GgaINT0011649 @ galGal4
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
collagen alpha-1(XX) chain precursor [Source:RefSeq peptide;Acc:NP_001004392]
Coordinates
chr20:9177119-9177868:+
Coord C1 exon
chr20:9177119-9177262
Coord A exon
chr20:9177263-9177709
Coord C2 exon
chr20:9177710-9177868
Length
447 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
TGTATTCGTTATTTCTGTAGTAG
3' ss Score
3.87
Exon sequences
Seq C1 exon
GGGACTCGGAGCAAGAAGTCATGCTGAAAACAAAGACTCCCAAAGCCACGGTGGGGGGGCTGAGCCCTACCAAGGAATACACGCTGCAGGTCTACGTGCTCAATGGCTCCCAGGAAGCCTTATTTGCCAAGAGGAAATTTGTGA
Seq A exon
GTAAGTAGAAAGATCTACATTTTACCATTCTGAGAGGTCTTGGAGATGTGACTCCTCAGAGCTCGTCCTCTGGCAGGTGAATAGTAGGATCAAGAATTTGTTTGAATTGGAAGAGATCTTTAAAAGCCATTTGGACCAACTCTCCTGCAGCGAACAGGAACACCCACAGCTCCATCAGTGCTCAAAGCCCTGTCCAGCCTGACCATGAGTACCTCCAGAGTTGGGGCATGCACCACCTCTGTGGGTAACCTGAGCCAGTGCCACCCTTACTGTAAAGGGATATATTTTCTTATATTCAGTGTCCCCATAGACTGTACTGAAGCCCGTTACCATTTTGTTGGAAGCTTGGAGAGGGGAGATGGTGAATGCTGATGGGATGAGGGGTGGACCACAACTCACAGACCCACCTGGATTGACTCCTCCTTCCTGTATTCGTTATTTCTGTAG
Seq C2 exon
TAGAGGACCTTAAAAATGCATCCCAGACTAGAAATAACCGAAGGAACTCAGGAGCTGCACCAGGAAAGAACCTCACCTCTGTGGGCAGCTCAACAGCGGAGCAGAGCCTGGGGATGGAGACTGCTCCACCACCCTTGAGCACCGTCCTGACACATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.388 A=NA C2=0.944
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(50.6=79.6)
A:
NA
C2:
NO
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:
GGGACTCGGAGCAAGAAGTCA
R:
CTGGATGTGTCAGGACGGTG
Band lengths:
303-750
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]