BtaINT0071804 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013065 | HFE
Description
Bos taurus hemochromatosis (HFE), mRNA. [Source:RefSeq mRNA;Acc:NM_001012399]
Coordinates
chr23:31617685-31618677:+
Coord C1 exon
chr23:31617685-31617948
Coord A exon
chr23:31617949-31618377
Coord C2 exon
chr23:31618378-31618677
Length
429 bp
Sequences
Splice sites
5' ss Seq
AGGGTGCGT
5' ss Score
7.22
3' ss Seq
ACCTGCTCCTTTGGTTTCAGTAA
3' ss Score
7.71
Exon sequences
Seq C1 exon
GGTCACACTCCCTGCGCTTCCTCTTCATGGGCGCCTCCAAACCAGACCTCGGGCTGCCCCTGTTTGAGGCTTTGGGCTACGTGGATGACCAGCTGTTCGTGTCCTATGATCATGAGAGTCGCCGTGCAGAGCGGCGCGCCCCATGGCTCTGGGGCAGGGCCACCAGCCAGCTGTGGCTGCAGCTGAGTCAGAATCTGAAAGGCTGGGACCACATGTTCATCGTGGACTTCTGGACGATCATGGACAACCACAACCAAAGCAAGG
Seq A exon
GTGCGTGAAGAGCAGGCCTCACCTTCCCAAGGTGGGCGGGGTGTGTCCCTGCTTCACAGATGCATCTTGAGGGAGGTTTGAGATCCTGGCTATTTGAGGTCCTGGGGGGCAGAGAAGAGGGCAAGTGTTTGCTTCCTGAGGTTGTTCAGTCCTTGTAATGGTTCCTGTAATCCCTGTAAGGGCTTCCTTGGTGGTCCAGATGGTAAAGAATCCACCTGCAATGTGGAAGACCTGGGTTCGATTCCTGGGCTGGGAAGATCTCCTGGAGAAGGAAATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATCCCATGGACACAGGAGCCTGGCAGGCTACAGTCCGTAGGGTCGTCGCGAAGAGTCAGACACGACTGAGCGACTAACACACACACAATGGCAGAAACAGGGACCTGCTCCTTTGGTTTCAG
Seq C2 exon
TAACGAAGCTGGGGGCGTTGCCAGAGTCCCACACCCTGCAGGTGATCCTGGGCTGTGAGTTGCAAGAGGACAACAGCACCAGAGGGTTCTGGAAGTACGGGTACGATGGGCAGGACCATCTTGAATTCCGGCCTGAGACACTGGATTGGAGAGCAGCAGAGCCCAGGGCCCAAGTCACCAAGCTGGAGTGGGAAGTGAACAAGATTCGGGCCAAGCAGAACAGGGCCTACCTGGATCGGGATTGCCCCGAGCAGCTGCTGCATTTGCTGGAGCTGGGGAGAGGGCCTCTGGAGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013065:ENSBTAT00000017371:2
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=0.010
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(47.6=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(51.9=95.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTGGGCTACGTGGATGACC
R:
GCTGCTCTCCAATCCAGTGTC
Band lengths:
352-781
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]