RnoINT0122574 @ rn6
Intron Retention
Gene
ENSRNOG00000021540 | RGD1563441
Description
similar to RIKEN cDNA A030009H04 [Source:RGD Symbol;Acc:1563441]
Coordinates
chr10:55940533-55941205:+
Coord C1 exon
chr10:55940533-55941049
Coord A exon
chr10:55941050-55941149
Coord C2 exon
chr10:55941150-55941205
Length
100 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
ACCCTTCTTCTTTTCTCCAGTGC
3' ss Score
10.07
Exon sequences
Seq C1 exon
ATGCAGCTCCTGATGAGAGTGCCCTCTCTTCCCGAGCTGGGTGAGCTGGACTGCAACATCTGCTTCCGACCCTACAACCTCGGGGCCCGCGCTCCCCGCCGCCTGCCTGGCACGGCGCGCGCCCGCTGCGGCCACACGTTGTGCACCGCTTGCCTGCGCGAGCTGGCAGCGCGGGGAGACGGCAGCCGCACGGCCGCGCGTGTGGTGCGCCTGCGCCGTGTTGTCACGTGCCCGTTCTGCCGCGCGCCTTCCCCGCTCCCGCGCGGCGGCATCACGGAGATCGCGCTAGATCCTGACTTGTGGTCACGGCTGGAGGAAGAAGCCCAGGCTGAGTGTGAAGGAGACCCGATGGGGAGCCCGGCCAAAGAAAGCGGAGAGGATGGAGAGGACGACGACGGGGAACAGGAGAGCGAGATGGGGGCGGGACCTTCAAGTGCCGGTTGGCGCGCGCTTCGCCGAATTTTGGACAGGGTCCTGGCGCCCGCGCGCCGCTTGCGGCGTCCGTTGCCTAGCAATG
Seq A exon
GTGAGGGACCGTGTAGGGAGGATACTGGGTATCTCGCGCTGAAGAATGCTGGGTCAGGTTGCATCCCCCTGTTGCCACTAACCCTTCTTCTTTTCTCCAG
Seq C2 exon
TGCTCTACTGTCCAGAGGTCAAGGACATTGCCCACATGACGCGTTGTACGCTGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021540:ENSRNOT00000012061:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.208 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF146341=zf-RING_5=WD(100=38.2),PF154511=DUF4632=PU(78.9=32.4)
A:
NA
C2:
PF154511=DUF4632=PD(19.7=73.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCGCTAGATCCTGACTTGTG
R:
TGACCTCTGGACAGTAGAGCA
Band lengths:
257-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]