RnoINT0015311 @ rn6
Intron Retention
Gene
ENSRNOG00000020205 | Agrn
Description
agrin [Source:RGD Symbol;Acc:2067]
Coordinates
chr5:173598286-173598972:-
Coord C1 exon
chr5:173598835-173598972
Coord A exon
chr5:173598414-173598834
Coord C2 exon
chr5:173598286-173598413
Length
421 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
TCACTGCCCCTCCCCCACAGCTA
3' ss Score
10.37
Exon sequences
Seq C1 exon
GACTTGAGCCCCCGGTGGGCAGCATTGTGGTGACCCATGGGCCACCCATCGAGAGGGCTTCCTGCTACAACTCACCTTTGGGCTGCTGCTCAGATGGCAAGACACCCTCACTGGACTCCGAAGGCTCCAACTGTCCTG
Seq A exon
GTAAGTGAACCTTGGGGAAGGGATGAGCTTGAGGAACAGCATAGATAGGAGTGCTGTCTTCACCCCTCGGCAGCAGGTCGGTATAAGGTTATGGTGTTCTGGCTCCAGCACTTCGAGTGTGTGGGGGGATTAAGTTTGGCACACACATGCACTCTGGTTTCAACCATTGAATATGCATGTGTGCCAAGGACCCGATACCTAACCCATCTTTCTCCTTGCAAGCCAGCTTGGGGCACCTGCTCCTAGGAATTGCCTGGTAACTGACGCCAGCCCAGCCCTGGGGTTCCCACTTACTAACCCCATGGTCATCTGACTAACACCCCCCGCCCTGCACCCCACATGGCTTGCTGTGGGCCTTGCTTCTGTGGCTGCCTCGGAGGCTAGATGGCATTGGCAGGGCCTCACTGCCCCTCCCCCACAG
Seq C2 exon
CTACCAAGGCATTCCAGGGCGTGCTGGAGCTTGAGGGGGTCGAGGGACAGGAACTGTTCTACACACCTGAGATGGCTGACCCCAAGTCAGAGTTGTTTGGGGAGACCGCAAGGAGCATTGAAAGCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020205:ENSRNOT00000045678:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.468 A=NA C2=0.163
Domain overlap (PFAM):
C1:
PF0139015=SEA=PU(0.9=2.1)
A:
NA
C2:
PF0139015=SEA=FE(38.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTTGAGCCCCCGGTGG
R:
GTGCTTTCAATGCTCCTTGCG
Band lengths:
265-686
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]