GgaINT0011657 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9184018-9184798:+
Coord C1 exon
chr20:9184018-9184147
Coord A exon
chr20:9184148-9184652
Coord C2 exon
chr20:9184653-9184798
Length
505 bp
Sequences
Splice sites
5' ss Seq
CATGTATGT
5' ss Score
5.71
3' ss Seq
CTGCCACATTTCCCTCCCAGTGC
3' ss Score
8.46
Exon sequences
Seq C1 exon
GTGCTTCTGGATGGAGCCATCTCCTCTCTGAGGCTTTCCAACCTGACCTCACACACGGAGTACCTGGTGTCAGTGTTTCCTGTTTATGACACAGCCGTTGGGGATGGGCTGAGAGGCGTCACCTCCACAT
Seq A exon
GTATGTCGTGAGTAGAGAACATTCCTCTGATGCATGTTTGTGGGAGGTGAACATAGCCCTGCCTATGCAACCACCTCAGTCTGGATCCTGGCACTGTACATTCCCCTTCCCTCTGGTTCAGACCGTTTGTCTGTAACTATCTCCATCCTTGGAGATGTTCAAAACTCGGCTGGACAAGGGTCTGAGCAGCCTTCTCTAATATGGCTCAGCAGGGTTGGACCAGAGACCCTCAAGTGTCCCATCCCACCTATGTCATTCTGCAAGTGACACCACTATGCTGAGCTCAGCCTTCCATGGGAGTAACACACCCCAGAAGAAATTTCCTACAACCCTTGTCCCTTTTCCACCCTTGGGCTGCAAATGAACTAATCCTACTCCTTGACAAGTGGCTGTGTTAGATGCAGATTGGATGTCCCCCAGCTTGTAAAACCAGCTCTCCTCTGGGGTTGGAGCTGTTGCAAACCTCACATGCTGAAGGTGTCTTTCTGCCACATTTCCCTCCCAG
Seq C2 exon
TGCCTCTGTCTGCCCCCCGCTCCCTGCGTGTCTCCGAGCTGAGCCACAACAGCATCAGGCTGAGCTGGAAGGCAGCCCAGGGAGCCGCGCAGTACCTGGTGCTCTGCTCTGCAGCCCCCGACGGAGCAGAGGACTATACGACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:12
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=0.041
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(43.0=77.3)
A:
NA
C2:
PF0004116=fn3=PU(55.6=91.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCTTCTGGATGGAGCCAT
R:
TGTCGTATAGTCCTCTGCTCCG
Band lengths:
273-778
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]