BtaINT0086099 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012025 | LMX1A
Description
Bos taurus LIM homeobox transcription factor 1, alpha (LMX1A), mRNA. [Source:RefSeq mRNA;Acc:NM_001191325]
Coordinates
chr3:3859102-3861034:+
Coord C1 exon
chr3:3859102-3859179
Coord A exon
chr3:3859180-3860964
Coord C2 exon
chr3:3860965-3861034
Length
1785 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATC
5' ss Score
7.46
3' ss Seq
CTGAGTTCTCTCCTCCCCAGATG
3' ss Score
9.95
Exon sequences
Seq C1 exon
GTGAGGGAGACCCTGGCTGCAGAGACAGGGCTGAGCGTCCGTGTGGTTCAGGTGTGGTTCCAGAACCAGAGAGCTAAG
Seq A exon
GTAATCTGCTTCTTACTTCTGTCTCTGTGTGGCCGCTTTCCTGAAATAATAGTAGAATGTTGTATTTGCCCGCAAATTTTCTAACTTCAATTCATTGGATAGACTGGTGCTCTCAATTCAGAAAGTCTATGATGAGCAGTCATTTCAGCCACAGCATACTTGCAGAAGGGCATTTGTTCTAGTGGGATACTGTTATTTTCCTTGTGACTGTGGCTGTCAGTCGTTTTCATGAAGAAATGCCTTTCTGTGTCTTGGTAAAAGCAGGTTCTTCAATTCCTATTCATTTAACCCAGATGCCAGAGTTCCTTTGAAATTTCAGAGGGAAACCAACATAGCACCCATATGATTGGTCTAAGACAACATTATGGCACACGGAATGGATGTCCTAACTCAGCTTTCCTAGTGCCCCGCCTGTCCCTGTTAGATCATGTTGTCCTCTGGATCCTGCCAAGGTGTGCATACCCCTGGCACGGCCTCTCATCTCTCTTAGACCTTTCCTTATTTATCTTCCTACCTGTACACAAGCATGTGTTGGGCTTCCCAGGTGGCACAGTGGTAAAGAATCTGCCTGCCAATGTAGGAGACACAGGAGATGTGGATTTGATCCCTGGATTTAGGAAGATTCCCTGAAGGAAGAAATGGTGACCCACTCCAGTATTCTTGCCCGGAAAACCCCATGGACAGATGAGCCTGGTGGGCTACAGTCCAGGGTGTTGCAAAGGGTTGGATATGACTGAGCACACGCACACACACACACACACACATACACACGTGTGTTAGTGGCCCATTTCTCTAGACCTCTAATCTTTAGTGGGCGATGGATTCATATCTCATTTGCTAATCGTGATTGGTTAAGATACTATTTCCCTAACTGAATTCCTCAGACTGGGCTTCTGGTGTGTAGTCCATGGTCTTTTCTATGAAAGAATTTCATAGTTCAGTAGGTTTGAGAGAACCTATAGCCTATATATTCATAAGCAGGGAGCATATTCGAAGTTCTGAGAAATCTTGCAGTAAAGAAGTTTTTTAAAAATCTAATGTTCCCTACACACACACACACACACACACACACACTCCAGAACCACCTAAAGGCCCAGTTTCCAGAGGATGAGAAACCCAGGAACTCTTCTTGAAATACATACCTAAATGTATGCTTATTCTTCTCTTCATTTACCTGGGGAATGAAGGTTTACCTAATGTTGCCTGCCCCCACCCCACACACACGCACACACACCAAGGATCTCATGGAACCCTAATGTTCCACAGAAGACACTTTGAGAAAGATTGGGTTGATGTGTCCCTTATGGGAAGTTAGTGTGCTTTGGGAGACAAGCTCCTTACCTAAAGGCATGCATGTCCTGGTAGGAGTCTCTGCCACAAGGGCCAGTGGGTGGAACGGCCTCTTGGCTCATGCCAAATCACAGGTGCCAGCAGGCCCTTACTGTACATCTAAGCTGAGCTGCAGACTGCACATCCCTCACTTACACCTCACATTAAACTGTGACGCCATAAGCAGCAGGTTTTATTTGTTGAGAGGGCATCCCTGTTCCTGCCAAGAGCAGCTGCCCTGAGGATTCCTAGCCAGCTGTCTTTCCATGGCTGCAGTGTAGAAATCCCTCAGCCGCCATGCATCAGGCTCAAGGCGCCTGAAACGTGGATTCTCTCCTGAGTAAAAGCTAGGGAAGGGGTCCCTCTGCTTTCCCCCTGAGCCGATGCCCCCTGGCCTAGCTGTGAGAACCTGCTGCAGGCCCCCTGACTTCTAATCCTGAGTTCTCTCCTCCCCAG
Seq C2 exon
ATGAAGAAGCTGGCCCGGCGGCAGCAGCAGCAGCAGCAAGATCAGCAGAACACCCAGAGGCTGAGTTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012025:ENSBTAT00000015947:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(43.9=100)
A:
NA
C2:
PF0004624=Homeobox=PD(3.5=8.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
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]