BtaINT0073262 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003829 | HPN
Description
Bos taurus hepsin (HPN), mRNA. [Source:RefSeq mRNA;Acc:NM_001080241]
Coordinates
chr18:45986206-45986663:+
Coord C1 exon
chr18:45986206-45986371
Coord A exon
chr18:45986372-45986472
Coord C2 exon
chr18:45986473-45986663
Length
101 bp
Sequences
Splice sites
5' ss Seq
TGAGTGAGT
5' ss Score
6.51
3' ss Seq
TCCCCTCCTTTCCCCGGTAGGCG
3' ss Score
10.42
Exon sequences
Seq C1 exon
ACTGTGGCCACCGAAAACTGCCGGTCGATCGCATTGTGGGCGGCCAGGACACCAGCCTGGGCAGGTGGCCGTGGCAAGTCAGTCTTCGCTATGATGGAGCACATCTCTGTGGGGGGTCCGTGCTCTCTAGGGACTGGGTGCTGACAGCCGCCCACTGCTTCCCTGA
Seq A exon
GTGAGTGTCCCCCAGGGCACTGAGGGGAGAGGCTGGGGAGTGGTGAGCTGGGGGAGGCTGTGCCCAGACAGGTGGCCACCCTCCCCTCCTTTCCCCGGTAG
Seq C2 exon
GCGGAACCGGGTCCTATCACGATGGCGAGTGTTTGCTGGTGCTGTGGCCCAGACTTCACCCCATGGCGTGCAACTGGGGGTGCAGGCTGTCATCTACCATGGGGGCTATCTCCCCTTTCGAGACCCCAACAGCGAGGAGAATAGCAATGACATCGCCCTGGTCCACCTCTCCGGCACCCTGCCCCTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003829:ENSBTAT00000004986:8
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=PD(6.4=12.5),PF0008921=Trypsin=PU(18.5=78.6)
A:
NA
C2:
PF0008921=Trypsin=FE(26.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGCAAGTCAGTCTTCGCTA
R:
CCAGGGCGATGTCATTGCTAT
Band lengths:
257-358
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development