GgaINT0011676 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9207202-9207490:+
Coord C1 exon
chr20:9207202-9207255
Coord A exon
chr20:9207256-9207436
Coord C2 exon
chr20:9207437-9207490
Length
181 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACG
5' ss Score
10.52
3' ss Seq
CCAGCAATTCTGATTTACAGGGC
3' ss Score
5.26
Exon sequences
Seq C1 exon
GGACCACCAGGTATTAAAGGAGAGAAAGGAGACACTGGAAGTCCTGGCATGCAG
Seq A exon
GTAACGGTAGACACTTTCCTTTTAATTGTATTGAAGATCTGTCCATTTCTCCCAGTAATTAATTAAAGCAAGCTTGAAAAGCCATAGTGTTGTCCCTATTGCCTTCTCATTTCCTTTGCTACAAGATGAAGTAGGACAATGATAAGCAGATGCCAACTTTACCAGCAATTCTGATTTACAG
Seq C2 exon
GGCATTCCTGGTGTGCAGGGAGCTCCAGGCAGAGATGGTCTTCAAGGTGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:31
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(30.4=100)
A:
NA
C2:
PF0139113=Collagen=FE(30.4=100)
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:
CCACCAGGTATTAAAGGAGAGAAAGG
R:
CACCTTGAAGACCATCTCTGCC
Band lengths:
100-281
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]