BtaINT0070460 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015784 | HAPLN2
Description
Bos taurus hyaluronan and proteoglycan link protein 2 (HAPLN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001075684]
Coordinates
chr3:14256163-14256821:-
Coord C1 exon
chr3:14256716-14256821
Coord A exon
chr3:14256517-14256715
Coord C2 exon
chr3:14256163-14256516
Length
199 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CTGTGGCCCCCTCTGCTCAGCAC
3' ss Score
6.07
Exon sequences
Seq C1 exon
ACTGGGCTGACTCCCATCATGCAAGGCAGGATCAGCCTCCCCACTCTCTGCCACTTCCTTCTCCCTTGGGCCTTCACCACCTTCCACAGAGCCCTGGGGAGCCAAG
Seq A exon
GTAAGACCTTAATTCGGCCCAGAATCTGGAGAACAGTGGTGGGGAAAGTGGGAAGGGTTGTTGGAGGTCCTCAGGGACTGAGTCATTTCTGAGTGAGCAATGGAGAGAGGTTTGGGGGGTCTGGGGAACGCTGGCTTTGGACAGGCACTTGGGCAGTGGGGGTCAGGGGGTTCCTGCCACTGTGGCCCCCTCTGCTCAG
Seq C2 exon
CACCCCACCCTGGCCCCCACTACCTCCTGCCCCCCATCCACGAGGTCATTCACTCTCGTCGTGGGGCCACGACCACGCTGCCCTGCGTCCTGGGCGCCCCGCCTCCCAGCTACAAGGTGCGCTGGAGTAAAGTGGAGCCCGGGGAACTCCGGGAAACGCCCATCCTCATCACCAACGGACTGCATGCCCGGGGCTACGGGCCCCTGGGGGGGCGCGCCAGGATGCGAAGAGGGCATCGGCTGGACGCCTCCCTGGTCATCGCGGGCGTGCGCCTGGAAGACGAGGGCCGGTACCGCTGTGAGCTCATCAACGGCATCGAGGACGAGAGCGTGGCGATGACCCTGCGCCTGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015784:ENSBTAT00000020956:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.008
Domain overlap (PFAM):
C1:
PF0768612=V-set=PU(0.8=3.3)
A:
NA
C2:
PF0768612=V-set=PD(98.3=97.5),PF0019312=Xlink=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCTGCCACTTCCTTCTCCC
R:
CATGCAGTCCGTTGGTGATGA
Band lengths:
248-447
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]