BtaINT0013322 @ bosTau6
Intron Retention
Gene
ENSBTAG00000009696 | ACTN2
Description
Bos taurus actinin, alpha 2 (ACTN2), mRNA. [Source:RefSeq mRNA;Acc:NM_001034635]
Coordinates
chr28:9443121-9445209:+
Coord C1 exon
chr28:9443121-9443267
Coord A exon
chr28:9443268-9445143
Coord C2 exon
chr28:9445144-9445209
Length
1876 bp
Sequences
Splice sites
5' ss Seq
AGGGTACCT
5' ss Score
4.24
3' ss Seq
TTCTTTCTTTTTGTTGAAAGAGG
3' ss Score
2.86
Exon sequences
Seq C1 exon
CACATTCGTGTGGGCTGGGAGCTGCTGCTGACGACTATCGCCAGAACCATCAACGAAGTGGAGACCCAGATCCTGACGAGAGATGCGAAGGGCATCACCCAGGAGCAGATGAATGAGTTCAGAGCCTCCTTCAACCACTTCGACAGG
Seq A exon
GTACCTCACTCCTACTTATTTGAAAGGCAGTGCTGGGGACATCAAAAGACATATTTGAAATAGCAGTCATGCTGTTATTTTTAAGTCGTCATGTCCTTAAAATTTACTGGGAAACAGGATGATTAAGGCCAGAGGAAAAGAGCCACTGAAATGAAGTGTGCTAAGTTCTGATGTTGCTCAAGGTGACATCAGACAAGGTCTAGGTTTGTGGGCCCTTTTATACAGATCACTTAACAAATGCCTTTGTAGTTGGGAGCAAAGCAAGATTTATTCTAAGTGAAAGTACATCCTTAACAGAATATAGTTGAAGGATTTAGGTCATTTTCTAAGCACTTAAATACAAAGCTCTAATGTACTTTTCCTAATTAACTATTTAGGTAAAGCACCTGATGAAAATTAGCCTACTCTTTTGCCATAAAACTTAATTTTCTTTTTTAACGAACAAAATCAGCTCATGAAATGTTGTAAGTAAAATGTATCAACAAAATGATGACCATATAAAAAGTTTAGTGCTGCCCTTAAAATATTATCTAATATTTTGATTTGAATATAATTGGGTAAAACCAGTTCTTCACAAGAAAATGCCCAGTTTGCTTATCATTTAGTTAATAGTGACTCTTAAGGCCACATTCCATTTGTTAAAAGATCCCTAACAAAGTATATTTCATTCTTTTGCTCAGGACCCTGTGTATGATTTACAGATATTAGTTAAATGGTTCTTAAAATGCCTGTGGACTAGACCAGCCATATTCAGGCCTATTAATGAGTTCAGAAAGTAGACTTCTGATCAGGGAGCTGAGGCATAAATAAAGTATTATATACAGACATGGATACTAAAGTTATTTTGGCTTCAGCACAGCTGTACTGTTGATGCTATCACACTGACCTGACTTCCTTCAGGTCGGGTCTTTTTCCTTCCATGGAGGGAAATAATTGACCATTGTTCCTGCATATATCACCTGGGCTTTTAGGAGGACAGCTCCGCTTGTTTGGGCCACTTCAGAGAGGGGAAATCCACATCTATTTGAATCCAGGGTAACGAGACTGTCTCTTGCAACAAAGGTGCAAAGGAGGACAATGCAGAACCTGCCAAGTTTAAAAGTTTAAGTAAAGCAACTATAGTCCAATAAAAATTAATTAAAAAACAAAAAACCCAGCTTCCCAGTTGCAGTGAATAATTTTCATTCATCTAACAAGAACTCCTTTCAAACACGTGTATACCTGTGGCGGATTCATGTTGATATATGGCAAAACCAATACAATATTGTAAAGTTAAAAAAAAAAAATAAAATAAAACTAAGAAGGAGTGAAAAATTAAAAAAAAAAAAAAAAAGAACTCCTTCCATACTAGCTTTCCCTTCCCGCCGCCCAGTAAAAGAATTAATAGAAGTTTAAGTTAAGGATTCTACGTCTTGGAGGGACTTGGGCCTGAGAGTGGCTGTAGGGTAACTGCAGCATGAATCCTAGCCCTGCTGTCATCTTTGGGGGACTTTTACAAGCGAGGTCTGCCTGGGGCCTCAAGAGTGTGAGGCGTTCTCACAACACTTACATTGTGTTCGGTCATCAGTGGGTGGCAGTGGGCAGCTTCTGACATGGTCATTTTCAGTAGCACTGGGTATTCCTCCTGCTTTCTAAGGTGTGGTCTCCATTTCTGACTGCTGTTTACCTTCCTTCCCTACTTTTTCCTTTTTAAGAAATTATTTTGTAATGTAATGTCCCTGTGTTGGGCCTGTCCTTTCTGTAAATCAGACCTTTAAAAATTCTTTGGCAGATGTCAAAGTGTCCCTTCTCTTTCTGGATTTTGTTCCCTGGTCAAGTCGAGTTGTTTATTTTGCGTCTAACACTCAACTTCTTTCTTCTTTCTTTTTGTTGAAAG
Seq C2 exon
AGGAAGAATGGTCTAATGGATCATGAGGATTTCAGAGCCTGCCTGATCTCCATGGGTTATGACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000009696:ENSBTAT00000012786:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.061 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PD(20.2=42.9),PF138331=EF-hand_8=PU(15.4=20.4)
A:
NA
C2:
PF138331=EF-hand_8=FE(32.3=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:
CACATTCGTGTGGGCTGGG
R:
TAACCCATGGAGATCAGGCAGG
Band lengths:
206-2082
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]