GgaINT0079942 @ galGal3
Intron Retention
Gene
ENSGALG00000016292 | COL21A1
Description
NA
Coordinates
chr3:90097487-90098065:+
Coord C1 exon
chr3:90097487-90097541
Coord A exon
chr3:90097542-90097864
Coord C2 exon
chr3:90097865-90098065
Length
323 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGT
5' ss Score
9.82
3' ss Seq
TTCTGTTTGAATTCTTCTAGCCC
3' ss Score
6.63
Exon sequences
Seq C1 exon
GCACGAGAATTTTCAGAAGAATTTATTCGACAGGTGTGTTCAGATGTACTGAGAA
Seq A exon
GTAAGTTTGAAAGACTCTTTACTGTTCTTGCCTTGTTTAAAGTGCTGAAGAAGTTTCCTTGTAATTATGAAGATGCTTTCTTGAAAACAACACCAATATTTTGATCTGATTTATCACTGGTTTTCATAGAGTTGTAGAAATACGCTTCCATGCCAGTGGCTCCATAACGTGCTAAAGGCGCCTTGTTTCCTAAAGATACCATAGCGCCTAAAGAAAGGAAGCTGGTTTTATTTTAGTGAAGAGGTAGAAATATTTTTATATTTCTATAAATATATAAATATATATATATATATAAAGCATTTTTTCTGTTTGAATTCTTCTAG
Seq C2 exon
CCCAGTTACCTGTGATCCTTCAGAGTGGAAGGCTACAAAACTGCAACCACTGTCAGTCCCAGAGCGCTTCCCCAGGACTTCCAGGACCACCAGGTCCAAGAGGCCCAGAAGGTCCAAGAGGGTTTCCTGGTTTGCCAGGGAATGACGGTGTTCCAGGTCTGACTGGCATCCCGGGTCGCCCTGGGGCTCGTGGGACAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016292:ENSGALT00000026273:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.842 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(6.5=21.1)
A:
NA
C2:
PF0139113=Collagen=PU(76.3=66.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACGAGAATTTTCAGAAGAATTTAT
R:
CTCTTGTCCCACGAGCCCC
Band lengths:
256-579
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]