DreINT0131742 @ danRer10
Intron Retention
Gene
ENSDARG00000063097 | scube1
Description
signal peptide, CUB domain, EGF-like 1 [Source:ZFIN;Acc:ZDB-GENE-050302-78]
Coordinates
chr4:8909222-8910929:-
Coord C1 exon
chr4:8910762-8910929
Coord A exon
chr4:8909384-8910761
Coord C2 exon
chr4:8909222-8909383
Length
1378 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTC
5' ss Score
7.46
3' ss Seq
CCTAATGTCTTTGATTCTAGTTC
3' ss Score
6.02
Exon sequences
Seq C1 exon
GTCAGTGTCCAGCCGGTCAGTTCTCTTCTGATGGTTTCCGCCCATGCCAACCATGTCAGCTGGGCACCTTCCAGCCTGAGCCAGGCCGTGTGCTGTGTTTTCCCTGTGGCGGAGGACTCATGACTAAACACACCGGCAGCACATCATTTAGAGACTGTGAAGCCAAAG
Seq A exon
GTACTCTGGCTGCACTATATATAAAAAAATAAATAAATATTGTGATATATAGTTCTGCGATATAAATAAAATTTTATCAGCAATTTATTATTATTTTTTATTTATTTAATGATCATACACAAATAAACAGGTTAAATATATACATTTTCTGAGCTATTAAAATAAAAACTAGCCTTTAAAAAACTGCAAATGACTGAAAACCCCGGCAGAAATTCTGATTCTTATTGGCTGTTGTCATTTTCCTCTCGTGTCTCCCAGCATTACTATTTATTTTCAGCTCTAGGTTCACCTAAACAGCACCTACTGGAGAGGATGATGATGAACACAGAGAAGGTCCCATCTGATTGATCAGATTTGGATAAACAATCAATGCATGCAGCGCGCAAATGCTTGACACATAAAATGAATGAAATTTTTTGCACTTCTCTGTGATATAGAAATTACATATACTATTATCGCAATAACAATACTTTATCGATATATTGTGCAGCCCTAATTAAATACAATATGCAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGTATGTATGTATGTATGTATATATATATATATATATATATATATATGTATGTATATATATGTATGTATATATACACACACACACACACACACACACACACACACACACACACACAAAACAATACAATACAATAGAGTGCAGGTACACATGAATTAAACAGTGCTTTAAGGTTTTCATACAGTATTCAGACACAGAACTTAAATTTAAAATCTAAAATATTACTGTACGGTTTTCATTGTACAAGTAAATCTTTGTTAAACCTACAAATATTCGAATTTTTTGTGCTATTACACACTCTTGAAATGCTTAATATTCCCACGTCTTAAAACAAATGCAATTGATAAACTTTGCAGATAAAATATGACAATTGCATGTGCTGCGATGTGACTATTGTGGATGTGTATATTGTAATATCAATGCTGATATAATATAGTGTGCAACTCGAAAAGGTATGCTGGGAAACACAGTGAGCTTAATGGTAATGCAAATCATCTGATCACAAATGAATGACTAAACACAGGCTTGTCCAATTTCCACACTGTAAAAAATGACTGGTTTCCTTAAATTTTTAAGCTGAATCAAATTCAGCTTAGTCTTTTGAACTCATATAATATTAAAGGGACTTAAAACAGTTTGTGCAACTTATCAAATTAAGTTAGAACATGATTAACTTAGTTTAATATGTTACAATTAACTAAAAACATATGTTGTCTTGACCAATTGATCATATCATTTTTTTACAGTGCACTATTTTCAATGATGGTCTCCTAATGTCTTTGATTCTAG
Seq C2 exon
TTCACTGTGCTCTTGGCCATTATTATAATGCCACCACACATCGGTGCATCCGCTGTCCAGCTGGTACCTATCAGTCTGAATCCGGACAGAACTACTGCATCACCTGCCCTGGAAACACCACTACAGATTTCGACGGCGCTAACAACGTGTCTCACTGCAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000063097:ENSDART00000091876:18
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
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGTGTCCAGCCGGTCAG
R:
TGCAGTGAGACACGTTGTTAGC
Band lengths:
326-1704
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]