BtaINT0039281 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015085 | CLIC3
Description
Bos taurus chloride intracellular channel 3 (CLIC3), mRNA. [Source:RefSeq mRNA;Acc:NM_001100301]
Coordinates
chr11:106229806-106230113:+
Coord C1 exon
chr11:106229806-106229915
Coord A exon
chr11:106229916-106229987
Coord C2 exon
chr11:106229988-106230113
Length
72 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
GCCCTGCCTCATGCCCACAGGTC
3' ss Score
11.02
Exon sequences
Seq C1 exon
GCCAGTGAGGACGGCGAGAGTGTGGGCCACTGCCCCTCCTGCCAGAGGCTCTTCATGATTCTGCTTCTCAAGGGCGTGCCCTTCACACTCACCACCGTGGACACCCGCAG
Seq A exon
GTGAGCCCTGCCCCGGGACCCTGACCTCGCACTCCTCTGCCAGCCACCTCCCGCCCTGCCTCATGCCCACAG
Seq C2 exon
GTCCCCGGAGGTGCTGAAGGACTTCGCCCCAGGCTCCCAGCTGCCCATCCTGCTCTGCGACGGCGACGCCAAAACCGACACGCTGCAGATCGAGGAGTTTCTGGAGGAGACGCTGGGGCCCCCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015085:ENSBTAT00000020075:2
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=0.023
Domain overlap (PFAM):
C1:
PF134171=GST_N_3=PU(41.1=81.1)
A:
NA
C2:
PF134171=GST_N_3=FE(57.5=100),PF134101=GST_C_2=PU(9.2=27.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTCTGCTTCTCAAGGGCGTG
R:
AGCGTCTCCTCCAGAAACTCC
Band lengths:
167-239
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development