RnoINT0125471 @ rn6
Intron Retention
Gene
ENSRNOG00000009196 | Rc3h2
Description
ring finger and CCCH-type domains 2 [Source:RGD Symbol;Acc:1304833]
Coordinates
chr3:21651137-21652725:-
Coord C1 exon
chr3:21652607-21652725
Coord A exon
chr3:21651250-21652606
Coord C2 exon
chr3:21651137-21651249
Length
1357 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
TAAATGTTTTGTTTGTGTAGCCA
3' ss Score
5.59
Exon sequences
Seq C1 exon
ATGCTGTTTCACCAACTTGGGAGCAACTGGAAAATGCAATGGTAGCTGTTAAAACAGTGGTTCATGGTCTTGTGGACTTCATACAAAATTATAGTAGGAAAGGTCATGAGACACCCCAG
Seq A exon
GTAAGTTGACTTATTACACTTCTAACTACTGCTGTATCCAACACAGCTTCATCCTGAACATACTAACAATTTTATTGGCAAATGGACTTGGATTCTAACCCTTTCCTATTAGACGTTGTGTGTGAGAGGAGGATGTTCATGTGTATGTGCATGTGTAGCTGCACAGACTTTGACACTGAGTGACATACATAGCCTTTGCAAATTTTTATTCTGTACTCTTGAGAGAAACTCCCTTCTTATTGTATTTGGTTAGCATTTCATTTTATAAAGAGTTTAGAGGTATTTTGAACATGAATTCACTGAATTTCAAGATGTTTGATCATTGATTTCTTCCACACATTTTGTCTAGTCCTTTTTACAGCTGAAGTTCTTTTTTTCCTTTGCTGTCTCTCAAATAAATTTGTTTTGTAATATATATGGAATTTGAAATTCCTCAATATTTGTAGTGTACTTTAGAAGGAGAAGTGGAAATACAATCCCTTATCCAAATGTCTTTTCATTTGTTCAGTTAAATATTATATTAAAAGTTATGCTATCAATATCTAACAAGGTAGGGCCAAAAGTACTCCAAAATCTGTTAACTTTTTAGTTTATTAAATAAAATTTTAATTTATTTAGACTACCACAGTATTTAATATCAAATGAATAATATTTTTATTTAAGGTCACAATAATAAAATTTTCTAAGAGTTTGATGCATATTATACACTTTTTTTCCTTTTTTTTTTTTTCTTGGTTTTTCGAGACAGGGTTTTTTTGTATAGCCCTGGCTGTCCTAAAACTCTCTATAGACCAGGCTGGTCTTGAAGTTACAGAGATTTGTCTGCCTTTGCCTTCTGAGTGCTGGGATTATAAGTATGCACCACTACCACAGGGTTGAATAGTGCATTTTTATATCTTCCCTCACTATTTGCCTGTGACTAGAGTTGTGCATGGAAGTCAACTATAAAGTAATAATTTTTTTACTCCAACTGTTTTGGGGAAGCTTTTAAATGGGTAAAGATCATCATAGTTTCCATTTTTTTAAATACCTTTAAAAATTATTTAATTTTGTTTTCACAATTCGAAGATTAAGAAATAGATAGATGGGCTGGAGAGATGGCTCAGCCGTTAAAGGCTAGGCTCACAACCAAAAATGTAAGAAATATATCAATTTCAGATAACCTTCAGAAAGAAGACCTGAAGGCTTCCTCAAGGATATCTACCACTCTTAAAGTAGGAAATAATGGATAGAACTTGTTTCGGCATGAGAATTACGTGTCTGATGTGAAAAAGACTTAAGTCTTTTAAGTTCTGAAGTCTAAAGAGTGAATAATAACTGATACCTTTTCCATCTGCTAAATGTTTTGTTTGTGTAG
Seq C2 exon
CCACAGCCAAACAGCAAGTATAAAACTAGTATGTGCCGAGATTTACGACAACAAGGGGGTTGTCCACGAGGAACAAATTGTACATTTGCCCATTCTCAGGAAGAGCTTGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000009196:ENSRNOT00000012354:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.350 A=NA C2=0.789
Domain overlap (PFAM):
C1:
PF0028516=Citrate_synt=FE(25.5=100)
A:
NA
C2:
PF0028516=Citrate_synt=PD(18.3=73.7),PF0064219=zf-CCCH=WD(100=71.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGTTTCACCAACTTGGGA
R:
TTTCAAGCTCTTCCTGAGAATGGG
Band lengths:
230-1587
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]