BtaINT0085454 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005525 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]
Coordinates
chr11:93078621-93081421:-
Coord C1 exon
chr11:93081201-93081421
Coord A exon
chr11:93078722-93081200
Coord C2 exon
chr11:93078621-93078721
Length
2479 bp
Sequences
Splice sites
5' ss Seq
ACGGTACTC
5' ss Score
4.58
3' ss Seq
GCCACTTCTGTCGCCCCCAGGAA
3' ss Score
10.98
Exon sequences
Seq C1 exon
CCGATTCGGGACCAAGTGCGCTCGGTGCGGCCGACAGATCTACGCCAGCGACTGGGTCCGGCGGGCACGCGGCAATGCCTACCACCTGGCCTGTTTTGCCTGCTTCTCGTGCAAGCGCCAGCTATCCACAGGGGAGGAGTTTGGCCTGGTCGAGGAGAAGGTGCTCTGCCGTATTCACTACGACACCATGATCGAGAACCTCAAGAGGGCTGCGGAGAACG
Seq A exon
GTACTCAACCCGCCCCTACCCCTCCCCACCCCCAGCCCTCTCTGACCCCCACGCCACCTCAGCACCCCAGGGACTGCTTGCAATTCTCTAGATCCAGGCGCCCCCCTCATCACCTGGGAGCAGCATGGGGGTGGGGCTGTGCATGGACTTTGCGCTTCTGGCTCCACCATTTGTTTGCTAGTCTGAAGTAACACTGCTGGTCTTTGCAAATTGTGTTTCCTACTCTGTAAAATGGGGCTAACGATAAGACACCTCAGAGATAGATGAGGCTGATGTTCGGAAAAGCCAAGAGGCACTCAATGGCCCTAGCAATGACTCTCATCACCAGCAGCCTACTCTGCCTTTGGATAGCTCTGGGTGGCCTGGAGGTTCATCCCCTCTCCTTTGCTGGAACCAGGCTTGGGCCAGTCGTCCAGAGATGATGCGACCCTCTCCTCCCAACTCCCACCCCAGCAGGTACAAGCCAGAGGTTTGGGCATGGGGTTTTCATTCTGGGCTGTAAGGAGAAAGGCCTTTGAGTCTAGAGACCGGAACTTCAGTTTTGCTTCTGGCAGGTTGTGCTGACCTACAAATTTGCCTTTTATCTCTGGGTCTCACTCTCCCTAGTGGGAAAATGGTTATTGGACTAGTGAAAGTAAAAGTCTCTCAGTTGTGTTCGACTCTTTGCGAATCCATGGATAGTCCATGGAATTCTCCAGGCCAGAATACTGGAGTGGTTAGCCTTTCCCTTTTCCAGGGGATCTTGGACTAGGAAGACCCCTAAATCTCTTCTGACTTTGATACTGAGATTTCCGAAGACACTTAGACTCAGGGACAGGACCCAGGTCTTCCCGGGTTTGTGGGGGCTAAGTCTGCCCCATCCCCAGTGCCTCTCAGGAAGTATGGACCATACTGCCTCAGTCTCTAGTCAGAGAACTAGTTAGGAATCCCCAGAGTGCTGTTGGCCATGGCCACAGCACCAGTCAGTCGCTCAGTCATGTCTTACTCTGAGACTACATGGACTATAGCCCACCAAGCTTGGTTATCCAAGGAATTTTCCAGGCAAGAATACTGGAGTAGATTGCCATTTCCTACTCTAGGGGATCTTCCTGACCGAGGGGTCGAACCCTTTGGCAGGTGTATTCCTTACCACTGCGCCACCTGGGAAGCCTTGGCCACAGCAGGCCGTCACTTTCTCCTGCCAGGATCAGGGCTGAGTGGGTCTGGGTGGGGAGCAAGTGAAGCTGGGGTGCTCTGAATTTACCTGCAAGCAAACTGGGCAAGTCAGTTGTAGAGCTGGGGTGGAAGTCCAGGAGTCAGCGTTTCCCCCACACCAGGAGCCATCAGTCACTCCAGGTTCCTTCCATATCTGGACCAAACAGGACCCGATAGCCACAGCCTTGCCAGTTACACTCCGCTCTCATAGCCAGACCTGACTCCAGACTCCTATCATGCAGGGAACCTGAAGGCTTATGACCTCAGATCTCCTTTACTGACCAGCCCTCAGTTTTGGCTACTGCTTTACTTGTAAAACTTAAACACACACATGTCCATTATAGAAAATTTAGAAAGGATGGTAAGCAAAAAGAAGAAAATAAAGACCACTCCAAATGCCACCACCCCACATTTTAGTGTATATCTTCCCAGATTGTATTCTATGTATGTATGTTGGAGTGTTTGTTTTGTTCTTTTAGCACACTTTTTCCTAATTAAAAAATTATGAATAGTGGTGGAGTTTCTGGAGATTTTAATTTTCTTCTTTGTGCTTATCTGATTTCTGAGTTATTGATAAGGATCATATATTAGCTTTTCATTCAGAAAAATGAGATATTAAAAGAATATATTTAGTGTGATTTAAAAAGTAATGTTAAGTGGAAAGAGAATAACACATACTCCAGTTAACAAAATTAAACCTTAGAAAAGGTGATGACATGTGATTGTTGGAAAAACTTCAGAAGCTGCAGAAACATTGAGTCTTCATAATTGCACTCCCTCTTCCTAAGCCTTTGGTGTATATCCTTCCAACCTTTTGCTTCCATCCTTTTTTTAAAAAAACAAAATTAGGATCACAGTTCTGTAACCTGCCTGTTTCCCATCTCCATCAGTCTTTGGTTTCCTCAGTATGTCAAGGAGGGAGACCAAACTGGGATGCTAGAGTCAGCTAGCTTTCAGAATACTAGTCGAAAGGTCCAGAGCTGGGACTTTCTTCTTTCTGAACCTCAGTATCTTCCGCTGTAACACGAGGATAATGTCACCAATCCTCAGGGTTGTGAGAAGTACAGGGCACCCCCAAAGAGAAGCGTCTGGCACTGATCAGATGCTCAGAAGTAGAAGCCCCTTCCCCAAAGACTGAGTTCAGGGGCTTAGGACCCTGGGATTCCCGCTCCCAGCCAACTCCGCTCCAGACACTTCCAGGGACCAGCTCCCCCCACCCCCGTCCTTTCCAGGCTGCCACTAGAAGAGATGGGGACGCGTGGTCAGCCACTTCTGTCGCCCCCAG
Seq C2 exon
GAAACGGCCTCACGCTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAGCCCAAGCCGGCTAAGCGCGCCCGGACGTCGTTCACCGCCGAGCAGTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005525:ENSBTAT00000007266:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.824
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.4=2.7),PF0041217=LIM=WD(100=77.3)
A:
NA
C2:
PF0004624=Homeobox=PU(21.1=35.3)
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