BtaINT0013313 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018255 | ACTN1
Description
Bos taurus actinin, alpha 1 (ACTN1), mRNA. [Source:RefSeq mRNA;Acc:NM_001035351]
Coordinates
chr10:81038469-81040040:-
Coord C1 exon
chr10:81039948-81040040
Coord A exon
chr10:81038700-81039947
Coord C2 exon
chr10:81038469-81038699
Length
1248 bp
Sequences
Splice sites
5' ss Seq
GACGTGGGT
5' ss Score
3.53
3' ss Seq
CTCCCCTTCTCCCTCCACAGCTG
3' ss Score
12.57
Exon sequences
Seq C1 exon
GCCGAGACAGCAGCCAATCGCATCTGCAAGGTGCTGGCCGTCAACCAGGAGAACGAGCAGCTCATGGAGGACTACGAGAAGCTGGCCAGCGAC
Seq A exon
GTGGGTACCCTTGGGTTCTCCTGGTCTGGCCCTGGCAAGGCCTTGCCACCCTGTCCTGAGAGACCAGGGAGCCTGCAGTACCCATCCATTCCTCCAAATCCATCTCCGGGCACAGTCCCAGCCTGGGCATTGCCCCTCATCACAGCAGCTGACCGAGGGCGGCTTGGGCTCCCCCAGAGATCGGGGGTGGGGGTGGGTCAGGGGCCAGTCGGGACTTTGAAGAGCTGAGTTCCGCGCTTTTTCTATCACCTCTCTGCTCTTGATTTTTTTTCACTTGACAAATGAAAGCTGTGCCAAGAGACCTCAGAGGCCTTTTGGGCCCAGTGTACTGTTACTCTGGGAGTTTCGTTTGAACTTAAAAGGAGCGTGCAGTTCTGAGAGGATGTGAACCAGGGATAAATCAGGCTGGCTCAGGCTAGCTTAGCGGCTGGGCCCACCCAGAGGACGGGGGGGACAGGATGGGTTTGCTGTTCTGCCACTGACTGCATTTGGGTTAGAGCACCACTTGCTCCTTCCTTAATTCAGCCCCTGAACAGCTTAGCCCGGCCTCTTGGTGGACTTACTGTCCCCCAGCATAGTAAGAGCCCAGGTTCTGGGGTCCCAGTGCCTGGATTTAATCCCTGCCCTACTTCGGTCACCTTGGCAAGTCACAGAAGCTCACCATGCTTTGGTTATGTCCTCTGCCACTGGCGGGGACGGTCACAGCACTTAATCCCGTGATGACTTAGCTTGTCATCATTATTCAGATGAGTTAGTCTGGGCCACGTGATCCAGTTGCAGGGGATCACGAGTTTCCTCTCATCGTTTCCACTCCTCCACCCCCCATCACCTCATTGAAGAAACAAAATTCAGGCTGTCCTCTGCAACCTTTTCTCTTTTGAGTCAAGGACCCACATTCTAGAATCCTCAAAGGTCAGATGGCAGGGCCTCTGGCCAGCAACCATTCACCCCTCCATGGTAAGATAGGGAAATTGAGGCCCAGCCAGGTAGTAGATGAAGAACTAGAGCTTGGGTCTCCTGCTGAGTTGAGCCATCTTGCCCCCAGGTTTCCCCTTGGGGAGCAGGGAGGTTGAGTGATGCTGGCTGTGGTTTGATATATCCTAGTGGCCAGGCGTCATGGAGCCTTTGATTCTCAGAGGCAGCCTGGCCCTGTGGCCTGGGAACGGCCTGGGGTGATGGTTGGGAAAGAGTGTGCCCTCAGGAGAGATGCGGCCCCCCTCCCAGCGTCCTCCCCTTCTCCCTCCACAG
Seq C2 exon
CTGCTGGAGTGGATCCGCCGCACCATCCCATGGCTGGAGAACCGGGCACCCGAGAACACCATGCACGCCATGCAGCAGAAGCTGGAGGACTTCCGGGACTACCGGCGCCTTCACAAGCCGCCCAAGGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGCTGCGCCTCAGCAACCGGCCCGCCTTCATGCCCTCCGAGGGCAGGATGGTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018255:ENSBTAT00000024301:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PU(9.9=35.5)
A:
NA
C2:
PF0043516=Spectrin=FE(68.5=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:
GAGACAGCAGCCAATCGCATC
R:
GACCATCCTGCCCTCGGAG
Band lengths:
318-1566
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development