RnoINT0015321 @ rn6
Intron Retention
Gene
ENSRNOG00000020205 | Agrn
Description
agrin [Source:RGD Symbol;Acc:2067]
Coordinates
chr5:173595410-173595755:-
Coord C1 exon
chr5:173595659-173595755
Coord A exon
chr5:173595575-173595658
Coord C2 exon
chr5:173595410-173595574
Length
84 bp
Sequences
Splice sites
5' ss Seq
AGGGTTAGT
5' ss Score
5.02
3' ss Seq
ACAACTCCACGTGACCCCAGGGA
3' ss Score
4.13
Exon sequences
Seq C1 exon
TCCTGGAGACTGCTGGCTCCCGGCCCTTCCTGGCTGACTTTAATGGCTTCTCCTACCTGGAACTGAAAGGCTTGCACACCTTCGAGAGAGACCTAGG
Seq A exon
GTTAGTAGGGCAGGAGGATTAAGGGAAGGGAGCTAACCTGATGAGGAGACCATGACACGCTCCCACAACTCCACGTGACCCCAG
Seq C2 exon
GGAGAAGATGGCGCTGGAGATGGTGTTCTTGGCTCGTGGGCCCAGTGGCTTACTCCTCTACAATGGGCAGAAGACAGATGGCAAGGGGGACTTTGTATCCCTGGCCCTGCATAACCGGCACCTAGAGTTCTGCTATGACCTTGGCAAGGGGGCTGCAGTCATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020205:ENSRNOT00000045678:28
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005418=Laminin_G_1=PU(33.8=82.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGAACTGAAAGGCTTGCA
R:
ACTCTAGGTGCCGGTTATGCA
Band lengths:
170-254
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]