
ENSBTAG00000021775 | SLC4A9
Description
Bos taurus solute carrier family 4, sodium bicarbonate cotransporter, member 9 (SLC4A9), mRNA. [Source:RefSeq mRNA;Acc:NM_001192206]
Coordinates
chr7:53242584-53243151:+
Coord C1 exon
chr7:53242584-53242744
Coord A exon
chr7:53242745-53243037
Coord C2 exon
chr7:53243038-53243151
Length
293 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCCC
5' ss Score
5.77
3' ss Seq
GCCCCACCTCTGTTCTCCAGAGC
3' ss Score
7.6
Exon sequences
Seq C1 exon
GTGGGTGCTGTTTGAGGAGAAGTTGGAAGTGGGTGCAGGCCGGTGGAGCACCCCCCACGTGCCCACCGTGGCACTGCCCAGCCTCCAGAAGCTCCGCAGCTTGTTGGCCAAGGGCCTTGTCCTGCTGGACTGTCCAGCTCTGAGCCTCCAGGAGCTCACAG
Seq A exon
GTGCCCTGGGACCCTTTGCTGGGAGGGCCTGGGCATCCTCATGATTTCTCTAAGATTTTCCCCATGAAGTCTTAGAATTTTCCAGAGCCCACCCCACCCTACTCTTGAGAATTATCCACCCCTGTATCACAAGGAAGAGGTGGAAATGCAGAGGGGAAGAGCAAGTCCATTGGTTGGACTTGTGTTCCCTGAGACTCTTGGAAGGGAAAGGAGCCTGGGCAGAGGGGAAAGGGGAAGAATTCAGGGGCAGGGAGTTCTCAGGAAAGGATGGGAGCCCCACCTCTGTTCTCCAG
Seq C2 exon
AGCAAGTGACCAGAGTGGAGTCGCTGAGCCCAGAGCTGAGAGGGAAGCTGAAGGCTTTGCTGCTGCAGAGACCCCAGCACCTCATCCAGACCCCATGCACCGGCCCCTGCTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021775:ENSBTAT00000029024:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.036 A=NA C2=0.026
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=PU(56.6=85.5)
A:
NA
C2:
PF075658=Band_3_cyto=PD(42.2=89.7),PF075658=Band_3_cyto=PU(6.1=23.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGGTGCTGTTTGAGGAGAA
R:
GTGCATGGGGTCTGGATGAG
Band lengths:
261-554
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]