BtaINT0117277 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004538 | PRDM9
Description
Bos taurus zinc finger protein 596 (ZNF596), mRNA. [Source:RefSeq mRNA;Acc:NM_001101948]
Coordinates
chr1:45028323-45029426:+
Coord C1 exon
chr1:45028323-45028482
Coord A exon
chr1:45028483-45029324
Coord C2 exon
chr1:45029325-45029426
Length
842 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGA
5' ss Score
10.53
3' ss Seq
GCTTCTGTTCTCCATCTTAGAAC
3' ss Score
9.19
Exon sequences
Seq C1 exon
AAGACAATGTCCAGAGCACCATTAAGTAAGGAATTTAGTTTGAAGGAATTGCCGGGAGCAGCCAAATTGCTGAAGACAAGTGGCTCCAAGCAGGCTCAGAAACTGGTGCCCCCTCCCGGAAAAGCAAGGACTCCTGGACAGCACCCCAGACAAAAAGTCG
Seq A exon
GTAAGAGAAAATTTGGGGAGTTCCTCTAATTAGTTCCTCTAATCCCTATAGAAAAGCTAGTAAGTATGGACTATGTGTGTGGCATGGACTTTGGGTAGGCTTGGGTTTAAGCTGGACTGATTTGAGACATGAAGTTAGCACTGGGGCCTTGGGAAAATCTTATATGTTTTCTGAGGTCCTGATTGCTCATCTGTAAAGTGAAGATAAGGATGCATAACTCATACAGTGTTTGAAAGCTTTACATTAAATGCAAAAGTGCTGACACTTTTTTGAGCTAAAAGTAGTTCAGTAAATCCAGCTGTGATGATAGGGACCATGCCTCGTTAGTGTTTATGCCCAGACCTCTGCTCAATGCCTTACATGTCATGTGCCCTCAATGTATGTTTTCTGAGTACATGTGTCAGTGAACTATTTCCTAAGTAAGAAGGTGGGAAGTTAAACCTACTAACGGGAAGTGCAGGAAGCTAACACTGAACTGGGCATCTGTGGTCAGTGAGGAGCCTCAGTCTCCTGAACCAGGAGTTAAAGGAAGAAGAAACAAAGTATAGAAAAGGGACTTCCTGGTGGTTAAGTGGTTAAGACTCCATGCTTCCACTGCAGGGGGTATGGGTTCCATTCCTGGTCGGGGAACTAAGATCCCACAAGCCATGCAGCTTGGCCAAGAAATAAATAATGTAACATTAAAACATAAAATTACAAAAGTAAAAGTTTAAAAAATACATGTAAACAAGTTTTAACAAAATGTATAAATGAACAAGTAGGAGATCTCACACTTTCCAATAAAACAGGGACTAACTCTCCAAACCCCACCAGCCTTGCTTAGCTTCTGTTCTCCATCTTAG
Seq C2 exon
AACTCAGAAGAAAGGAGACTGAAGTGAAGAGGTACAGTCTACGAGAAAGAAAGGGGCATGTGTACCAAGAGGTCAGCGAGCCCCAGGATGATGACTACCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004538:ENSBTAT00000002795:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.759 A=NA C2=0.543
Domain overlap (PFAM):
C1:
PF0230512=Phage_F=PD(3.2=5.6),PF095145=SSXRD=PU(0.1=0.0)
A:
NA
C2:
PF095145=SSXRD=WD(100=94.3)
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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGACAATGTCCAGAGCACCA
R:
AGAGGTAGTCATCATCCTGGGG
Band lengths:
262-1104
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development