GgaINT0011653 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9180701-9181155:+
Coord C1 exon
chr20:9180701-9180820
Coord A exon
chr20:9180821-9180990
Coord C2 exon
chr20:9180991-9181155
Length
170 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
CCATCTGTCCTCGTCCCCAGGCC
3' ss Score
12.27
Exon sequences
Seq C1 exon
GGCTGTCCCAGTACAGCAGTGATCCCCGCACAGAGTGGGATCTGAGCGCTTATGCTACGAGGGACCAGGTGCTGGAGGCAGTGAGGAACCTGCGGTACAAGGGTGGCAACACCTTCACAG
Seq A exon
GTAACTCCATCTCTCAGATCACAGCAAGACTGTGCTGGGGGAAGCTGTTCCCATGGGATAGCATCTTCTTGGGGGGATAAGGTGAATGAGTGAATGGAGCGAATGAGGAAGGATAAAGGTGGAGGCAGTCTGTTGGCTGTAGCCCACCATCCATCTGTCCTCGTCCCCAG
Seq C2 exon
GCCTGGCACTGACCCATGTCCTGGAACAAAACCTGAAACCAGATGCTGGTGCCCGGCTGGAAGCTGAGAAATTGGTAATTCTCCTGACTGATGGAAAATCCCAGGACGATGCCAACCTGGCTGCTCAGACCTTGAAAAACATGGGCATAGAGATATTTGCTATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.049 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(23.1=100)
A:
NA
C2:
PF0009223=VWA=FE(31.8=100)
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:
TCCCAGTACAGCAGTGATCCC
R:
TTTCAAGGTCTGAGCAGCCAG
Band lengths:
252-422
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]