GgaINT0107555 @ galGal4
Intron Retention
Gene
ENSGALG00000014178 | SCUBE1
Description
signal peptide, CUB domain, EGF-like 1 [Source:HGNC Symbol;Acc:HGNC:13441]
Coordinates
chr1:68727342-68728900:-
Coord C1 exon
chr1:68728697-68728900
Coord A exon
chr1:68727504-68728696
Coord C2 exon
chr1:68727342-68727503
Length
1193 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGT
5' ss Score
11.37
3' ss Seq
TTCCTCTTTTCTTTTCTCAGTTA
3' ss Score
9.53
Exon sequences
Seq C1 exon
ACACCTGTAACATTGACTGTGTTCGGAAAAGGATGGAGCAGAAGCTGCAAACTGCAATCAAAACATTGAGGAAATCTATTAATAAACAGCAATTTTACATTCAGTTTTCTGGGACAGAATATGAAGTGGCTCAGAAGCCAGCTAAAGCTACTGAAGGGCATGAAGCTTGCAGTACGGGGCAAGTGCTGCAGGATGGAAAATGCG
Seq A exon
GTAAGTCCCAATTGATTCAGTTCAGCCATACCCCAAAAAACATCTCGCCACAGTATGTTAGCAGCTATTTCCCAGTTACTCCCAGTATCTAATGAAAATACATTTACAGTTCTGTAAAACAATGAAGTAGTGTTTGCCTAGATGCTGTGTATTTACTTTGAATTTGTCTCTTACTTTCTTCATCACCAGATGATCTGTGACCTGTACGTATATTTATACTTAACTCTCAAAAAGTCCAATTAAGAAAGAAAAGGAACGATCTATAGAAATCTATTTTAACTTTACGTGAAATATCTAATTTCTTTAAGCTTCTTCCACAGTTACTAGGCTGTAGTGCTAAGGTGATGATGCAAAACTACTAGTGGCAGTTCTCAGCACTGCAAGGTTTCTAATCACTTGGAGTCACATTTTCAATATCAGCATATCTGTTTTTCCAGCCGCTTTTAGACACCAAGTCATTTACAGGCAAAAAGGAGTTAAGAGCAGATCTGATAGATGCCTCTAATGAGTTGTTTCTGAGGCTGTTTTCATCACGTAGAAACAGTGATTTAGAAGCAGTTATTGAAAGGCTGCTTCTGTTAGTGTCTAGAAGCCCATACATTTTAACTACTAATATCCAGCAGAGGAAAAACCTTTAATGTAATTGTGACCTGTTACTATAAGAAGAGTATAAGGATTCATTTGTATACTTAAAATGCCTTCCAGTTGGGCTATTTGAGTGTCAAGAAAAAGAAAACATTGCATGGGATACACTGCCCTCAGAGAAATCGCCAGAACTGATTACAGGAGACAGATTTCCCATAAAACTTACACATAAATGCACATAAATTAAACTAAAAATTCACATCATTTCTCATGCATTATGTAACACTGCCTTAATTAAACTGCAATATACTGTTTGCAGACTGCATTAACTTTATTAGCAACATATATCTGGTAATGCTTCAGCACAGTAGAATGCTATTTAATGGGCTAAACAACAGAAGAAGGACCTTGCTTGCACTGATGTAAATTGACCACAGATCCCAGATGGTCCTCTTTACATCAGGTGAGGATCCTTGCCTAATGCATGCAAAAGTGCTACTAATGATACTGGAACTAAAAAGACCCGTCTTCTGTAAATGTCTAATATATAGGAAAATGATGTGATCAAAATGAAAGTCCTTATGCAAATTCCTCTTTTCTTTTCTCAG
Seq C2 exon
TTACCTGCAGCACGGGCACCTTTTATAGCGGAGAACATAATCAGTGCATTCCTTGCTCACCAGGAACATACCAAGACACAGAAGGTCAACTTACCTGTGAGCCTTGCCCAAGTAATGATGGACAGGGAGTAGCGGGCGCCCGGAATGTGTCAGAATGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014178:ENSGALT00000022933:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.072 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=87.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTCGGAAAAGGATGGAGCA
R:
ACATTCTGACACATTCCGGGC
Band lengths:
343-1536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]