BtaINT0117276 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004538 | PRDM9
Description
Bos taurus zinc finger protein 596 (ZNF596), mRNA. [Source:RefSeq mRNA;Acc:NM_001101948]
Coordinates
chr1:45026490-45028482:+
Coord C1 exon
chr1:45026490-45026539
Coord A exon
chr1:45026540-45028322
Coord C2 exon
chr1:45028323-45028482
Length
1783 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
GTTGTCTTTTATTCATGTGGAAG
3' ss Score
-2.19
Exon sequences
Seq C1 exon
GTAAACTTTCTTCGATGGCCTTCAGAGTGGAGCACAATAAACACCAGAAT
Seq A exon
GTGAGTATTTCCCAAATCCTGTTGCCAAAATATCCTCCTCATGGATCCAGTCACAGGTGAGAATAGGAGAAAACAGAGATCCTGGAGACTGCTGCCTTCCTGTCCTGAATCTTTAGCACAATGTCTGATATCATCACCATCTTTATAGTTAGTAAGAACAAGAACAATAGTAGGCTGTTCTGTTGTTACATTATTTTCACAATATTTCAGACTTTAAGCATTTTATGTGAATAAACTTACTTAAACCTTAAAACAATCCTACAGTACCTATAAGTAGGTATATAGCTATCACCATTATAGATCACAAAACTGAGGTAAAAAAAATGATTGATTATATGCCTGAGATCACAGTATCACTGGTAGTGCAATCTAATCCAAAGCACTTCTTCTAAACTCCTTACAAAATGATTAAAACTTCCATAGTTCTATGAAGTTTATTCATACATCTTTATATCATTCATCTGAGAGATGTTTTCAACCTCAGTTCTTTTGTGCTGTGCTAGGGAGGGATATGCTAAGACATCTGACTAAGGGAAGCTTAAGGACCTGCTGGGCAGTTTGTAGAGTGGACGGTCCAAGATGAAGAAGCTTAAGGACATGCTGGGCAGTGTGTAGAGTGGACAGTCCAGGATGATGAAAGTGACAGGATCCCTACTTCAGAGCCTCCCAGTCCAATAAGAGGAAGCAACTCGCAACACTGACAAGCCTCAGGTTTATGACTGAAAAGCAACAAATAAGAAAATAACTGAAGGACTTCACATAGGTTACCCACTTTTGAGTAGAAACTCATCATCTGGGCGTCATTTCAAATGCTCATTCTTGCAGGAGGAAGTAACAAGTCCTTCCCCTGAGCTATGATTAGGCAACTCTCATGTTTGGAATCATTTGTTTAGCCTGCCCTGTGTTGTGAGCTTTGAGAGCCTAGCCCATACCCGTTAATTCTCAGAAGTCAAGGCCCAGCTTAAAGCCCCTGAGAGCCCCCTGAATGTTTTGTGAATGAGTGACTCCACATTTAAACATTCATCTAGGAGTAAGAAGATCAAAGAATGCTGAAGATAGTATCTGTGAGCTAGACTTCAAATATAGAGACAGTTGAAGGGATAAATTGATGGCAGGGATGTACACTCACATTCATACTGTATTAAATAGCTCACACAATGATTTATTGAAATGTTATTAAATTTCATGTCCACTGTAACATTAAAAATTAGCATGTATACCAATTTATGGATCAGGAAACTGAGGAGAACCAGCTAGTCATACAGCCTTTTTCAAGCAGAATTGATTAGGTCAGCTACTTTAATTCCAAACATTGTCTCTAAGAGGACATGGCAACCTGCAACTTTCAGCTCATTTTCTTTATTGTCTAAATGTGTTTCTGCCGATCGTCTTTTCTCTTCTCAATCTCACTGCTTTGTCACCTTATCTTCCAGATGTGTTTTGTCCCCTCTGTAATTTTCCATACTTCCTCGTCCATCAAAGGGCCACTAATTAATAGAAAACCCCCCGGATTTCTCTATGAGCCCTTACCCACTTCTTTCCCTGACCTCCAGCTATTCTCCTTGCCTTGCTCTCACTTTTCTGTAGAAAGTTGAAGGGAAAGAACCTTAAGATATGAATTCTAGTTTTGATTCACTACCCACTTAGGTCCTTATTTTACACTCCAGTGTTCAGACCCCTCCTCCACCAGGTATTTCCAAGAATTGTCAAAGTCATGCATGTGAAAACACTTCATAAAGTCCTAAAGAACTAAAGAAATTCATGTTGTCTTTTATTCATGTGG
Seq C2 exon
AAGACAATGTCCAGAGCACCATTAAGTAAGGAATTTAGTTTGAAGGAATTGCCGGGAGCAGCCAAATTGCTGAAGACAAGTGGCTCCAAGCAGGCTCAGAAACTGGTGCCCCCTCCCGGAAAAGCAAGGACTCCTGGACAGCACCCCAGACAAAAAGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004538:ENSBTAT00000002795:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.759
Domain overlap (PFAM):
C1:
PF0230512=Phage_F=FE(17.0=100)
A:
NA
C2:
PF0230512=Phage_F=PD(3.2=5.6),PF095145=SSXRD=PU(0.1=0.0)
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:
ACTTTCTTCGATGGCCTTCAGA
R:
CGACTTTTTGTCTGGGGTGCT
Band lengths:
206-1989
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development