RnoINT0143947 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78104949-78105368:+
Coord C1 exon
chr4:78104949-78105119
Coord A exon
chr4:78105120-78105203
Coord C2 exon
chr4:78105204-78105368
Length
84 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
TGGTGTGCTGTGCCCTGCAGTCG
3' ss Score
7.31
Exon sequences
Seq C1 exon
CAAGTCCTGAGCCCTTCACTGTGCCTACTACTGCCCTCCCTGGGTTGCCAGCCTCAAGGGCCCTCTGTTCCCCAAGTCAGCTGAGCTGTGGCAGTGGGGAGTGCCTACCCCTTGAGCATCGATGTGACCTTCAGGTGAACTGCCAGGATGGCTCTGATGAGGATGACTGTG
Seq A exon
GTACGTGCTGGCCTGAGGCACAGTCCCAAGGGCCCTGTTCCTGCTTGAGCCCCCTTCTAAGCCCTGGTGTGCTGTGCCCTGCAG
Seq C2 exon
TCGACTGTGTGTTGGCACCTTGGTCTGGCTGGAGTGACTGCAGCCGCAGCTGTGGCCTGGGCCTCATCTTCCAGCACCGAGAGCTGCTGAGACCTCCCCTGCCTGGAGGCAGCTGTCTGTTGGACCAGCTCCGTAGCCAGCCCTGCTTTGTGCAAGCCTGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:48
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.103 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005713=Ldl_recept_a=WD(100=63.8)
A:
NA
C2:
PF0009014=TSP_1=WD(100=87.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGGATGGCTCTGATGAGGA
R:
CACAAAGCAGGGCTGGCTAC
Band lengths:
181-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]