BtaEX0017370 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000003829 | HPN
Description
Bos taurus hepsin (HPN), mRNA. [Source:RefSeq mRNA;Acc:NM_001080241]
Coordinates
chr18:45972571-45985453:+
Coord C1 exon
chr18:45972571-45972640
Coord A exon
chr18:45979118-45979219
Coord C2 exon
chr18:45985324-45985453
Length
102 bp
Sequences
Splice sites
3' ss Seq
CAGCATGGTGTCTATTGCAGGTG
3' ss Score
8.93
5' ss Seq
TTGGTGAGA
5' ss Score
6.29
Exon sequences
Seq C1 exon
GTCCCGCCCCGGCCCCGGAGGTCAGCCGGGGAATCATTAACTAGAGGCTGTGACATGGCGGAGAAGGAGG
Seq A exon
GTGGCCGGACTGTGCCATGCTGCTCCGGACCCAAGGTGGCCGCTCTCACTGTGGGGACCGTCCTGCTCCTGACAGGCATCGGGGCAGCGTCCTGGGCCATTG
Seq C2 exon
TGCAGGTCGGCCCGGCGGATGCTCGGCTCACGGTGTTCGACCAGACAGAGGGCACGTGGCGCCTGCTTTGCTCCTCGCGCTCCAATGCCAGGGTGGCGGGGCTCAGCTGCGAGGAGATGGGCTTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003829_MULTIEX1-1/2=C1-C2
Average complexity
C3
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.167 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
PF092725=Hepsin-SRCR=FE(39.1=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGTCAGCCGGGGAATCATTA
R:
CTGAGGAAGCCCATCTCCTCG
Band lengths:
182-284
Functional annotations
There are 1 annotated functions for this event
PMID: 15627507
Both exons together encode a transmembrane domain and cause cytosolic retention when skipped. Hepsin/-TM (skipping) overexpression does not affect the growth of a human cancer cell line.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development