RnoINT0143962 @ rn6
Intron Retention
Gene
ENSRNOG00000025848 | Sspo
Description
SCO-spondin [Source:RGD Symbol;Acc:1549716]
Coordinates
chr4:78111539-78112471:+
Coord C1 exon
chr4:78111539-78111684
Coord A exon
chr4:78111685-78112376
Coord C2 exon
chr4:78112377-78112471
Length
692 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGT
5' ss Score
8.78
3' ss Seq
CAAAGGGCTTTCTATTCCAGAAC
3' ss Score
6.62
Exon sequences
Seq C1 exon
GACCAGTGCCAGGTGTGTGTCCCAAGGACCAGCAATGGCTGGACTGTGCCCAGGGTCCAGCCTCCTGTGCCCATCTCAGCACCCCTAGAGAAGCTAATCAGACCTGCCACCCTGGCTGCTACTGCCTCTCTGGAATGCTCCTGCTA
Seq A exon
GTAAGTATCCCACTGCCTGGCTACGACTGGAACTGCTTCATGGTTTAGCAGGGAAGGGATAGCCAGGGGCCTGAGCAAGGGTGCCAAAGGTTTCCGACTGGTGACAGCCTGCTGAGTTAAAGACACCCTCGATAGCTGGTCTCTTGTTTATCAAAGTGGTGGTGGATCAGAGAAGTGTTTCATACATTTTACTCATTCAAATGTGTGTCCTCTTACCCACCACCAACTATGTGCTGAGCACCTACTGAGCGCTCAGGTGAGTGGTGCTGAGCACCTACTGAGCGCTCAGGTGAGTGGAATGGATAGGTAAGGCATACTCAGGGTTGCCTACTGGTGCTGGCTGGAGACACAGCTACCGTCTGTAAAGAAAATGGTTGCAGTGGCTGCTGGAGGGTGTTCTGCTGTTGTTTAAGTTACATGGTTTATACGACAAATATGTATCTCACACAGTTGGTTTCATTTAACAGCTTAGCCTCACGCCTTGCCATAGAAGGTGTGGTTTTCTTCTGAAGGAGAGGATGCATGTGTCCATGTGATCCTCAGCTGAGGCTCTGCTCTGCCCATTGAGGGAGGGACCTGTGTGGAGCTCTGTGGAAGGTGCCTGGGTGACGCTTGAGATGGACTAGGAAACTGAGTTCTAGTTTTGACTGGAGCAGGCTGGAGCCAGGATAACAAAGGGCTTTCTATTCCAG
Seq C2 exon
AACAATGTATGTGTACCTGCCCAGGACTGCCCCTGTGCCCACAGGGGGCGCCTTCATTCCCCAGGCAGTGCTGTGATTCTTCCGTGTGAGAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025848:ENSRNOT00000035906:61
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:
PF0182612=TIL=PU(79.2=85.7)
A:
NA
C2:
PF0182612=TIL=PD(17.0=28.1)
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
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:
GACCAGTGCCAGGTGTGTG
R:
TTCTCACACGGAAGAATCACAGC
Band lengths:
238-930
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]