BtaINT0073255 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003829 | HPN
Description
Bos taurus hepsin (HPN), mRNA. [Source:RefSeq mRNA;Acc:NM_001080241]
Coordinates
chr18:45991140-45991833:+
Coord C1 exon
chr18:45991140-45991304
Coord A exon
chr18:45991305-45991500
Coord C2 exon
chr18:45991501-45991833
Length
196 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAA
5' ss Score
4.51
3' ss Seq
CCCTAGTTGTCTTTCCCCAGACT
3' ss Score
7.01
Exon sequences
Seq C1 exon
GGCGACAGTGGTGGCCCCTTCGTGTGTGAGGATAGCATCTCTCGGACGCCACGTTGGCGGCTGTGTGGCATTGTGAGCTGGGGCACCGGCTGTGCCCTGGCCCAGAAGCCAGGCGTCTACACCAAAGTCAGTGACTTCCGGGAGTGGATCTTCCAGGCCATAAAG
Seq A exon
GTGAAATTTGAGCCCAGATGGGAGCCAGAGGGCGGGAGGGTTTGGGACTCTGAGCGGGAAAGGGAGGCAGGGTTTTCTGGAAACCTATAGGGCTTAGAAGCGGTCACCCTAGGGAACAGATGGCTTTCACGGGGCTCCTGGGGAGGGGTGGGCACTTGTGGGACGTTGGGGGGAGCCCCTAGTTGTCTTTCCCCAG
Seq C2 exon
ACTCACTCCGAAGCCAGCGGCATGGTAACCCAGCTTTGACCTGTGGCTTCTCCTCGCTGTGCACGCCTCCAGGGCCCGAGCTGATCTAAGGGGCCCCAGCCCCACGTGATGGGGTTCACCCTGGGCCAGGGATGGAACATTTTTCTTCTTGGGCCCAGCCCACAGGTCCAAGGATACTCTTCCCTCCAAGGTCCTCCACAGTGGCGGGCCCACTCAGCCCTGGGACCACCCTCCTGCCCCCCATGTAAATATTGTTCTGCCATCTGGGACCCCCCCCCCATCTTGTGCTCCTGAAGACAGGATGCTCTTTAAATAATAAAGATGGTTTTGATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003829:ENSBTAT00000004986:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=PD(20.6=89.1)
A:
NA
C2:
NO
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:
CCAGGCGTCTACACCAAAGTC
R:
GGAGGACCTTGGAGGGAAGAG
Band lengths:
254-450
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development