BtaALTD0020219-2/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000002348 | SLC4A4
Description
Bos taurus solute carrier family 4, sodium bicarbonate cotransporter, member 4 (SLC4A4), mRNA. [Source:RefSeq mRNA;Acc:NM_174605]
Coordinates
chr6:88354378-88396527:+
Coord C1 exon
chr6:88354378-88354530
Coord A exon
chr6:88354531-88354557
Coord C2 exon
chr6:88396451-88396527
Length
27 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATG
5' ss Score
5.46
3' ss Seq
GTCTCCTTCTGTTTTTACAGGTA
3' ss Score
11.89
Exon sequences
Seq C1 exon
AGATGATTGTTGACCATCAGATTGAAACAGGCCTATTGAAACCTGACCTTAAGGATAAGGTGACCTATACTTTGCTCCGGAAGCACCGGCATCAAACCAAGAAATCCAACCTTCGATCCCTGGCTGACATTGGGAAGACTGTCTCCAGTGCAA
Seq A exon
GTAGGATGTTTACCAACCCTGATAATG
Seq C2 exon
GTAGCCCAGCCATGACCCACAGGAATCTGACTTCTTCCAGCCTGAATGACATTTCTGATAAACCAGAGAAGGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000002348-14-8,15-8-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.233 A=NA C2=0.808
Domain overlap (PFAM):
C1:
PF075658=Band_3_cyto=FE(23.8=100)
A:
NA
C2:
PF075658=Band_3_cyto=FE(9.9=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGACCTATACTTTGCTCCGG
R:
GATTCCTGTGGGTCATGGCTG
Band lengths:
122-149
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development