BtaINT0039278 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010948 | CLIC2
Description
Bos taurus chloride intracellular channel 2 (CLIC2), mRNA. [Source:RefSeq mRNA;Acc:NM_001081727]
Coordinates
chrX:38520083-38521056:+
Coord C1 exon
chrX:38520083-38520189
Coord A exon
chrX:38520190-38520874
Coord C2 exon
chrX:38520875-38521056
Length
685 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGA
5' ss Score
5.73
3' ss Seq
CTATTATTTCATTGCCTCAGCCT
3' ss Score
5.67
Exon sequences
Seq C1 exon
GTATCCTCACTTGAGTCCCAGGAACAAGGAGTCCTTTGATGTGGGCTGTAATCTCTTTGCCAAGTTTTCTGCATACATTAAGAATACACAAAAGGAGGCCAATAAGA
Seq A exon
GTAAGACATCTTTATTTAAATCTTTTTGTTTTTCTCACATTGTCACAATCACATTCTGACTCAACTAAAATAGGGTTTTCCTGAATATATAATATATATTGGGAAATACTCTTCATCTTGTTCTCTTTTCTCTCTTCCGAAATTCCCTTGAATGAAGTTTTATTGGATTTAGAACCTAATATTCAATATAGTAATCACCAACTTAGCTCAACTCGAACATTGGCATGCCAGATGTGAACTAACTACAGGATTGTATTTCTTAACCCTCCAACTCTCCCAGCTGTGTGTACCTTTAAGGTTTCTTAAACCATAGCAGCTACCATTTCCCACAAACACTCTTGAACAGGTTTACTATTCTCTGAATCAGAAGAGCTATGAGTCTCTTTTCCCACTTTCTGACTCTCCTTTAGTGATAATATGCATCACCTTTCTTTCTTTGACTCTCCTCCCAATGTACTTCCTCAAGAAAAGTCCAAAAATATTTCCACTTGCCATTTGATTAAACATCTGCCTCTGTCTTATCAGTGTGTAGTTGAGCATTTTGGTTAAATATATAGATTTTGAAGAGTCAGTGTAAGCAATATGAAAAGACAGAGATATCTAAATGTGTGAAAAGTGTATTGAGAATGTATTCAGTCATGAAGACAACAAATGTATATGTAACCCTATTATTTCATTGCCTCAG
Seq C2 exon
CCTTTGAAAAATCTCTGCTTAAGGAATTTAAGCGTCTGGATGACTATTTGAACACCCCACTTCTGGATGAAATTGATCCAGACAGTACTGAGGAACTCACAGTCTCCAGAAGATTGTTCTTGGATGGCGATCAACTGACCCTGGCTGACTGTAGTTTGTTACCCAAACTGCACATTATTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010948:ENSBTAT00000014537:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.016
Domain overlap (PFAM):
C1:
PF134171=GST_N_3=PD(0.1=0.0),PF134101=GST_C_2=FE(25.0=100)
A:
NA
C2:
PF134101=GST_C_2=FE(41.7=100)
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:
GTATCCTCACTTGAGTCCCAGGA
R:
AATAATGTGCAGTTTGGGTAACAA
Band lengths:
286-971
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]