BtaINT0010542 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018137 | A2M
Description
Bos taurus alpha-2-macroglobulin (A2M), mRNA. [Source:RefSeq mRNA;Acc:NM_001109795]
Coordinates
chr5:101309603-101309967:+
Coord C1 exon
chr5:101309603-101309717
Coord A exon
chr5:101309718-101309857
Coord C2 exon
chr5:101309858-101309967
Length
140 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
ATTTTTTCCTTCTTTTTCAGAGG
3' ss Score
11.26
Exon sequences
Seq C1 exon
CTGAACAATGAGGGCTGCTTCTCTCAGCAAGTAAACACCAAGATCTTCCAGTTGAAGAGACAAGAGTTTGAAATGAAAATCGAAGTGGAAGCCAAGATCCAAGAAGAAGGAACAG
Seq A exon
GTGTGTATACTTCCTGGGTATGGGAAAAGAACAACGGACACTGATTTAGTTCCTTTGCCAAATTATGAAAGGGAGGTGGTGGTGTAAGTTCAGGGAGAAAATCCTTCCAAATGAGAATGTATTTTTTCCTTCTTTTTCAG
Seq C2 exon
AGGTGGAATTAACTGGAAAGGGGGCCACTGAAATAACAACAACCATCACCAAACTCTCATTTGTCACAGTGGACTCAAACCTTAGACGAGGAATTCCTTTCACGGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018137:ENSBTAT00000006167:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.189
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0236911=Big_1=PU(34.0=86.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAATGAGGGCTGCTTCTCTCA
R:
CTTCCCCGTGAAAGGAATTCC
Band lengths:
220-360
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]