GgaINT0011681 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9210752-9211226:+
Coord C1 exon
chr20:9210752-9210818
Coord A exon
chr20:9210819-9211037
Coord C2 exon
chr20:9211038-9211226
Length
219 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
TTTCTGTCTTGCCTTCTCAGGTC
3' ss Score
12.16
Exon sequences
Seq C1 exon
GGGGAACCACAGTCCTTGGCCACAATTTACCAGCTCGTTAGCCAGGCTTGTGAGAGGATGATCCAGA
Seq A exon
GTGAGTATAACCACCCTGAGCTTGTTTTGATGCTTCTCCAGCAGCAGTGGACAAAAGCACGGGGGAAGATGGCATGAAGCTGTAGTGAGCCAGGGATCCCCTCTGTCCTGTGCAATGCGTGGTCCCACCACATTGTCCCGTCCATTGGTTTCATTGGGTGGTTTTAGCACAGAGACTTTTGTGCCCTTGCAAAGGTTCCTTTCTGTCTTGCCTTCTCAG
Seq C2 exon
GTCATGTGTTGAAATTTGACTCATTCATTCATGAACATGCAAGGAAGCCGGTTCCTGTTTGGGAAGGAAGACTGAAGCCAGGAGAGCCAGGATCACCGGGTCCTCCAGGTCCTCCAGGGAGCAATGGAGAAAAAGGAGAAAATGGCCTCCCTGGTCAGACAGGAAAAGATGGGTATCCTGGAGAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:36
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.826 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(8.3=21.7)
A:
NA
C2:
PF0139113=Collagen=PU(69.6=60.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACCACAGTCCTTGGCCAC
R:
CTCTTTCTCCAGGATACCCATCT
Band lengths:
253-472
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]