GgaINT0107549 @ galGal3
Intron Retention
Gene
ENSGALG00000014178 | SCUBE1
Description
NA
Coordinates
chr1:70759779-70761513:-
Coord C1 exon
chr1:70761397-70761513
Coord A exon
chr1:70759902-70761396
Coord C2 exon
chr1:70759779-70759901
Length
1495 bp
Sequences
Splice sites
5' ss Seq
GAGGTTTGG
5' ss Score
3.53
3' ss Seq
AACATTAATTATATTTTCAGATA
3' ss Score
6.43
Exon sequences
Seq C1 exon
ATATAGACGAGTGTTCCTTTGAGAGGACCTGTGATCACACCTGCATCAACTACCCTGGAAGCTTCGAATGTCTCTGCCATAAAGGCTACACCTTGTACGGACTGACGCACTGTGGAG
Seq A exon
GTTTGGAAATCGTTTCCCTCATCTGTTTGCTTCTTTGCTTTGTGAGCTGTTTACTGAGCCACGCATTCTTAAGCTGAATATTTTAGAACTCGAGGTGATAAGATGAACCAAAACAGTTAAAGCGAGAATAGCTTGAGCTGAGTGTCACTGAAATTTCAGTGTCTCTAATTGTCTGAACTATTCCCTGAAGAATGTAAAACAGTGGCCTGGCATTTTTGTCACGGTGGTATACTCAGCAGCCTCAGAACAGACCAGAAGACTGCAGCTCTGAGCCTTACTGTGTGGGTGCTGCTGTTCTTCCACAGGTTCCAGAGGAAGGTGTGGCTAATTGGATGAGGCTTGTGTTTATTAATTGGTGTAGGACCTAGTGTGCACTGGAACCTGGTCCCTCATTTGGTTCCTACCTGTACCTCACATCTGACTTCAGACTGCGTCACGAGGCTCCAGAGCTGAGGACCGGGGAGAATTGACTAGAACTCTAACACCGTTCCTGCAGGCCATGTAGATTCACTCAGAGCCAGGCACATGGCAGTTGGAGTTTAAGACGTGATTCAGGCATGGTTTGGAACGGTAGGCAGGCACTCAGCCTGTCAGCCTTTATGCCCTGACCTCCCTTAGAAATACATGCAGCGACAGTTTTCTATTACTGTCACATTTTGAGGCCTATCATTACACTAGAGTCTGAGCAATTAAGCCTTTGACATTTTTCTATATAATGTAATATACATTGTTGTCATTATTCAAGAGGCATCTGGATGAGGAGCTACGAGATGTGGTTTAGTGGCTTGTGGTAGCAAGAGTAACGGGAGGACGGTTGGCCTAGATGATCTTGTAGGTCCTTTCCAACCTTGAGATTCTATGATTCTATGCTGCACAGACTTTCAAGAATGTTTTGCATCTCGTGAGGACTTCCAAGAATTTCAGTGTAACTAGTCCCAACAAGTAACTTGTATCATATGGCCTTATGGGAAATGGCCTTAAGTTGCACCAGGGTAAGTTTAGATTGGATATCAGGAAACACTTCTTTACAGGAAGGGCTGTTAAGCACTGGAATAGGCTCCCCAGGGAGGTGGTTGGGTCACCATCCCTGGATGTGTTTAAAAACCATTTGGATGTGGTTCTCAGGGACATGATTTAGCGGAGGGTTGTTAGATAGGGTAGTTCGGTTAGGTTGTGGTTGGACTTGATGATCTTCAAGGTCTTTTCCAACCTGAGCAATTCTGTGATTCTATGATTTTATGATATGTGTAAATCGTTACAGGAAAAGCAGCTATGTATGTGTCTGGAGACAAATGCATGCTAAGTACGCTGAACTGTTTGACAAGACCGTTGTCTGCATTACACATTTATAATAGATGTAAATGTAGAAGATGTAGTAGGTAGAGATATTCTTACGCACACAACATTTCAGTGCACAGTACATGTGTGTACAGTATACATGGGGATACTGTGCACGCATTTTTAATACTCCTCTCAACATTAATTATATTTTCAG
Seq C2 exon
ATATTGATGAATGCAGCATCAGCAATGGCAGCTGTGACTATGGGTGTCTGAATACAATGGGAAGCTATGAGTGTGTCTGTCCACCTGGAAAGAAACTGCACTGGAATAAAAAGGACTGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014178:ENSGALT00000022933:8
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:
PF0764510=EGF_CA=WD(100=95.0)
A:
NA
C2:
PF146701=FXa_inhibition=WD(100=85.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATAGACGAGTGTTCCTTTGAGAG
R:
AATGCAGTCCTTTTTATTCCAGTGC
Band lengths:
238-1733
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]