BtaINT0085440 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011124 | LHX3
Description
Bos taurus LIM homeobox 3 (LHX3), mRNA. [Source:RefSeq mRNA;Acc:NM_001038620]
Coordinates
chr11:103734904-103737286:-
Coord C1 exon
chr11:103737115-103737286
Coord A exon
chr11:103736409-103737114
Coord C2 exon
chr11:103734904-103736408
Length
706 bp
Sequences
Splice sites
5' ss Seq
CTGGTACGG
5' ss Score
8.6
3' ss Seq
GCCCTCTGCTTCCACCGCAGACG
3' ss Score
9.84
Exon sequences
Seq C1 exon
GTGTGGTTCCAGAATCGCCGGGCCAAGGAAAAGAGGCTCAAGAAGGACGCGGGCCGGCAGCGCTGGGGCCAGTATTTCCGAAACATGAAGCGCGCCCGAGGCGGCTCTAAGTCGGACAAGGACAGCGTCCAGGAGGAGGGGCAGGACAGCGACGCGGAGGTCTCCTTCACTG
Seq A exon
GTACGGGCGGAGTTGGGAAGAGCGTTGGGTTGATTGACTGCCGGAGCCTGGGAATCAATCCCCGTCTCTATAGACCCTGGCGCCCATCCCCAAGCCCTGTGGTTTGGCCACTCAGGACCATTGCCCTTCTTCTGAAGGGGGACAGAAACCCTGTGACCTGCATGCGTGTCCTTGGCAGGCTTTGTCCTGGAGGGAGGGTCTGACCATGCTCCCCCCTGCCCCCACCCAGGGCACTTGGCACTTACAGTGATTTTTTAGGGAGGCAGCAGCACAGTCTTGGGGTGATTAAAGGTCCTAGCTGCTTGGCGTTGGAGGAGGGTCCACCCTCGTCTCTGGAACCCAGTTACCTCCTTTTTCCAAAGCAGAGAGCCCCTCCCCCACCAGCTCTTAATGTCCATCCTCAGAGAGTTTGTTTAGGAGATTGTTTGGCTGCATTGTGACCTTAGGCTACTCACCTAGCCTCTCTGAGCCTCAATTAACTTGTCTGCAAAATTGGGTAGCCTTGGGATCATACTGGATCCCAGCACAGGAGCCCACAGTTTCATAGGAATCAGGTGGGATGGAGCTGAACAAACTCAGGGGTGAAAGGGTAAGAGATGTGGGCTGACCCGCCCTGGTGGGGCACACGGCGCCTGCAGGGGGCACCGAGGAGCACCAGAGGTGGCAGCAGGTGTGCACTAAGCAATGCCCTCTGCTTCCACCGCAG
Seq C2 exon
ACGAGCCAGCCATGGCCGACATGGGCCCCGCCAGCGGCCTCTACGGCAGCCTGGGAGAGCCTGCCCCGACTTTGGGCCGGCCCTCGGGGGCCCCGGGCAGCTTCCCGCTGGAGCACGGAGGCCTGGCCGGCCCGGAGCAGTACAGAGAGCTACGCCCCGGCAGCCCCTACGGCGTTCCCCCTTCGCCTGCTGCCCTGCAGAGCCTCTCTGGCCCCCAGCCCCTCCTATCCAGCTTGGTGTACCCCGATGCCGGCTTGGGGCTCGTGCCCACGGGAGCCCCAGGTGGGCCCCCACCCATGAGAGTGCTGGCAGGGAACGGACCCAGCTCCGACCTTTCCACTGGGAGCAGCGGGGGCTACCCCGACTTCCCTGCCAGCCCCGCCTCCTGGCTGGACGAGGTGGACCACGCTCAGTTCTGACTTGAGTCCCCGTTCCCTCAAGCCTCGGACGTGAGGAGTCTGGGCAGCAGCTCTCCTGCCGGAGGCACGAACTTCTGCAGGACGCGGTGCCACGGGGAACAGGATGCAGGCTCGGGAGGGTCATTTCTGGGAGTGCCCTCTCCCACCCAGGCAGAGGGACTCTCCGGGTTCGGGTCTGAGAGGCTGCTGCTGCTCAAACTGGGGGCCTCTCGGCAAGCCTTGTTTTGTAAGCAGATTTTTCCCTTTATCGACCAATTAACCCAGTGCTTGCCACCGTTTCCAGACAGGAAATGTCACCCCAGGGAGGCCAAGCCTTCACTCCCTTCAGGGGCCTCTGCCCAGACCAGCACAGCCCTCAGGCTGGAAGATGCTTTAATTTCCAAAATTAAAAATAATTCTAATTGTGCTTTTGTTTCCCAGGTTCTATATGTCTGAGTTCTCTAGCCCCCTGCTCCACCTCCCCCCCAACCCCCTCTTTAAGTCAGAGATCAAGCTGTCCGTCCAGGCAGGAGGTGGCTGCGGGGAGGCCACACCTGAGAACTTCCTCTTCCTCTGGGGGCCTCCCTGCCACCAATTCCTGTCTTCCCCGGGACCCTCCCCACCCCTCCCCTGGGGCCACTGGCTCTAGATCTTTCGATCCTTCTGGACCCCACTACCGTGGGGGGAGGGGCGGACTCTTGGAACGCTTAAGGAGCTTCCTCCAGTCCAGACTAGGTGTTCGTCCCTGCACCCCCTCCCCTCGACCTGTCACAGCTGCCCTCAGAGCTCAGGCCAAGCCCAGCCCACCGATTTCCATTGCCAAACATCCCCCAGCTCCCGTTCTCCCTGTGGGCTCCGACTGCCCACGGATTGGACGCCCCACAGGCAAAGGAAGGCTGGGGCGGGGGCTCCTCCGAGCTGCCTCCCTGCCAGATGCTTCTGCCGCTGGCCACCACGGACACAGAGGCCGGCCGCGTGTGGATTCAAGTTATCCCTCAAACCTGCATCCCCGGCTACCTGTTGTTTCTGTGGCGTTCCCCTGTCTTTTATTTATTCTCTGACCATCGGGTCTCTCCCAGACTTCAATAAATTCGTCAGTTACAGTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011124:ENSBTAT00000055580:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.741 A=NA C2=0.928
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=19.0)
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:
GGGGCCAGTATTTCCGAAACA
R:
ACACCAAGCTGGATAGGAGGG
Band lengths:
348-1054
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development