RnoINT0146217 @ rn6
Intron Retention
Gene
ENSRNOG00000033389 | Susd2
Description
sushi domain containing 2 [Source:RGD Symbol;Acc:1308595]
Coordinates
chr20:13965121-13966660:+
Coord C1 exon
chr20:13965121-13965266
Coord A exon
chr20:13965267-13966452
Coord C2 exon
chr20:13966453-13966660
Length
1186 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
CACCGGGCTTTCTTTTCCAGGTA
3' ss Score
11.53
Exon sequences
Seq C1 exon
GGCCCGCAGGGAGAAAGCCTGTCCGGCAATCTCTGAGCCACTGTGCTGCCCGCTGGTTGCAAACGCAGGGCACATCATGAAGCTGGCTGTGCTGCCCTGGATTTTGATGCTGCTCTCGACAATCCCAGGCCCCGGGCTTACAGCAG
Seq A exon
GTATGCCTCACTTTGCTCTTCTGACCCCTCCCCTGTTCATTTGCCTGATCAGCCAGGCCCTAAGCAGATACCTCTCCGGGCTCAGCGTCTGCCCATCTGGTAGTCCATCTGTGACTGTACTGGGGGGTACTGGGAAGAAATTGGGAGGCTCCTGGATCTAGACACTTCTGGGAGAGATGGGAGGCCTGAATCAAACTCATCGTGCACTCACATAATGGCCTGGGAGGGAATCCGGGAAGACCAAAGAGCATGCGCCCCAAACCTCGGTGAAGGGTGCAATCACACAGAGGACCTCTGCCTCTCATCTGTACCTGCGCTGGTCCCTATCAGCTCAACCAAGAAAGTCTAGCAAGAAGGATGAGCTCAGAGCTATGGTCTTTGACTGAGCTGAGCTGGGAGTCAACCAGCCTATAGTCTCCTGCTTCGACCTATCATCCCTTGCAGGGAAGTGCCACCACCCTTCTGGTATTTTATCTCACAGCATCTTGAAGCCTCTTCCCACACCCCTTGTAGTCATTAAACCTTAGCCGATAGATAAATAGTTATTGCTGCTCCTGGAGTAGAAGCTTAGAGAAGTGGCCTAGTAGCTTGGTCCGCAGCCTGTCTCCTGTAGCATATCTATCAAAGATCTGAGGAAGGGACCAATTGGAGTTGTGGTCTGGCCTGGAGACTTGTACCCCACCCAGGTCTCGACCGTTCAGTTCTGGGGCTGAAATACAGCCCTGCCACAGGTCTCCACCGCCCACAGAGGAAGTGGGCTGATCAGCTGGGCCTAGGCAGGATATCCACAGCTCCGTATGGTGCACTACTCTGCACCAGAATTCTCATTGGAATGTCCCTCCTGCCCCCTAAAAAGGGAGTGTCCTGGCTGCCTTCTCAGAGGGTGGGGCTCTCTGGGATTCAGCTTGACCCACCCCCAGGAAGAGATGGACAAGTTCAACCCAGAAACCATTCCCTCCTGGGCCTTTCAGTAGGACTCTTGGTGACTATGTGCTCTGGCCTCAGAAAGCAAAAGGACCCTTTTTGTAGCTGGGAGGACTCCATTACCTGTGCTAAAACGGAGCCCAGCCCATGTGTCATTTGGTAGCCAGAGCAATTCCTGGTCAGCGCCATGGATGCTTCTCCTGGGGAAAGGGGTCCTTTTTGTAGGGCAGCTGACCCCAGTACACCGGGCTTTCTTTTCCAG
Seq C2 exon
GTACCCCGGGGAGCTGCTCCCTGCGCTGTGGGGTACAGGATGAAATCTGTTCCTGTCATCCAACCTGCTCAGGCCTTGGCACCTGTTGTAAAGACTTTCTGAACTACTGTCTAGAGATTTCACCCTCCTCGGGCTCCATGATGGGCGGTAAAGACTTCGTGGTGCAACATTTAAAGTGGACTGATTCTATTACCAGTGTCATTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000033389:ENSRNOT00000066773:1
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:
PF0103312=Somatomedin_B=WD(100=58.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCAGGGAGAAAGCCTGTC
R:
TGACACTGGTAATAGAATCAGTCCAC
Band lengths:
343-1529
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]