BtaINT0024956 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005938 | BARHL2
Description
Bos taurus BarH-like homeobox 2 (BARHL2), mRNA. [Source:RefSeq mRNA;Acc:NM_001192297]
Coordinates
chr3:52694203-52696492:+
Coord C1 exon
chr3:52694203-52694428
Coord A exon
chr3:52694429-52696179
Coord C2 exon
chr3:52696180-52696492
Length
1751 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
ACATCTGTTTTTTTTTTCAGGAC
3' ss Score
12.68
Exon sequences
Seq C1 exon
GAACAAAGGAGGAAGGAGACCGGGAGATTTCAAGTAGCCGAGAGAGTCCCCCTGTGAGAGCCAAAAAGCCTCGTAAAGCCAGGACGGCTTTCTCCGACCACCAACTCAATCAACTGGAGCGTAGCTTTGAACGACAGAAGTACCTGAGTGTGCAGGATCGCATGGACCTGGCGGCTGCACTCAACCTCACTGATACCCAGGTCAAGACCTGGTACCAGAACCGCAG
Seq A exon
GTAAGGGAGGCTGTGGTGGGGAGCAGAGGCATCTGGTCATCTGGGTCAAGACAACTACACCAGTCTTCCATCCCATGTGGCCTCGGAGTCACTAGGGAGTCAGAGGGCCTGGAGTGGGCAGTTGGGGGGTTTTCAGACTGGAGTAGGGATTAGCCATACCTCCCAGGTGATGAGTAGCTGGAGTTTGGAGAATTTTGCACTTCTAAGTGTCTTTCATGTATGCTGTTTTTCTCTCTCAAATCTGAGTGGCTGAAATATCTCCCACTTTGCCTCCAAATCAATCAAGCCACACCTTCTTAAATCGAGACATCTGTGTAGCAGACACTCAGGCCCATAAAACCGATGCACTGCACCCTTTTGGGCCTGCCCCAGGATGGCTCCAAATATCTATAACCAGTCACTAAATCTGGCTATAGCTGTTCTGAAGAGCGGACCCACTGGCCTCGGCTTAAAAGTCCTTGCCTGGCCTGTGAGGCAGCCTGGAGGAAGGTTAGGGTTGGCAGCCAGTCAGGCATCTAGACTGAGGGTCTGTCCCCTATTCTGGCCACGTCAGAGCCCTCCAGGAACCACAGCTTCCCTTGAAAGGAAATTAGGAAAGGAGCTGGCAGTACTTGTAGGCCCCTGAACTGCAGTGCGAACACCCAAACCCGGCAATCTGGGGCCGAGGTTATGCCGGGTTTCTAAGCCTGACGGTTGTCTCCCTTGTCTCGATTTTCTCTCTCCCGCCTTTTCCCTCGTTTGTGTTCTAATCGTCCATAAGTGTGGTTGGAAATGCCCATCCAGTTGTCATCTTTACCATAATTTTCTGTCTCATTACATACGGTTTCAGCCACCCTAATTCTGTCGGAAAACATTAGTGTCATTTGTCGCCAATTTAAAACGGGTGACATGTTTATTAATTTGGCTGGAGCTGCCGGGTATGGAGGGCCCACCAGCCCTGAGTTCCTTCAGGAGGCATGTGAGCAAAGGCCTGCTGCCTCTTCTTCCTAGTGGGGGTGCGGTGGGGGAGGGAGGAGACCAAGAAAAGCGGATCACAGGTTTTAATTGTTACTCTCTCCCAGAGGAGACAAGATTTTGAAATGCATTTTTCCCCTCCTGGAATGGCCCCGAGGTACTGTCCCCTTGGGAGAGCCCTCCCTCAAACGAATTCCGTTTTGAAACCTTGTCACCTTCCTCACTCTGAGCCGCCCGCCTGCTGTAAGGTCCTGTCAGGCTGATGAGAGAGATGTGTCTCCACAGCCTTGGGGACCAAAAGGGGCAGGGGTCCCAGGCCCAAGAGCCTCTGTGTCCCTTTGTTTGCGGTTTCTTCTCACTCGGTCTGGAGGAAAGGGGGAGGGCAGAGAGCATACACTCTGGGATTGTTGGGGAGCCACTTGGGGAAGAGAATTAAAGGAGGGAGGAAGAAGACTGCCATAGAAAGAGTGGTCTCAGTTGATCTCTAGAGAAGTTTCCGCAAGTAGCCAAACTATAAGGGTGGCAACAGCAGAGCAAAACGTCCGGAGAAGGCAGCAAAGCTTGGGGAATTTCATTTATGAATGTCTGTTTGGGAAGCCAGCTTGGATTTGGGTGATTCTGTGAGGGAGAGGGTGGGATGGGGGCCAGGAGGTGTGGTTCCTTCCCGATTCTCAGCGCTCTCTAAGTCCTCCTTGTCCTCCCCGAGGAAGAAGAGGCCAGTAGGGGAGAGAACGGGCCTTGGGGCCTGGACTGTGCCCCCAGCCGCGGGGTGCATGCACATCTGTTTTTTTTTTCAG
Seq C2 exon
GACCAAGTGGAAGCGGCAGACCGCGGTGGGCCTGGAGCTACTGGCTGAGGCGGGGAATTACTCGGCACTGCAGAGGATGTTTCCATCGCCTTATTTCTACCACCCAAGCCTGCTGGGCAGCATGGACAGCACGACCGCGGCGGCGGCCGCTGCCGCCATGTACAGCAGCATGTACCGGACTCCTCCCGCGCCCCATCCCCAGCTGCAGCGGCCCCTGGTGCCCCGAGTGCTCATCCATGGCCTGGGGCCCGGGGGACAGCCAGCCCTCAACCCCTTGTCCAACCCCATCCCAGGTACCCCGCACCCCCGGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005938:ENSBTAT00000007796:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.579 A=NA C2=0.365
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(89.5=67.1)
A:
NA
C2:
PF0004624=Homeobox=PD(8.8=4.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGAGAGCCAAAAAGCCTCG
R:
GTCCGGTACATGCTGCTGTAC
Band lengths:
354-2105
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]