RnoINT0131930 @ rn6
Intron Retention
Gene
ENSRNOG00000013123 | Scube2
Description
signal peptide, CUB domain and EGF like domain containing 2 [Source:RGD Symbol;Acc:1563998]
Coordinates
chr1:174468413-174469582:-
Coord C1 exon
chr1:174469466-174469582
Coord A exon
chr1:174468536-174469465
Coord C2 exon
chr1:174468413-174468535
Length
930 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGCT
5' ss Score
6.77
3' ss Seq
TTAGTGTTTGCTCATTACAGATA
3' ss Score
6.72
Exon sequences
Seq C1 exon
AAACGTGTGCTGTCAACAATGGAGGCTGCGACCGCACCTGTAAGGACACGTCAACAGGCGTCCACTGCAGTTGTCCCTCTGGATTCACTCTCCAGTTGGATGGGAAGACATGTAAAG
Seq A exon
GTAGCTCTCGCTTGTCCTGGAGCTGGGGGTTATAGGGCTGGGGGCCTGGGTGGAGGGGGTCCTGCACAGCGTTCAAGCACTTCCGGATTTGCTTATGATTCCTACTGATGAGAGCTTCTCTTCCCTGGGCTGGTGGACGGTTGTAATTGAGCAAGCTTAATTAGAAGCAACTTAATTACGCTAACTGCTGAAAAGGTCAGCTTCTGCAAGCGCCAAATAATCCATTTCAGGCAAATGGCTTTATTAGCAAGGGGAGGTTCATGGGACATTCATCGGCAGCAGATAATATCAACCAATCATGAATAATAGCCTCGAGATTACATGTAAATAACGGCCAAGATTATTATCCGGAGCACTTAACGAATAACTGTACCATTAACTTTTAGTAATGAAGACAGACCCTAATGACTTGCTGGTCTTTCATGGGCAAGACTACAAAGGGGTTGTTAGTTCTTTAGCACGATAAAAAAAACAGATAAGCTGGTCATGAGATGAAACAGCGGAGAAGGTAAGATTAAGTATCAGGAATCATTAAAAAACGTTGAGACCGTTTGGTCCGTGTGTAGTTTGCCAAAACAGAAGCTCCTGTCCCTTATAACTTTAGTCATTAAGCTAGAATAGAACACATACTAATGGGGGTGGTCTTATCTTTGGAGGGCATTAGAAGGCGAGAATAAAATAAAGCATGCTAGCACCAATTCTTTCCAGGGTTTGTGCCCTTAGTGCTTGCCAATGGCATGGCTGAAGTCGGAGCTGTTAGCTGGGTGAGGTACTCCTTCAGCCAGACAAGAGAATGCTTGTAAGACTGAGACCATCAGTGAGCACTGGAAAGTGCTCTCGCGGGTGTGCTTTCCTTTCTGAGGATAGGGACTGGGGGAAGCCAGGCAACTGTTGCTCTCCTGTTGCTTCCTTAGTGTTTGCTCATTACAG
Seq C2 exon
ATATCGATGAGTGCCAGACCCGGAATGGAGGTTGTAATCATTTCTGCAAAAACACTGTGGGCAGTTTTGACTGCAGCTGCAGAAAAGGATTTAAATTACTAACAGACGAGAAGTCTTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013123:ENSRNOT00000052377:8
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=90.0)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=85.7),PF0764510=EGF_CA=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAACGTGTGCTGTCAACAATGG
R:
AATTTAAATCCTTTTCTGCAGCTGC
Band lengths:
214-1144
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]