BtaINT0117278 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004538 | PRDM9
Description
Bos taurus zinc finger protein 596 (ZNF596), mRNA. [Source:RefSeq mRNA;Acc:NM_001101948]
Coordinates
chr1:45029643-45030558:+
Coord C1 exon
chr1:45029643-45029914
Coord A exon
chr1:45029915-45030490
Coord C2 exon
chr1:45030491-45030558
Length
576 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
ATCTCTTTTCTGACACTCAGATC
3' ss Score
7.04
Exon sequences
Seq C1 exon
ATTGTGAGGAGTGTCAGAGCTTCTTCATCGACAGCTGTGCTGCCCATGGGCCCCCAATCTTTGTAAAGGACTGTGCAGTGGAAAAGGGGCATGCCAACCGCTCAGCCCTCACTCTGCCCCCTGGGTTAAGTATCAGAGAGTCAAGCATCCCTGAGGCTGGGCTTGGAGTGTGGAACGAGGTGTCTGATCTGCCGCTGGGCCTGCACTTTGGCCCCTATGAGGGCCAGATCACAGACGATGAAGAGGCCGCCAACAGTGGATACTCCTGGCTG
Seq A exon
GTGAGAAACACCCCTGTTTCCCTGTTCTCTGGCCTTGAATTGCTTGTGTGTGGTGACGGGTGCTTCATGTCTACATGCAAGGATGCAGATGGTGATGACATGGTCAGCAATGACACGGGCAGCCCTGTGTACTGTGCACTGGGCATGAACATCTAAAGGTCAGAGGAGAGGTGGGAGACACTGTGTACAGACACACAGGACCTCTATCTAAAGCTCAGAGGAGAGATGGGAGACAGTGGTCCAGGCACACAGCACCTCTGTCTACAGGTCAGAGGAGAGGTGGGACCACAGTGTACAGACACGCAGGACTCCTATCTAAAGGTCAGAGGACAGGTGGGAGACAGTGGTACAGACACACAGAGGTGACTCCTCCCTTGTGTAGCCCTTGCCTTCAGTGAACCAAGAGACTCAGACTTTGAATGATGATTAAGCAGCTTACCATTTGGCCTGACTGGCAGTTGAATCCATGCAGGCTGAAGAGCACCAATGACTGCAGAGGGAAATAGTTCTTCTATTACTTCCTATCAAAAAAAATAAAAGAGAGAGGAAAGCTTGTATCTCTTTTCTGACACTCAG
Seq C2 exon
ATCACCAAAAGGAGAAACTGCTATGAGTATGTGGATGGAAAGGACACGTCTTTGGCCAACTGGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004538:ENSBTAT00000002795:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0085623=SET=PU(20.7=18.7)
A:
NA
C2:
PF0085623=SET=FE(26.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGAGGAGTGTCAGAGCTTCT
R:
TCATCCAGTTGGCCAAAGACG
Band lengths:
337-913
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development