BtaINT0136208 @ 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
chr7:53245292-53245889:+
Coord C1 exon
chr7:53245292-53245379
Coord A exon
chr7:53245380-53245734
Coord C2 exon
chr7:53245735-53245889
Length
355 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
CTCTGTGCCCCTATCCCCAGCAA
3' ss Score
8.03
Exon sequences
Seq C1 exon
GTTTTTCTGCCTGCTCCTCGGTCCCCCTACACTGGGAAGGGGCTACCATGAGATGGGCCGAGCAGTGGCCATCCTCCTCAGTGACCTG
Seq A exon
GTGAGCTGGACAGGCATGTGTGTCTGTGTGCATGCACATAGGCTTGTGTCAAGTGAGTGTGTGTGTACTCTCTAGGTGTGACTGAGTACGACAGTGAAGCAGAATGTGGCTTCCTGTCTGTGAGCAGGAGGATTGAAATTGCCTTGGCTACCACCACAGCCCCCCTTACCTAGCACAGAGCTGGCACACTGTAGGCACCCACAGATACTCCCTGAATGCATGCATGCCTGAATGAATGCTTAAATGACTCATCTGCCTATGTGACCTGTGTCTAGTTTTGAAACTGTGAAAATGCATGTAAGAACAGATCTGTATTTAGACTGTATTTAGTGCCTCTCTGTGCCCCTATCCCCAG
Seq C2 exon
CAATTTCAGTGGAGAGTTCGGCGGGCCAGCAGCCTTCATGACCTTCTGGCAGCCCTGGATGCTTTCCTAGAGGAAGTGACAGTGCTCCCTCCAGGTCGATGGGACCCAACAGCTCGGATTCCCCCACCTAAATGCCTGCCCTCTGAGCACAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000021775:ENSBTAT00000029024:7
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=0.154
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(19.7=100)
A:
NA
C2:
PF075658=Band_3_cyto=PD(24.5=69.2)
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:
GTTTTTCTGCCTGCTCCTCGG
R:
CTTTTGTGCTCAGAGGGCAGG
Band lengths:
243-598
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]