BtaINT0085445 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003992 | LHX4
Description
Bos taurus LIM homeobox 4 (LHX4), mRNA. [Source:RefSeq mRNA;Acc:NM_001192785]
Coordinates
chr16:62912552-62915247:+
Coord C1 exon
chr16:62912552-62912723
Coord A exon
chr16:62912724-62914852
Coord C2 exon
chr16:62914853-62915247
Length
2129 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CTCCGTTCTTTTGTCCACAGAGG
3' ss Score
10.55
Exon sequences
Seq C1 exon
GTTTGGTTTCAGAACAGAAGGGCCAAGGAGAAGCGACTGAAGAAGGACGCGGGGCGGCACCGCTGGGGGCAGTTCTACAAGAGCGTCAAGAGGAGCCGGGGAGGCAGCAAGCAGGAGAAGGAGAGCTCTGCGGAGGACTGTGGGGTTAGTGACAGTGAGCTGAGCTTCCGAG
Seq A exon
GTGAGCAGGGCTGGAGGGGCGAGGCCAAGGCCCTAGGAGAGGCCCCTGGGAAACAGTGACCCCCGACAGGCAGGAGGGGTCTTTCTGGAGGCCTTGCCAGCTCTCTTCTGAACACAGGCCCCACCCTGTGACTTGCAGTAAAGGGTGGGGGGAAATGGTCGTGGCCCTTCCAGAGGGGACAGGGCAGAGGAAACCAGAGCTCTGCTGCTGACCCATGGAAGCTGGGCTCCCAGGCCTGCGGGGCCCAAAGGCCTCCCCTCCTTGCCCGCTGCCCGGGGCTCCCTCATCAGCCCACACAGCTGCAAAGGACCCCTGTGTCTCAGTCTGTGCCCCAAGCCCCTCTCCGGCATTTCTCCCCTCAATGGGGGCAGTGGCCTTCCTCCCGTTACCCACTAGGTGAGCCCCCTCCTCTGCTGGTGGTGGGAGGATGTGCGTCACAGCCCTTGGCCCTGGGGAGTCAGTACTGCGAGTGCATGTGAGGTGGGGGCTGGCCTCATTCTGGAATCCCTTCCCCCACCGCTCACTTCATCCTGTCCCCAGCACATATGCTTTGCTGCATGTGCTACATTCAAATTTTGTGCATCAGTAGAATTGCAAATGGCTGCATGTTTTGGATCCTTTGGTTGTTTGCAAATAGCCATTCTCTTGTATCGAGTCCTCAAACGTGGAAGGTCTTCTGTTGCGGCAGGAGAAGGGAAGAGGCCTGAGCTGGGGGAATCAGAAATCTGGTTTCCAGTTGTGGCTTTGTCAAATTGATTTACTTTTCTTGAGCCTCAGTTTACCCATCTCTAAATGGGTTTAACAGTATCGTTGCCCATATCCCAGTGGTCTTGTGGGAATCCGTGAATACAACTGACTGGATGCGTTTGGAGAGAGCTCAGCACATTTTTACTCTTATAAGACACAACCATTTTTAGGCAGCTTGTGGTTCCCACAGAGGGCCCTGGTCACTGGGGATGACAGGTGTAGGCAAAACACCAGTTAATGGCCATTTTACAGTGTAGCTGAGCCTTCATCTCCTGCCCCCTTTAAAGGGCATGACTCTCCTCCACCTTTTCATTTTCATGGATGGGATGCGGGACAGCCTAGGGCAGGTTGTCAGAAGGGATGAGTGTTGAAGTCCACTCTGGGGTGGCCTTGGTAGGAATGGACACACAGGCCCAGTGGGAATAGAAAGGAAGTCTGTGGGGCAGCAGATGGCAAGAGCTGCCTGTGAGGGCCATGATTTCCTGAGAGGACCGTAAGTCAGCCCAAAGGTCTGCCCATGAGGCCCGGGGCATGTTCCAGGCTCACCTTCCAGGCCTCTTGGGGGTGGAAAGCCACTCAGTCTCCTCTAAGATGCTGAAATCAACATCTGGAACATACAGGATGGTTAAGTCTTGGTTTGTAGCTCCTTTTTGTTGGGTGCAGGTGGGCCCCCAGGTTGACATATCACTGGTCTCTCCACATAACTGTATAATCTTATTTTTCTTAAGACTAAAATTGTTCACCTCTGTTGGAGAGATGAATTCTTCCAGGTGGTAAAGATTCCACGAGATCCCCTTAATGAAATTCCTCAAGAAACAAGAAGGTCCATTTGCCTTAATCAATCCAATGCTTTGTCCCCAGTGAAGAACTTAGAGAAACCAAGTCCTTTGATACTGAACCTCTTTCCCAGGTACAGCAGAAAGCTTTTGTGTATACATGTCTTGAGTCCTCAGCTCCCTTGAGCCTACGGCCCTGCTTGTTTCCCTACAACTGAATCAAGCACTTTTCTCAGCTCGAAAGCTTTCAGATGAAATCTTGTTAGCATGGAGTTTATTCCCTTTGTGCTGTGGATGACATGTGACACAGCAAACCTCAGGCACTGGCACTCCATAGCTGTCAGTGTAGCCCTCTTCATACATGACCCACCTGAGACCCACAAGCTCACGAAACATTTGTCCAGCCTTCTGGGACCTGGGCATGTGGTCTCTGGAGGTGTTTGTTCTGTTTTTCCCCCTTGACGTGTCTGGATGCCAGGCTGACATGCTGGTGTCTGGTTCATGCTCGGGCTTCTTTCCTGGTCATGTGTATTCCTAGGTTGTGAAGAACAGGGGAGCGCTGGAGTCCTGGCGGCTGACAATAAATCTCCGTTCTTTTGTCCACAG
Seq C2 exon
AGGATCAGATTCTCTCAGAACTTGGCCACACCAATAGGATTTATGGCAACGTGGGGGACGTTTCAGGCGGACAGTTAATGAATGGGAGCTTCTCCATGGACGGGACAGGACAATCCTATCAGGACTTGAGGGATGGGAGCCCCTATGGAATCCCCCAGTCTCCATCCTCCATCTCGTCCCTGCCATCCCACGCTCCTTTGCTCAATGGGCTGGATTACACGGTGGACAGTAACTTGGGCATCATTGCGCACGCAGGGCAGGGAGTAAGCCAGACGCTGAGAGCCATGGCTGGGGGACCCACCTCTGACATCTCCACAGGAAGCAGTGTAGGCTACCCCGACTTTCCAACTAGCCCGGCCTCTTGGCTCGATGAAATGGATCATCCTCCTTTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003992:ENSBTAT00000005216:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.618
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:
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