BtaALTD0012248-2/2 @ bosTau6
Alternative 5'ss
Gene
ENSBTAG00000010228 | LMX1B
Description
LIM homeobox transcription factor 1, beta [Source:HGNC Symbol;Acc:HGNC:6654]
Coordinates
chr11:97480497-97481276:+
Coord C1 exon
chr11:97480497-97480638
Coord A exon
chr11:97480639-97480659
Coord C2 exon
chr11:97480945-97481276
Length
21 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
CGCCCCTCCCCCACCTCCAGGCA
3' ss Score
10.13
Exon sequences
Seq C1 exon
GTCCTGTCCAGTCGCATGGAGGGCATGATGGCCTCCTACACGCCGCTGGCCCCGCCACAGCAGCAGATCGTGGCCATGGAGCAGAGTCCCTACGGCAGCAGCGACCCCTTCCAGCAGGGCCTCACGCCACCCCAAATGCCAG
Seq A exon
GTGACCACATGAACCCCTATG
Seq C2 exon
GCAACGACTCCATCTTCCACGACATCGACAGCGATACCTCCTTAACCAGCCTCAGCGACTGCTTCCTCGGCTCCTCGGACGTGGGCTCCCTGCAGGCCCGCGTGGGGAACCCCATCGACAGGCTCTACTCCATGCAGAGTTCCTACTTTGCCTCCTGAGAGCCAGCCGGGCGGCACGGACGCTTGGGCAAGGGTCCTGGAGGGGAGGATTGCTGGCCACAGACGCTGCCTCACCACCCCCAGCCCCACCGCCCGCACAGACTCTGCAGACAGCCATACGGTGCCCTCCCCTCGGCCAACCGGGCCTGGCTAATGTGCCCACTGGGCACAGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010228-4-5,5-5-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.982 A=NA C2=0.250
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCATGGAGCAGAGTCCCTA
R:
GCTGTCGATGTCGTGGAAGAT
Band lengths:
102-123
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development