RnoINT0131927 @ rn6
Intron Retention
Gene
ENSRNOG00000013123 | Scube2
Description
signal peptide, CUB domain and EGF like domain containing 2 [Source:RGD Symbol;Acc:1563998]
Coordinates
chr1:174474847-174476199:-
Coord C1 exon
chr1:174476074-174476199
Coord A exon
chr1:174474964-174476073
Coord C2 exon
chr1:174474847-174474963
Length
1110 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
TTGATTCGTTTTGACCTCAGTGA
3' ss Score
5.47
Exon sequences
Seq C1 exon
AGGGCCTGAGCTGTATGAACAAGGATCATGGCTGTGCTCACATCTGCAAAGAGGCCCCGAGAGGCAGCATTGCCTGTGAATGCAGGCCTGGTTTTGAACTGGCCAAAAACCAGAGAGACTGCATCT
Seq A exon
GTAAGTATGAACTGTCACTGGGCTGAGGTGAGGACAGCCTACACAGAGATCAGAAAAACAGCCATGGCCACGGCCACGGCGTGTGTCCTGGGGATTGAACTCAGTAACAGATGTCTTTACCCTGCTCTGTCTCACCAGACCAATGTCCTTTTTCTTCCTTCTTTCCTTCCTTCCTCTCTCTCTCTCTCTTTCTTTCTTCCTCTTCCTCGTCTTCTTTTTGCTTTTACTAAATGTTTTTAAGATGTCACTGCTTAAATGCTTTTGTTTAAAAAAATAACATTTGAAGAATTAAAAAAAAAAAAGCCACACTCCTGTGATCCCAGCACTTAGGGGGTAAAGGCAGGAGGATCAGGAGCTCAAGGGTCATCTTCGGATACTTGGTGATAGAATAAGTTGGAGGCCAACCTGGGCTATATGAGGTCCTATCTCAAAAGACCAAACAAACAAACAAAAACAACCAACCAAACAACCAAACAAACCCTCAAAAACCAAAAAAAGAGGGTGAGGAACATATCCCAGAATCACACAACCTAGCCAGCTCATTTTTTCTATATTCCCACTTAGTCATCGTGCAAATTAAACATTGTCAGTCTGTTCCAAACATGAAGTACTAGAGAATTTCTAGCGGTCCCGGCACAGCCTGGCTAACAGGCAGACTTCACCAGAGAGAGGGAAGGAACGGTCTAGAATCACACGGCGTGGGGGGCTTCCCTGCCCCAGCCTTCCCAGCTCCATCTCCCTGTATCACTCTGTTTAAGCCTTGTTACGGTTCTATATGGTTTACACCGAGACACTGTATACCCTGTATACATTGCATATCAATGGCAGCATCTGCTTGGAAGTCTTTTATCTCAAGAGTCAGGCATGCACTGGATGCTCAGATTCTTGCAGAGAAAAAGAGCCACCGCTTGGGGGACGTCTTTAATCTCAGTGCTCTGGAGTAGAAGCTGGTAGGTCTTGTGAGTTCAAGGTCAGCTAGGGTTACGTAGTTATGCAGGCCAGTTACATAGTGAGACCTTGTCTTTGAAAATAAAACAATTCGTTGGACACGAACCCAGCCCTGGTTGTGGAAACCTCAGCACTTTAAGCATTGATTCGTTTTGACCTCAG
Seq C2 exon
TGACCTGTAACCATGGAAATGGTGGGTGTCAGCACTCCTGTGAAGATACTGCAGAAGGCCCCGAGTGTAGCTGCCATCCACACTACAGGTTGCATGCTGATGGGAGAAGCTGCCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013123:ENSRNOT00000052377:5
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:
PF146701=FXa_inhibition=WD(100=86.0)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=90.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGGCCTGAGCTGTATGAACA
R:
CAGCTTCTCCCATCAGCATGC
Band lengths:
238-1348
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]