BtaINT0086102 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010228 | LMX1B
Description
LIM homeobox transcription factor 1, beta [Source:HGNC Symbol;Acc:HGNC:6654]
Coordinates
chr11:97475306-97477847:+
Coord C1 exon
chr11:97475306-97475540
Coord A exon
chr11:97475541-97477665
Coord C2 exon
chr11:97477666-97477847
Length
2125 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGC
5' ss Score
8.69
3' ss Seq
CTGCATCGTGTTCCCCACAGTGA
3' ss Score
8.71
Exon sequences
Seq C1 exon
AGGCTCTTTGCGGCCAAGTGCAGTGGCTGCATGGAGAAGATCGCCCCCACCGAGTTCGTGATGCGGGCGCTGGAGTGCGTGTACCACCTGGGCTGTTTCTGCTGCTGCGTGTGTGAACGGCAGCTACGCAAGGGCGACGAGTTTGTGCTCAAGGAGGGCCAGCTGCTGTGCAAGGGTGACTACGAGAAGGAGAAGGATCTGCTCAGCTCCGTGAGCCCCGACGAATCCGACTCCG
Seq A exon
GTGAGCTGCGGCTGGAGCCGGGTGGGGGGCTTGGCACCCATGCCGCAGAGGGTCGCCCTGCAGGAGAAACCCGCTTCTGACCCTGGGACCCGTACCCCACACAGACACTGCACCCACACCCACAGCCAGTGCACACATGCACGGAGGTGTTCACATGCGGGGTGCACACAGACACGTGTGCATGGCCCCACAGGCCCACAAACGCACCTGGACACGATCACGCACAGGGATAGGTGCATGTGGTTGTACGTGCACACACACAAGCACATAAGATGTGTGTGTGGATACCTACGCCCAGGAATGTAAAAACATGGACACATGTCCACTAGACATGTGCTCACATGCCCAAGCACGCCAAAGCCCACACCCATGTAAACACACATGTGTACACATGCCCTAGCACACTCGTGCAGTAAGTCTGGCTACACGTTTATCCATGTGCTCACAGGTACTATACTTTGCACACACATGAATGCATGCCCTGTGCTCTCTGGCCCAGCAGTCCCCCTTTCCCTTGCTGTGACCCCACCGCAGCCCCACCTCACAGGGGTCTCTCCCAGCATCGAGTCTACAGGCATCTGATACGACGCATCCTGTCTCCATCACGCCCCCCCAAGTCTTCAGCAGTGGGCAGACTGGAGTCCTCGGTAGTGGAGGGAAAGCCTCCATTTCCTGGGGTGAAGGCTCCTCTCCACCCTGCTCCAGCCTCCCAAAGACTGCCAGTTTGGAGCGCTCCTGGCAGGAGGGGCAGGGCCAACCAGGGACAAGTTCTTAAGGAGGAGAAAGTCAGGAAGCAGGCTGGCACCTGGTCATTCCTGGGGGCGGCAAAGACAGCCTGGAGCAGGGGGCGTGGGGAGGAGGTGCCCTGGTCTGCCAGGCCCTTGTGGGGAACCCGGAGCCCATGGTCAGAGGACCTGCCCACACAAAGGAGCCGTGTCCCTGCCAGAGCCCTTGAAGGGGGGCATGAGCTGCCCATGCATCTGTCCCTCTGCCCACCCCTGGGCAGGGCACCGTGGTGGCCAGGCTGCCTGGGCTCCTGAGGGAGAGCGGGGACCAGCCAGGTGCCATTGGCACATTCCTGCCAGGCCTAGGAAGGGGGTCTCAGAGGGAGGCCCTCCTCTGCAGGGACTCATGCTCGGAGGAAGATGGGCTGGGGGCAGCAGGAGGCATGGGGGTGGGGGAGGCTCTGCTGTCTGTTTGGGGCCCGCATCTCTGAGACCCATAACTCGGGCATGCAAGTGGGTATGGGGTCGCTGGGTGAAGACGCATGCTTCTGCATTCAAGGGTGTGTGTGTGTGTGTGTGTCCAGACGTGTGCATGCCTGTATGTCCCTGCTTCAGAGCATGCACCTGTGTGTACGTGTGTGTGAGTGTATGTTTTGCTTGTCAATCCTTAGTCCCTGGAAGCTCCTTAGAGCCTCCTCTCTGGGCCCTGATGCCCGGCTGATGCTGGGCTAGTGCCATGGGAACTGGTTTTCCTGAAAGCCAGCATTCTGGGCTGGGGTCCCCCAGGGCCCGGAGGCCACAGGCCAAGGTGGGGCCCAGGCAGGTTGGGTCAGGGGAAGCCCAGGGCCAGACTGAGCACAGCTGCCAGCTCCTCTCATCAGGAGGGCCGTGGGCCTGATGGCAGATCGGCTGCCTGTGAGTGTCAGCATAGCTGTGCTCCCTTCCGTGTGCCAGCCACACATGTGTGTGCCATACGTGTGCACCTGCACATTTCTGCAGTGCCCGAACCTGTCCCCATGTGGGCCTGTCTCTCTGCCCTTCTGAACGTGAGTGCATCTGAGTGGGCAGCGTGTGTCCGTGCCTGCTCACCAGGGTGCCCTCCTCTGCCTGTCTGGTCAGCAGGGCAGGTCTGGTGGCTTTGGTTCAGGTCTCCCCAGGGGGCTGAGATAAGGGCGCGAGGACCGTTTGCTGAGGAAGGGAACACACCGGGCTGGGTGGGGCAGTGGGTGGACAGGAGGTGAGAGGTGAGACGAGGCGGGGCCTGTGGCCCAGGGAAGGGGGCAGTCTCTACCCTGAGGGCCCTGGGGAGTCGTGCTGGGTGATGGCAGGAGGTGACGGGACCCCAGCAGCAGCGGGTTCCTGAGGATACGGGCTGATCCGCTGCATCGTGTTCCCCACAG
Seq C2 exon
TGAAGAGCGAGGATGAGGATGGGGACATGAAGCCGGCCAAGGGACAGGGCAGCCAGAGCAAGGGCAGTGGGGACGACGGGAAGGACCCTCGGAGGCCTAAGCGGCCCCGGACCATCCTCACGACGCAGCAGCGCAGAGCCTTCAAGGCCTCCTTCGAGGTCTCCTCCAAGCCCTGCCGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010228:ENSBTAT00000038767:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.114 A=NA C2=0.770
Domain overlap (PFAM):
C1:
PF0041217=LIM=WD(100=74.7)
A:
NA
C2:
PF0004624=Homeobox=PU(47.4=44.3)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development