BtaINT0010519 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018137 | A2M
Description
Bos taurus alpha-2-macroglobulin (A2M), mRNA. [Source:RefSeq mRNA;Acc:NM_001109795]
Coordinates
chr5:101325097-101325688:+
Coord C1 exon
chr5:101325097-101325220
Coord A exon
chr5:101325221-101325566
Coord C2 exon
chr5:101325567-101325688
Length
346 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGA
5' ss Score
6.95
3' ss Seq
TACTGGTCCCCATTTTCTAGGGA
3' ss Score
7.72
Exon sequences
Seq C1 exon
GTCAGTGTGCAACTAGAAGCCTCTCCTGCATTCCTAGCTGTTCCAGAAAAGGAACAAGAGACTTATTGCATCTGTGGGAATGGCCGGCAGACTGTGTCCTGGGCGGTAACTCCAAAGTCCTTAG
Seq A exon
GTGAGAGACAGCCTCTCATAGGCAATTCTGTACCTAAAGATTGTATGTATATATGGGATCCTTATATCCAAGCAAAGAATGTGCCCCCTCTCCACCAGATGGTAGAATGTTTTTCTCTCTTTCATTCTAGGATGTCTAGAAGGATACCCCCTTTCCCTCACCTCCATCTCTACCTTGGATTCTCAGTATCATTAGCCTCTAGTCTATGCTACTTACATTCCTGTTCCTATATTTTTATAAACCAAAATAAAAAGTCACATAGCATTAAACATGTATAAACCTTGGGGTTTGGAGTCACTGAAGAAGACAGAGATGGGGCTCATCTCTACTGGTCCCCATTTTCTAG
Seq C2 exon
GGAATGTGAATTTCACAGTGAGTGCAGAGGCAGTGGAGTCTCAAGAGCTATGTGGGAGTGAAGTGCCTGTGGTCCCTGAGCATGGAAGGAAAGACACAATCATCAAGCCCCTGTTGGTTGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018137:ENSBTAT00000006167:20
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=0.024
Domain overlap (PFAM):
C1:
PF0020717=A2M=PD(4.4=9.5)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCAGTGTGCAACTAGAAGCCT
R:
TTCAACCAACAGGGGCTTGAT
Band lengths:
246-592
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]