BtaINT0015704 @ bosTau6
Intron Retention
Gene
ENSBTAG00000014420 | AGER
Description
Bos taurus advanced glycosylation end product-specific receptor (AGER), mRNA. [Source:RefSeq mRNA;Acc:NM_173982]
Coordinates
chr23:27009687-27010158:+
Coord C1 exon
chr23:27009687-27009751
Coord A exon
chr23:27009752-27010000
Coord C2 exon
chr23:27010001-27010158
Length
249 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
CCGGGTCTTCCACATTGCAGGCA
3' ss Score
7.04
Exon sequences
Seq C1 exon
AGATTCCTGGGAAGCCAGAAATTGTTGATCCTGCCTCTGAACTCATGGCTGGTGTCCCCAATAAG
Seq A exon
GTAGAGGATGAAAAGGGGAGACGTGGAAAGGGGTCCTGAGGATGGGAGGGGAGTGTAGCTCTGTGTGTGTGTGTGTGTGTGTATGTATCACTCAGTTGTGTCTGACTCTTTGTGACCCCATGGACTGTAGCCCGCCAGGCTCCTCTATCCATGGGATACTCAGGGCAAGAATACTGGAGTGGCTTGCCAGTTCCTTCTCCAGGGGATCTTCCTGACCTAGGAATCAAACCCGGGTCTTCCACATTGCAG
Seq C2 exon
GCAGATTCTTTACCATCTGAGCAACTGGATTCTCTTATTTCCAGAGATGATGAAGTTGATTTTTCCCCAGGTGGGGACATGTGTGTCCGAGGGGGGCTACCCTGCAGGGACTCTTAACTGGCTCTTGGATGGGAAAACTCTGATTCCTGATGGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000014420:ENSBTAT00000065259:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.239 A=NA C2=0.056
Domain overlap (PFAM):
C1:
PF082057=C2-set_2=PU(16.7=72.7)
A:
NA
C2:
PF082057=C2-set_2=PU(41.9=66.7)
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:
AGATTCCTGGGAAGCCAGAAA
R:
TGCCATCAGGAATCAGAGTTTTCC
Band lengths:
220-469
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]