GgaINT0011678 @ galGal3
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
NA
Coordinates
chr20:8851678-8852855:+
Coord C1 exon
chr20:8851678-8851731
Coord A exon
chr20:8851732-8852783
Coord C2 exon
chr20:8852784-8852855
Length
1052 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
CTTGTAATTGATGTCTGCAGGGT
3' ss Score
6.57
Exon sequences
Seq C1 exon
GGGGTGAGGGGACTGGAAGGCACAGCTGGGCCCCCAGGACCTCCTGGACCAAGG
Seq A exon
GTGAGTACAGGAGCAATGCGGATCTGTTTGAAATCTCTTCCTCAGAAGGAGCTTGGGATAACTGCTGTCATCCAGAGGTGTCTGGGCAAACCCTCTTCTTGGGTTGTCACAAGGGAATATCCTCACACGTATTGCAGAAATCCACTTTCTCTGCCACTGTCTCACGGCTTCTTAAGAAATAAAGAGAAAAAGCCTTCAGCTTGCCTCTTGGAGGCAAATGGAACCTATTTACTGCTGCATTTGCATTAAATCCCATAGCAGCTGTGGTAAGGTATCTATAGCGAGGGCCACATTCAGCTCCTGACTTGGACTTGCTTATCCTGGGAAGACAGGGAGCCAGGGCTGAACCTCAGCTTTTAAATGTGAGGAAAGCACTGCAGCCTTTGGACCAGGCTCTGAAAGATGGCCTGGTGCTGCCTTAAAGTTTTCTTTCTTTCATTTTCCACTGATCTAAAGAGCTATTAATCTCCATTGAGCTTAAACATAACAGCTGAAAAAAACTACAAAAGCAAGTATTTTTAGTGCTTTTTTGCCTTATTTTTTTCTTCCCCATATGGCTCCAAAAGGCACAGAAACTTCTCAAAGAAGAGATAACCAAAGAAGACTCTTTCCAATCTCTAATCTACAGTTGCTATTGTAAAGACTTAGCAGCAAAACACAGGTCTTAAAGGGGAAAAAAAAGCAGTGGCATGGTATTAGCAGGCTGAAGAAAAGGGTTATGCTATAGGCTGTGCCTAAATCTGAATGTGTAATGAAGGATCTAAAGCCAGTAGGCTAAAAATCACATTGCAGTTTGTTGGCAAAACTCAGCATTGCTGGCTTGACAGTAGCTGAGACAGTAATAAGAAATGATGTGAAGATGACGCATACGTGATACACTCTTAACATTGTGCTCATGGCTGGATGAGGTACTGACATAAACCTTAAGGCAGCAGTGCTCTTGTTGGAGTCCTCCAAGCTCAAACTGCTGGTGCCCCTGGAGCTGCAAGGAGATGTCAGTCAGAAAGAGAACAGTGGGACTTTCATCTTTGTCTTGTAATTGATGTCTGCAG
Seq C2 exon
GGTTTCCAAGGAGTGACAGGCTCCCGGGGCAGCAGCGGAGAGAAGGGACCTCCAGGTGATGTTGGGCCAACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(23.2=72.2),PF0139113=Collagen=PU(28.3=94.4)
A:
NA
C2:
PF0139113=Collagen=FE(38.3=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]