BtaINT0117274 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004538 | PRDM9
Description
Bos taurus zinc finger protein 596 (ZNF596), mRNA. [Source:RefSeq mRNA;Acc:NM_001101948]
Coordinates
chr1:45021761-45022299:+
Coord C1 exon
chr1:45021761-45021884
Coord A exon
chr1:45021885-45022191
Coord C2 exon
chr1:45022192-45022299
Length
307 bp
Sequences
Splice sites
5' ss Seq
TAGGTAACA
5' ss Score
6.25
3' ss Seq
AATATTTTGCTTCTTTCCAGGTT
3' ss Score
9.85
Exon sequences
Seq C1 exon
GCCAAAGATGCTTTCAAAGACATCTCTGTATACTTCTCCAAGGAAGAATGGGAAGAGATGGGAGAATGGGAAAAAATTCGATATAGGAATGTGAAAAGGAACTACGAAGCGCTGATTGCTATAG
Seq A exon
GTAACAGGAAGTGCTGGGTGCCCATAAGCCTGGGAAACATGAAACAGGTCTTCACCCTTGGTGTTCACTTGGCCCTCTCTTAGGTGGCTTCATTTGCTTACAGTTCCCTTTTGTGTGGAGACTAACCTGGAGGAAATGTTTATTGTTTTGTACTAAAGGGAGGTTGACCCTGCAGTGCAGAGCTCACCTCTTGCCTTTTTCTAGATTTTCCCAGCCCATCCTACTGATTTCCCTGACTTTGTGACACTTTCCATTGCTTCTGCGCTTTGTTCCTCCTTCTTATAACAAATATTTTGCTTCTTTCCAG
Seq C2 exon
GTTTCAGAGCCACTCGACCAGCATTCATGCATCACCGCAGGCAGGTCATCAAACTCCAGGCAGATGACACTGAGGATTCTGATGAAGAATGGACACCAAGGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004538:ENSBTAT00000002795:2
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=0.730
Domain overlap (PFAM):
C1:
PF0135222=KRAB=WD(100=92.9),PF0230512=Phage_F=PU(39.4=88.1)
A:
NA
C2:
PF0135222=KRAB=PD(0.1=0.0),PF0230512=Phage_F=FE(38.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAAAGATGCTTTCAAAGACA
R:
TTGCTGCCTTGGTGTCCATTC
Band lengths:
231-538
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development