GgaINT0107557 @ galGal4
Intron Retention
Gene
ENSGALG00000014178 | SCUBE1
Description
signal peptide, CUB domain, EGF-like 1 [Source:HGNC Symbol;Acc:HGNC:13441]
Coordinates
chr1:68723640-68724853:-
Coord C1 exon
chr1:68724686-68724853
Coord A exon
chr1:68723802-68724685
Coord C2 exon
chr1:68723640-68723801
Length
884 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAT
5' ss Score
6.38
3' ss Seq
ATATGGCTCATACTTTGCAGTTC
3' ss Score
5.62
Exon sequences
Seq C1 exon
GGCAGTGTTCTCCTGGACACTATTCGTCAGATGGTTTTAAACCTTGTCGAGTCTGTCCTCTTGGTACGTATCAGCCTGAACCAGGAAGGACCCTCTGCTTTCCATGTGGTGGAGGGCTTGTGACCAAGTACGAAGGTGCTGTTTCTTTTCAAGACTGTGAAACCAAAG
Seq A exon
GTGAATTTCATGTCTTTCCATGATTCATTTTCCTGCTGCTTGCTCTTTTGTTTGTGAGCTTCGATACTAACAGACTTTGAAAGTCTCCAAAGCAAACATAGTCACTGCATATAGGAACACTGTGTGTGATCAAATTAAATGTTCGGGCAATCTGTAAACTAGTCATGATCTCCCAAGGTTGTGGAGACTGAACAGGATTTATTGTATTTGGAATTTACCACTGGCACTTATAGTGTTAGCTTTGCAACTGGGACGTAAATCAGCTTCATTGCATGGCAAGAAACAAGCTGGCATCAGAGAATGATTTAGCCTTCCATTGCTGCCTGTTTTTATTTTCCAAATTAGAAAAAGTAAATAATAAAAAATTATATGAAGTTAAGGATTCTTTACGAATGGGCTGGGAAGCAACTGTAAGTATGGAACGTGCTGCATGTCCTGTAATGACAACTTCCAATGTAAACTTTGAAGAAGGAATCTGCCCAAACTTATTTTGGCTTACATATTTGAATTACATGCGGATCCTGGCAAACATAGGAACTTCCCTCTTGCTATTGTGAAAGACGGTTTTGTTGTTGAGGCAGATATGTATCATCTTCCATTTTTTATTAGCTCATAGGAAGCCCCTGTATCAAATATAGTGAGAGGCATATGCAGCATGAGTTACTAGTTCATCAGTCTTCAGAAGAGCATTCTAGTTAGAAGGTCCTTTGTAATCAGAAATACTGTGAGCTTATGTCCTTTTTGCCTTTTATTGCCTACACATAAGTATAGCATAGTAAGTATATTGCAGTTTGGGGATCATAGGTTATGTCCAGAGCAGAGGGAAGATGTTTCTACAATGCAGATTGTTACTTTCTGAAAATAATATGGCTCATACTTTGCAG
Seq C2 exon
TTCATTGCTCTCCTGGACACTACTACAACTCCACAACGCACAGATGTATCCGATGCCCTGTAGGAACTTACCAGCCTGAGTTTGGTCAAAACTACTGCATCACCTGCCCTGGGAACACAAGTACGGATTTCGATGGCTCCACTAATGTTACGCACTGTAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014178:ENSGALT00000022933:17
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:
PF076998=GCC2_GCC3=WD(100=84.2)
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:
GGCAGTGTTCTCCTGGACACT
R:
ACAGTGCGTAACATTAGTGGAGC
Band lengths:
326-1210
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]