BtaINT0015703 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014420 | AGER
Description
Bos taurus advanced glycosylation end product-specific receptor (AGER), mRNA. [Source:RefSeq mRNA;Acc:NM_173982]
Coordinates
chr23:27009314-27009751:+
Coord C1 exon
chr23:27009314-27009506
Coord A exon
chr23:27009507-27009686
Coord C2 exon
chr23:27009687-27009751
Length
180 bp
Sequences
Splice sites
5' ss Seq
ATCGTAAGG
5' ss Score
5.84
3' ss Seq
AGGAATTTTCCCTCCTTCAGAGA
3' ss Score
7.26
Exon sequences
Seq C1 exon
AACACAGGCCGGACAGAAGCTTGGAAAGTCCTGTCTCCCCAGGGAGACCCCTGGGATAGCGTGGCTCGGGTCCTCCCCAACGGCTCCCTCCTCCTGCCGGCTGTTGGGATCCAGGATGAGGGGACTTTCCGGTGCCGGGCAACGAGCCGGAGCGGAAAGGAGACCAAGTCTAACTACCGAGTCCGAGTCTATC
Seq A exon
GTAAGGGTTCCCAGGACCTCTTCACCACCCACCTCTCATCTAAGGAAAAGCCTTCGACCCCAGCCCTTGACTCCTTGGCCCTGGCCTGGGAGAACTTGACTTCAGCTGCCCCCATTCCCACACCCAGGGTGTGAGAATCTTCAAAGCTGTGGCCTCTGATAGGAATTTTCCCTCCTTCAG
Seq C2 exon
AGATTCCTGGGAAGCCAGAAATTGTTGATCCTGCCTCTGAACTCATGGCTGGTGTCCCCAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014420:ENSBTAT00000065259:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.249 A=NA C2=0.239
Domain overlap (PFAM):
C1:
PF138951=Ig_2=PD(62.6=95.4)
A:
NA
C2:
PF082057=C2-set_2=PU(16.7=72.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGACAGAAGCTTGGAAAGT
R:
GGACACCAGCCATGAGTTCAG
Band lengths:
242-422
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]