BtaINT0164927 @ bosTau6
Intron Retention
Gene
ENSBTAG00000040072 | ZNF140
Description
zinc finger protein 140 [Source:HGNC Symbol;Acc:HGNC:12925]
Coordinates
chr17:45107093-45107581:+
Coord C1 exon
chr17:45107093-45107231
Coord A exon
chr17:45107232-45107482
Coord C2 exon
chr17:45107483-45107581
Length
251 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
TGTATTTCATTTTCCACAAGCAG
3' ss Score
1.71
Exon sequences
Seq C1 exon
ATGTCATTTCAGGAGTCAGTGACATTCAGAGATGTGTCCATAGACTTCTCCCGGGAGGAGTGGGAATGGCTCCAGCCTGCTCAGAGAGATTTGTACAGACATGTAATGTTGGAGAACTATGGCCACCTGGTGTCACTGG
Seq A exon
GTAGGTATTTCCTCTCATCTCCTCTCATGCAGAACTTGACCTTTAGGATGACTGTTGTGAATCTTGATTATCTGACTGAATATTCCCAAGGAAGGAAAGTTTTTTTTGTTTTTTTTTTCTTTCAAGAGGAAGATTATAACTTCAACTAGTGTTTTGACATCTTTCATATTTATATCTGGCATTTCTAATAATGGCCTCTTTTTTGGTAAGGATTCAAGGACTAATTTTGAATGTATTTCATTTTCCACAAG
Seq C2 exon
CAGGTCTTAACATGTCTAAGCCAGATGTGGTTTCCTTATTGGAACAAGGGAAAGAGCCCTGGCTGGGGAATGGAGATGTAAGCAGAGAGCTGTTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000040072:ENSBTAT00000052977:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.029
Domain overlap (PFAM):
C1:
PF0135222=KRAB=WD(100=87.2)
A:
NA
C2:
PF0135222=KRAB=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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:
TGTCATTTCAGGAGTCAGTGACA
R:
GCTCTCTGCTTACATCTCCATTCC
Band lengths:
228-479
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development