GgaINT0011660 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9186578-9187018:+
Coord C1 exon
chr20:9186578-9186717
Coord A exon
chr20:9186718-9186888
Coord C2 exon
chr20:9186889-9187018
Length
171 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
CTCATCCCTCTCCGTTGCAGGTT
3' ss Score
11.21
Exon sequences
Seq C1 exon
TGGCCTTGAGCCCTCCCAGGTACCTGAGCTTCTCAGAGCTCAGCCACTCATCCGTGCGGGTCAGCTGGGAGCCAGCATCACCGGCAGTGAAAGGTCATCGCGTCACCTACATGTCTAGCAGAGGGAGCAACACCGGGGAG
Seq A exon
GTGAGTCCTCAGGGGCTGCTGGAGGGAGAGCTGGGAGGTAACACGCTGCCCTGTTCTCTCTGGTGCGTGGAGGGAGGGTTATCTCTGAAATGGGCACTTTTGAGGGATGTGCTAAGCCCTCTGCAGCTGTCTCCATGTCCTTCTCTCCCAGCTCATCCCTCTCCGTTGCAG
Seq C2 exon
GTTGAGGTTCCCGGCACTGCGATGTCCACTGTCCTGAGACCATTGTCCTCCCTCACCCAATACTTCATCAGTGTCCGATCTATGTACGATGAGGGTGACTCCTTTCCAATCACTGGCAATGTCACCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.277 A=NA C2=0.227
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.8=79.5)
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:
CCCAGGTACCTGAGCTTCTCA
R:
GGTGGTGACATTGCCAGTGAT
Band lengths:
255-426
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]