BtaINT0030538 @ bosTau6
Intron Retention
Gene
ENSBTAG00000022000 | CACNB2
Description
Bos taurus calcium channel, voltage-dependent, beta 2 subunit (CACNB2), mRNA. [Source:RefSeq mRNA;Acc:NM_175789]
Coordinates
chr13:33280515-33282494:+
Coord C1 exon
chr13:33280515-33280666
Coord A exon
chr13:33280667-33282398
Coord C2 exon
chr13:33282399-33282494
Length
1732 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
AAAAACCTCGTCTTTTGCAGGTT
3' ss Score
9.23
Exon sequences
Seq C1 exon
CGGAAGTTCAGAGTGAAATCGAAAGGATTTTTGAACTTGCAAGAACACTGCAACTGGTGGTCCTTGACGCGGACACTATCAATCACCCAGCCCAGCTCAGTAAAACCTCTCTGGCCCCTATTATAGTGTATGTCAAGATTTCTTCTCCTAAG
Seq A exon
GTAAGCAGGGCTGTTAACCGTTTGTTCTGCAGTGAAACTGTACTAAAATGTGTGCTTACAGTCTGCTTTCAGAACAGGCTGCTTCTTAATCCGTCACTAAGGCTTTGAAGATAGATGTGGTAGATGAGAAGCGTTAAGATTCATATAAGCAGAGAGTGATGATAAGTTTCATGGCTGAGAACAGTGATTTCCAAAGTGTGGCCTGTGGAGTCCTGGTGGGGGAGGTTTGGAGACACTTTCAGAGGACCTAGGTCATTTCCCTGATAATCCTCATTGTCCTCCTCTTCCACTGGCCTGACCTTTGTACTGATGGTGCAAAAGAAGTGGTGGGAATGTCTAAGCAGGAAGCAAGACCACACCAGCACCGGCAGCTGCTGCATTCTTCCTCACCATGAGCTACCAGGTTATAAGTTTCACTTAATGTCCTAATGAAAATCCATCTACTGCCACTTTTTTAGAGGGGTTTGAAAACACTGGATACGTTAGTTCCTGGTATGTATTTTGACAGGAGATCCTTACTGTTGTCTAAAGGCATTACTAAAATATAAAACTATGTCCCAGACTAGGTCAGAATAAGGTACATTTTTTTTACTGGCAACCTTTAAGTTAGATGAGAAGATGCCTCTTTCGCCTATGATTTTAGATGGATTCTTGTGAAATGTCTGAGTATTAATAAGTTAACTGTGCTAGAAATTAAGATTTTACAATCATTAACTCTTACAATTTCTGGTGTCCACACTAAAAATACAAAAACTGGTGATATTAGTTTTAAGAATGTATTTTATTTAAGCCAAAAATATCCTATTTGTTATTTTAATATTTAGTCAATAAAGTGTTATTTGTGGTACTTTGAAGTAGCAAAATTGTTTATTAAATTTTGACTCTTCAAAAAGGTGCTACCAGCCTTTTTAATATTCTACGTAACAAAATGGGAGGCACACGTCAAGTTCTTCATCTGCACACTCAAAGTCAGTTACTTGAGGACAACTACTGGTATGACTATTGCAGTCATCTTAGAACACCATTTTTATTGGAAAGAACAAATGACATGCCATTCAAATTTCAGGACAAATCAATGGAATTTAATAGAGTAGGGTTTCAGATGTTCCATGGCAGCTAATCTTTAAAAAGCTACCACTTGTTTACTGTAGTATCAAAGAAAAATATCCACAATTATCTGAAAAGGTTACTAAAATAGTCCTCCTCTTCTAAATTATGTATCTGGAAGAGGCTGGATTTTCTTCACGTATTTCAAAGTAATGTACTGTGGCAGATTAAATGTAGAAAGAGGAAACATTGGTTATCTTCTGTGAAGTCAGGTTGTAGAGAAATTTGCAAACAATTTTTATCGAAATAAGTGATGTAAGTTAACATGCAACAAGTTTATTGGTCATTCTTAAATGAATTTCTCAGTTTTAATGTCTAGTATGTAATATTCTAGTTCACATAAAAAGCTCTTGGGATTTCTCAACAGTTTTTAAAAACATAAATCATGAGTGATAAAGTTTGAGAAGTGCTAGCCTTAAAAAAAAGGTTCAGAATAATACATCCTGGTGGTTTTTGAAGCTTGCCACCAAGATGTATTAATTTTCCAGATCATCTTAGATATTGTTTTCTTGCCTAGTAAACCGTGAGTGCTGTATGAAAAAGGTCCCAGAGAAAAGCGTGAATAATGAACCTTGTTGTCTACCTGAGTACAGACGCTCCTGTTTAAAAACCTCGTCTTTTGCAG
Seq C2 exon
GTTTTACAGAGGTTAATAAAGTCTCGAGGGAAATCTCAAGCGAAGCACCTCAATGTCCAGATGGTGGCGGCAGATAAGCTAGCTCAGTGTCCTCCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000022000:ENSBTAT00000029344:10
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=0.000
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=FE(27.6=100)
A:
NA
C2:
PF0062516=Guanylate_kin=FE(17.1=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:
CGGAAGTTCAGAGTGAAATCGA
R:
TGGAGGACACTGAGCTAGCTT
Band lengths:
248-1980
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development