RnoINT0036164 @ rn6
Intron Retention
Gene
ENSRNOG00000017939 | Chn1
Description
chimerin 1 [Source:RGD Symbol;Acc:620139]
Coordinates
chr3:60525576-60526514:-
Coord C1 exon
chr3:60526341-60526514
Coord A exon
chr3:60525654-60526340
Coord C2 exon
chr3:60525576-60525653
Length
687 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CTTCAGTCCTTTCTCCTCAGGTC
3' ss Score
8.92
Exon sequences
Seq C1 exon
ATTGTGGGTTGAATGTTCATAAGCAGTGTTCCAAGATGGTCCCCAATGACTGTAAGCCAGACCTGAAGCACGTGAAGAAGGTGTATAGCTGTGACCTGACAACACTCGTGAAAGCTCACATCACCAAGAGGCCCATGGTGGTAGACATGTGCATCAGGGAGATCGAGTCCAGAG
Seq A exon
GTGAGGCGTTTCTGTGCAGGCTGCCAACGCCTTCACTCGAGCCACTCTAGGCGCATCTTCAGTGGTGGTGTTGTCTTCAGTGATGTGGAACAGTGTCAGGAAATGTGCTCTCACAGTGTATTAATGAGCAAGTAGCTTGATTTCAAGGAACATTTAACCGGTTATGGAAAGTAGTATTTAGGAGACATTAATGGATGATGTCTGCGGTCTGCAGAGATCTCTGTGCAGAGATGGATTCATCTTTCGGGTTTTAAGTTCTTCTCACGCCAGGAAGCAAGGCAGAAATGCCCTATTAAAACGTCAAGAGCAGAAATCTGAGCTGCACCCTAATTATTCTTACCCACTTGGGAAAACAGCCACAGGCCTGCTGATGCAGCTTTCTGTTATGTAAAAGGCTTTATGATGGAATTGGGTGACAAATGATTTCCCTTAAGATTTAATGTTATTTGGTCTAATTAGGCAACATGATGGCCAAATTATAAATATCCAGGTGACAGTAGGTCAGAAGTAGAAACAATGGGACAGACTCACTTTTGGAGGATGTGGAAGACGACTTGTAGCGTGTGTGAGTGAGTTATTTTTTTCTAACACATATTTGCCCAGCTTGAAGTATGAGAAAAGTTGAAATGTGAAAGAAGGTGTGAGTTAACAGACAGTCAGCCCCATGCTTCAGTCCTTTCTCCTCAG
Seq C2 exon
GTCTGAATTCTGAAGGACTCTACCGAGTGTCGGGATTTAGTGACCTAATTGAAGACGTCAAGATGGCTTTTGATAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017939:ENSRNOT00000068745:5
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:
PF0231811=FYVE_2=PD(38.4=72.9),PF0013017=C1_1=PD(37.7=33.9),PF0062022=RhoGAP=PU(14.9=23.7)
A:
NA
C2:
PF0062022=RhoGAP=FE(16.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGTGGGTTGAATGTTCATAAGCA
R:
TCAAAAGCCATCTTGACGTCTTCA
Band lengths:
246-933
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]