BtaINT0070309 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019322 | HABP2
Description
Bos taurus hyaluronan binding protein 2 (HABP2), mRNA. [Source:RefSeq mRNA;Acc:NM_001014868]
Coordinates
chr26:34333686-34334478:+
Coord C1 exon
chr26:34333686-34333941
Coord A exon
chr26:34333942-34334335
Coord C2 exon
chr26:34334336-34334478
Length
394 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGC
5' ss Score
5.78
3' ss Seq
ATTATACTTTCCTCTTACAGGAT
3' ss Score
11.66
Exon sequences
Seq C1 exon
ACGTTGCCAACCCAGAGGGAAGACCCACTGAGCCCTTGACCAAGTTTCCTGAGTTTGGGTCCTGCGGGAGGACGGAGATAGCAGAGAAGAAGGTCAAGAGGATCTTTGGAGGCTTTAAGAGCACGGCCGGCAAGCACCCGTGGCAGGCATCCCTGCAGACCTCCCTACGACTGACCGTCTCCACGCCCCAGGGCCACTACTGTGGGGGGGCGCTGATCCACCCGTGCTGGGTGCTGACTGCTGCCCACTGCACTGA
Seq A exon
GTAAGCGCCTGCTGCGAGCAGAGGCCAGGGTGGCCAGAATCCCCAGGGGGTGCTGTCCCCTTCCCATCTGATCAGCATCTTGACAACTCTGGCAGGACTAGGGGGTCTGACCTAGCTCCAAGGGCAAAAGTGTGTCTCCTTAAAACCAGACAACAGAAGAAAGCTCCCGTGTGTAGAATGCTTACCACATGCATTACATGTGTTATGACAGTCAAGCCTCAAAACTGACTGCTGAATGACCGGCAGGAGAGCTCTGTGAGCAAGACCATGATTACAGATGAGGATGCCACCGGGCGAGAAGTCAGGTCATCTGTGAAGGTCACAGCTCACGGGTGTGGCTCCAGCCTCTCAAATTCCAGGACTAGTTCCTGATCATTATACTTTCCTCTTACAG
Seq C2 exon
GATAAAAACCAAATATCTGAAAGTGGTACTTGGAGACCAGGACCTGACGAAGACGGAATTCCATGAGCAGAGCTTTGGGGTGCAGAAGATTTTCAAGTACAGCCACTATATTGAAATAGACGACATTCCCTACAACGATATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019322:ENSBTAT00000025732:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=PU(21.5=59.3)
A:
NA
C2:
PF0008921=Trypsin=FE(20.3=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:
TTTCCTGAGTTTGGGTCCTGC
R:
TCGTTGTAGGGAATGTCGTCT
Band lengths:
350-744
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]