BtaINT0139747 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010048 | SPC25
Description
Bos taurus SPC25, NDC80 kinetochore complex component, homolog (S. cerevisiae) (SPC25), mRNA. [Source:RefSeq mRNA;Acc:NM_001034230]
Coordinates
chr2:27297968-27298290:+
Coord C1 exon
chr2:27297968-27298120
Coord A exon
chr2:27298121-27298224
Coord C2 exon
chr2:27298225-27298290
Length
104 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCT
5' ss Score
8.16
3' ss Seq
CAACTCCTTTCCTCTTTCAGAAA
3' ss Score
11.06
Exon sequences
Seq C1 exon
CCTTGTCTTACAAAATGGTAGAGGATGAACTGGCACTATTTGATAAAAGCATAAATGAATTTTGGAATAAATTCAAAAGCACTGTCAGTGACACCTCCTGTCAGATGGTGGGACTAAGAGAAACCTACAAGGACTCCATTAAAGCATTTGCAG
Seq A exon
GTACCTATATTTAACTCATAACATGCTGTTATTCTTTGTTGTTCTTGTCTGTTTTTTAGTGTAATTTCAGCTGAATTGAAACTTCAACTCCTTTCCTCTTTCAG
Seq C2 exon
AAAAGCTGTCTGTGAAATTAAAGGAAGAAGAACGGATGGTTGAAATGTTTCTGGAATATCAAAATC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010048:ENSBTAT00000013248:2
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=0.000
Domain overlap (PFAM):
C1:
PF083176=Spc7=PU(24.6=91.5),PF131661=AAA_13=PU(25.2=85.1),PF086146=ATG16=PU(27.9=76.6),PF039618=DUF342=PU(21.0=63.8),PF101864=Atg14=PU(20.0=53.2)
A:
NA
C2:
PF083176=Spc7=FE(12.6=100),PF131661=AAA_13=FE(13.8=100),PF086146=ATG16=FE(17.1=100),PF039618=DUF342=FE(15.4=100),PF101864=Atg14=FE(17.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTGTCTTACAAAATGGTAGAGGA
R:
ATTCCAGAAACATTTCAACCATCCG
Band lengths:
210-314
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]