BtaINT0086106 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010228 | LMX1B
Description
LIM homeobox transcription factor 1, beta [Source:HGNC Symbol;Acc:HGNC:6654]
Coordinates
chr11:97480495-97481276:+
Coord C1 exon
chr11:97480495-97480659
Coord A exon
chr11:97480660-97480944
Coord C2 exon
chr11:97480945-97481276
Length
285 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
AGGTCCTGTCCAGTCGCATGGAGGGCATGATGGCCTCCTACACGCCGCTGGCCCCGCCACAGCAGCAGATCGTGGCCATGGAGCAGAGTCCCTACGGCAGCAGCGACCCCTTCCAGCAGGGCCTCACGCCACCCCAAATGCCAGGTGACCACATGAACCCCTATG
Seq A exon
GTAAGCTGCCCCACCCCTCATGGCCCAGCACCGCCCCTGCCCCCCCAGCCTGACCTGGCAGGCCCTTCCAAATCAGCCCACCTGCCTCCTCCTGTCAGGAAGGGGGTACCCTGGAAACCCCCACCCGCAGCCCCCCAAACCCCCGCCAGCTGGCAGTCATCCTTTCCCTCCCTCACCTCCAGCCACACGGCCTGTAGGGCCAGTGGGGCCCCCAGAAGCCCCCTGCCTGGAACCCCCGGTGCTGACGCCCACCCCCTCTGCCTGCCGCCCCTCCCCCACCTCCAG
Seq C2 exon
GCAACGACTCCATCTTCCACGACATCGACAGCGATACCTCCTTAACCAGCCTCAGCGACTGCTTCCTCGGCTCCTCGGACGTGGGCTCCCTGCAGGCCCGCGTGGGGAACCCCATCGACAGGCTCTACTCCATGCAGAGTTCCTACTTTGCCTCCTGAGAGCCAGCCGGGCGGCACGGACGCTTGGGCAAGGGTCCTGGAGGGGAGGATTGCTGGCCACAGACGCTGCCTCACCACCCCCAGCCCCACCGCCCGCACAGACTCTGCAGACAGCCATACGGTGCCCTCCCCTCGGCCAACCGGGCCTGGCTAATGTGCCCACTGGGCACAGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010228:ENSBTAT00000038767:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
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 Inclusion 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:
ATGCCAGGTGACCACATGAAC
R:
CGTATGGCTGTCTGCAGAGTC
Band lengths:
307-592
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development