BtaINT0070462 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015784 | HAPLN2
Description
Bos taurus hyaluronan and proteoglycan link protein 2 (HAPLN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001075684]
Coordinates
chr3:14255529-14255965:-
Coord C1 exon
chr3:14255849-14255965
Coord A exon
chr3:14255712-14255848
Coord C2 exon
chr3:14255529-14255711
Length
137 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CCCCCGCCATCTCCCGCCAGCGT
3' ss Score
8.05
Exon sequences
Seq C1 exon
GTGTGGTGTTTCCGTACCAGCCCAGCCGGGGCCGGTACCAGTTCAATTACTACGAGGCGAAGCAGGCGTGCGAGGAGCAGGACGGACGTCTGGCCACCTACGCCCAGCTGTACCAGG
Seq A exon
GTGAGTGGCCGGGTACCGCCCAGGTTCTCTCCGGGCTGTCGCCTGGACCCCAGGGGAGGCAAACTCCGGGTTTGGCTCCCGCCTGTGATGCGTTTGATCCCGCTACCCGCCTTCCTTCCCCCGCCATCTCCCGCCAG
Seq C2 exon
CGTGGACCGAGGGTCTGGACTGGTGTAACGCGGGCTGGCTGCTAGAGGGCTCCGTGCGTTACCCTGTCCTTACGGCGCGCGCGCCCTGCGGTGGCCGAGGTCGGCCCGGGATCCGCAGCTACGGGCCCCGCGACCGGAAGCGCGACCGCTACGACGCCTTCTGCTTCACCTCCGCGCTGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015784:ENSBTAT00000020956:5
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=0.081
Domain overlap (PFAM):
C1:
PF0019312=Xlink=PU(41.1=97.5)
A:
NA
C2:
PF0019312=Xlink=PD(57.9=88.7),PF0019312=Xlink=PU(0.1=0.0)
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:
GGGCCGGTACCAGTTCAATTA
R:
AGAAGGCGTCGTAGCGGTC
Band lengths:
251-388
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]