BtaINT0073260 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003829 | HPN
Description
Bos taurus hepsin (HPN), mRNA. [Source:RefSeq mRNA;Acc:NM_001080241]
Coordinates
chr18:45985522-45985826:+
Coord C1 exon
chr18:45985522-45985644
Coord A exon
chr18:45985645-45985785
Coord C2 exon
chr18:45985786-45985826
Length
141 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGG
5' ss Score
6.13
3' ss Seq
CATCCTTGTCCCTCCCACAGCGA
3' ss Score
10.45
Exon sequences
Seq C1 exon
GGCGTTGGACTTCTCGGAGCTGGACGTGCGGACGGCGGGCGCCAATGGCACGTCGGGCTTCTTCTGCGTGGACGAGGGGAGGCTGCCGCATGCCCGGAGGTTGCTCGAGGTCCTCTCCGTGTG
Seq A exon
GTGAGGAGGGCGGCGGGCAGGTGGGGCGCACGCCGCGGGCCCCACCACCCCTGAGTACCCACTATCCCCTGGGTGCCTTTCCTCTGTCTTAATTGGCCTCTTTTTTTTGTCTCTGTGTCTTCATCCTTGTCCCTCCCACAG
Seq C2 exon
CGACTGTCCCAGAGGCCGTTTCCTGGCTACCAGCTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003829:ENSBTAT00000004986:6
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=0.000
Domain overlap (PFAM):
C1:
PF092725=Hepsin-SRCR=FE(37.3=100)
A:
NA
C2:
PF092725=Hepsin-SRCR=FE(12.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTTGGACTTCTCGGAGCTG
R:
CTTGGCAGCTGGTAGCCA
Band lengths:
162-303
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development