BtaINT0086098 @ bosTau6
Intron Retention
Gene
ENSBTAG00000012025 | LMX1A
Description
Bos taurus LIM homeobox transcription factor 1, alpha (LMX1A), mRNA. [Source:RefSeq mRNA;Acc:NM_001191325]
Coordinates
chr3:3856080-3859179:+
Coord C1 exon
chr3:3856080-3856252
Coord A exon
chr3:3856253-3859101
Coord C2 exon
chr3:3859102-3859179
Length
2849 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAG
5' ss Score
8.04
3' ss Seq
TAATGTTACGTATTTTTAAGGTG
3' ss Score
7.35
Exon sequences
Seq C1 exon
GGAAAAGTGATGATGAGGAAAGTCTTTGCAAGTCAGCCCACGGGGCAGGGAAAGGAGCCTCTGAGGACAGCAAGGACCATAAGCGCCCCAAACGTCCCAGAACCATCTTGACAACCCAGCAGAGGAGAGCATTCAAGGCCTCGTTTGAAGTATCCTCCAAGCCGTGCAGGAAG
Seq A exon
GTACAGAGGGGAAGAAGGGAAGAAAGGGGATAAGGCCCCTCTTCTCTGTGTGTACCCTGGACTCTGGGGTGTCGATGGGCACCTGGTGGGGATCGGGGTGGGAGTGCTGTTCAGACAGTCTGGGCGGGTGGCCTTGAGCCCCATTGGAGGCTCCAGGGATCCCTGTAGTTGTGGCGGGGGCAGTGGTAGAATTTCCTTTTGCTTTTCAGCATGCACCATTCCAACTGGCTACTTCCTCTTACCTTTCATTTCATGGAGAGCAGGGGTTCCATTTGGGGTATAGGTCAAGATGTTACAATAGAAGAAAAATACAGTGGGTTGTAGCATACGTTATTTTTTTGGTCCAGTTTGTTCTGCTTAAGGTGGTGATTTTGGCATTCATCCATGTTGCTGCTCACCCATTTTTGTTGTTGCATGGTATTCCATGGGTATACCATGGTATACCTGTTGATGGGCATGTGGGTTGTTTCCAGTTTGGGGCTGTTACAGACAGGGCTGCTCTGAATAGATATGTAAAAAAATACAGTGACTTAAAGAGATAAGAGTTCATGTTGCTCTCATATCATAGTCCAGAGGTGAGCAACACAAGATTGGCCGGGAAACTCTGTCTCATCACATGGGTCTAAGGGACTGCTCCAGATGTCACCATTTTTTGCAGCTACCATGGTGGAAAAAGAGGGAGTAGGGCGGGGAGTGGGGGGCAAGCAGTTGCTTTTTAAAGGACATACACACCCTGGGATTTTTTGCATCACTCTCATGTGTTGGCTAGAATTTAATCCCATGATTACAAAGGGACCTGGGAAATGAGTCCATCTGGGTATCCATATAAATCCCTAAAACTTAGGAATTCAGTTGCTAAGAGGAAGAAAGAGAGAATTCATTTTGGAGACAATTAGTAGTCTCTGTCACAAATAGCTGCATTTACTTATTAAGTACCCGCCATTTATTGACTCTGCCAGACCAGATACTGTCTTTTATGCAACAAAGATAAAAAAAGAAACGTTCTTGAAATTGAATTGAAATTCATAGAAGAACGATATTTAAACATTTTAGTGTTGTTTTTCCTCTCTCCTTCTGTGTAGGAATCAGTTTTTGCTGCGGTAGCAAACAAAATCTTAGCGGCTCCAACAAGCATTTATTTCCTACTGCTAGGCTGTGGGTTGGCTGCTGGTTCAGGTTCAGGTCTGCCCGCATGTCTGTCATTAAAGGGTCCAGGCCACAGGAGCAGCAGCCACCTGGGCACATGGGTCTCCTGACAATGGCAGGAGGCAAGAGGCTGAGTCCCACCGGGCATGCCCAGTGGGTCTCCATGGAGATCACTCACTTCACATCCAGTAACAGTCCATGGGCCACAGCAAGTCACGTGAGTAAGCCCACTGTGAGTGCAGGGGAAGCACATACCCATCCAGGAGTGGGAAGGATGGTTATTTGCTGAACCATGATACATCCTCCCACCACTTCTGACTTTTGAAGTTTCAACTGCAGAGTGCTTTCTTTCCCTGACCTCACTGCCCCATAAGTTCCAGCAGAACGAGCTGGTAGAAAGTGAGCCCCAAAGTAGACGTGCATAAGGGCCAATTCCCACCTCCCTCAGCGGTTTGCTTGTTCTGCATGTACTAGACCCCCAGCCTCTGTGTGGCCTGTGCCCACCGCCTGTCTCCGGGCCACCAGCAGGGAGGAGCTGTGTGCTGGGACCCTGGGGAGAAAGCGCAAGGGCCAAGACAGAGGGGCAGCCTGGAGCTGGGAGAAGGGAGAGGCCACTCGTGTCTGGGAAATCAGGCGAGGCTTTGTGGGACAGGTGGCTTCTGAGCCGGGCCTGTGAAGGATGGATAGGGTTTCTGCAGGTGGCCGTGGGCCCCTGCGTACACTGCTGTTTAAGTTGGCTTAGCAGAAGGATGTGCTTTAAAAATTTGCTCTAATTATCCCGTTTCTCCTAAGCTTGAGCCTGAGTGGCATGACAAAGGTAAACGCTTCCCTAGGCCTCCAGCTTGCTCTATTTTCTATATTTACTCAAGGAGCTCCTAAGTCTCATCTCCTCAGAATCTAACCATGAGGGGTCAGTGTGTCTCAGGGCCACTCTTGGGAGATCTGTGCCTCGTCCCTCTTCCCTTCTGGCCCGTCCCTCGCCATGTGCCTGTACAGAGGGCAGACGTTTAAACCCCTCTCTTCACGAGAGGGGCCTTGATTGTCCTGTCTCTTCATAGCCCCAGGCCACGTACCCACCTCAGTGTGGTCTGCCTTGCTTTGTCAGATCCCAGATGGCTCTTATCTTATCTTTTTTGAGGGCTCGCTGTAACTGAATATTCCTGAGACACCCAAAGTGACCTAGAGCTATAAGGAACAAAACCAAACATTTAAGTCAGTGAATTAAGACAGGAGAAGAGAGCAAGCGAGAACTATTTGTTTTTGCAAAGTGATTTTTCACCCTCAGTTCTCCTTAAGTAGGTTATGGCATATACCTGGCATATAGCTGAAACCCCAAAATAGATTTTGCTAGTATCTAAGAACTGCTTGAAGGCCCAGGTTCCAGAGGATGAGAAATCCAGGAACACTTCTTAAAATACAAACCTAAACGAAAGCTTCTTCTTCTCACTTACCTCGGATGCACTGTCTCTCCATACAAACCTAAATGAATGCTGCTTCTTCCCCTCAATTTCCTGGGGACGCACTGTCTCTCCCACTGAAGGGAAGCAATGCTCTGTGTTTGGGATTTCGCTGAGCATTGAATATTCACCAGCTGCTGTGTGGGATGTGGCCTGTTGGGCTCCCTGTGCACTGCACAGGAAGTGTTCTGCCTTCTACTATGACATGCCAATATTTCTCTATTTCTAATGTTACGTATTTTTAAG
Seq C2 exon
GTGAGGGAGACCCTGGCTGCAGAGACAGGGCTGAGCGTCCGTGTGGTTCAGGTGTGGTTCCAGAACCAGAGAGCTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000012025:ENSBTAT00000015947:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.552 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=46.6)
A:
NA
C2:
PF0004624=Homeobox=FE(43.9=100)
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]