RnoINT0036169 @ rn6
Intron Retention
Gene
ENSRNOG00000009411 | Chn2
Description
chimerin 2 [Source:RGD Symbol;Acc:620140]
Coordinates
chr4:84423892-84424881:+
Coord C1 exon
chr4:84423892-84424016
Coord A exon
chr4:84424017-84424803
Coord C2 exon
chr4:84424804-84424881
Length
787 bp
Sequences
Splice sites
5' ss Seq
AATGTATAA
5' ss Score
-3.61
3' ss Seq
AGCTCTTTGCCTGTTCACAGATC
3' ss Score
9.31
Exon sequences
Seq C1 exon
AAGAATCCTGCAGTGTGGCAGCCTGCTTCTCACCTTCTCACCTCGGAGTTGGCTGAACCCAGAACCAAATGCTTTGCACGTCTCCCGTCAACTGCTTGGACTCAGTTTGTTGCACTTCGATAAAT
Seq A exon
GTATAAGACTAAAGATAAGGTTTTCTAGTACCAGACAGCTTTTATAAAATAGATGTGACTTGATCACTTTAAGATTAAAAAATCATCTGGGTTTAAAGGGATAGTCTGCTGGAAGTCAGCTCAGAATGAGGTTCATAAGCCCAGAATAAATGGACACAGCTTTCACTTTGAACATCGCAACGACCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGTGTGTGTGGGTGTGGGTGTGGGTGCGTATGTCTGTCTGTGTCTGTGTATCTGTGAGTGCTGTACACATTGCTGCCTCCCTGGATCCCCTGCCTCCCTGGATCCCCTGTGCTGACTGGATATTCTGGGAGTTGCTATATATGAATGTGTGCTATTGTTCCAGGCACATGCCAGCCTTAAGAAACAGCACAAAGCAGGCCCATCCCTCTTCAGCCAGAGCCCCCTCCATCACTCAAACAGTCCCTTCCAGGTCACATGCCTCTCAGACCTCTACAGACAGAGCACAGCTGCCTCAAGTCTGCTGCCCAACATTAGCGGCAGTCCCAGAACTCCGCTGGCTGAGGAGAGCGTGCTTCCACAGGAGACACCCAGAAGAGCTGAGATCCAAGTGCTATGTTCTCTCAGGAATTGTGGCTGGAAAATGAGAGAAAATGCACTGTGGTTCGGAAGTCCAAGCCCAGCAGGAAGCGCCAAGAGCTGTTGGCCATTGCATTTGGGGTAAAGGTGGGACTCAAAGGTGGCTTTCTCTGGTCTCCTCTCAAGCTCTTTGCCTGTTCACAG
Seq C2 exon
ATCTCTTCACTGGTCCGAAGAGCTGCCCTCACACACAATGACAACCACTTCAACTATGAGAAGACACACAACTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009411:ENSRNOT00000012655:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0013017=C1_1=PU(5.7=11.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGAATCCTGCAGTGTGGCA
R:
CTTGAAGTTGTGTGTCTTCTCAT
Band lengths:
203-990
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]