GgaINT0011658 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9184653-9186173:+
Coord C1 exon
chr20:9184653-9184798
Coord A exon
chr20:9184799-9186049
Coord C2 exon
chr20:9186050-9186173
Length
1251 bp
Sequences
Splice sites
5' ss Seq
GAGGTACGC
5' ss Score
9.4
3' ss Seq
TGAACTTCTCCCTGTGACAGATT
3' ss Score
8.63
Exon sequences
Seq C1 exon
TGCCTCTGTCTGCCCCCCGCTCCCTGCGTGTCTCCGAGCTGAGCCACAACAGCATCAGGCTGAGCTGGAAGGCAGCCCAGGGAGCCGCGCAGTACCTGGTGCTCTGCTCTGCAGCCCCCGACGGAGCAGAGGACTATACGACAGAG
Seq A exon
GTACGCTCCATGAGAATGGTGGCAATACTGCTTTTCCTTTGCCTGGGCTCTCCTCAGTTAAAGAGTCCAAAATGAGTGCCTGTCTCTCTGTGTGGGGTTAAGTTCTGACAATATAATACAGAGCAGACCTGAAGCACGGAAACCTTTGGCAGCCCAGGGGCTGAGCTCACACCTCTGCAGCCCCAAGAGTGACTTCTGCATCCTCGAGGCTGCACAGAAATATCTCTGCTTTGCTTATCTTTACATGTTGATTGAGAATTTGTTAGGGCAGCTTTCACTGACCTTGAAAAAGAGAGCTGTGGCACTGTATAACAATAAAGCAATGCCAGATGAGTGGAAAATCCTTACAAACTTCTAAGGTGAAGTTCACAATGTGAACATTTTAAAGTGAACATTCAAAATGGGAACATTTCAATGAGCTGTCAGAAGTACCGGCATTACAGCGTTCCCATCCTTTTACAAACCTCTGCTCTGCTGCATGCAGCCTCCTGGAAGTCACTGAGGGGGGTTCCTGCAGCAGGGAGGGCTGTGACATGCAGTGTTAGCGGCAGGTGGCAGCAGCCCGGCTGCTATAGCCCTGCTTGCAGCAGGCAGCTCTCATGCAAGCTTCCCAGGCCGTAGAGGAAAAGAGGCTCACCGTCTCTCACTTAAAACCTTGCTTTCTTGAAGCCCCTTTCATCCAGGGATGCTGCACCCTGTGCACACTCTGAGTGCTGCAGGATGGCTGGAAATGGGAGCGAACTACGCAAGCTTCCTGCTCTGTTGCCTTTTCTGGGGGGGGGGGAATTTTCACCAAGAATATATATATATTTTTTGGATCCTACTATCAGAAATCAGCCCCCAGCTTTGTATTTTCAGTAGTGGAAGCCACCCTGCTTTTTACATCCATACTCATCTTTCCATTATAGTGTCTTTCCCAGGAAAATCTCGATATATTCCTTACAAAAGTGACTTGTTTGAGCTTACTTCAGGTACCCTGATCCAACCCAGAATAATAGCATCACCTCTGTATAAGAGATACACCTCTGCAGGCCTTGGGAGAAGGTGGTGTGACCCCTCAATATATTTGGTGTCCCCTGGGGAGGGAGGGAGGGAGGCAGAGAAGCTCTGACAGTGCAAAGCCCATGTCCACGTGGTCAGAGGGTGTTAGAGGGCAGCCCAGAATGGAAGGGTGTCCTAGAAGTGAAGTGTTCCTCAGGACTGAGGCGTACCCAGAACTGAAACATCTCCCTGAACTTCTCCCTGTGACAG
Seq C2 exon
ATTAAGGTGGCTGAGCCCGAGGTCCTGCTGGACGGGCTGTCACCCAGCACTGAGTACTCCATTGCAGTGTATGCGTTGTATGGGGAAGATGCCAGTGATCCAGCCAGCATCCAGGAAACCACCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.041 A=NA C2=0.071
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(55.6=91.8)
A:
NA
C2:
PF0004116=fn3=PD(42.0=81.0)
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:
CTGCGTGTCTCCGAGCTGAG
R:
GGTGGTTTCCTGGATGCTGG
Band lengths:
246-1497
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]