GgaINT0011648 @ galGal3
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
NA
Coordinates
chr20:8818961-8820449:+
Coord C1 exon
chr20:8818961-8819074
Coord A exon
chr20:8819075-8820305
Coord C2 exon
chr20:8820306-8820449
Length
1231 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGT
5' ss Score
9.8
3' ss Seq
GTGGCTTCATCCCACCTCAGGGG
3' ss Score
5.26
Exon sequences
Seq C1 exon
GGTCATCAGGCCGGCTGAAACTCACAGTCCTTTCAGAAGACAGGCTCCAGATGAAATGGAAAGAAACCGAAGGAAGCATCAATGGCTACAAAGTGCGGGTAAAGCCCATGGCAG
Seq A exon
GTATGTGCTACCCAGCAGAGTGCTCTGAGTGAGGGATGGGCCCCCAGCTTCTGTCTGGCACTGGGTATGTGCTGGATGCTCTTTCTCCTTGTCTGCACCATTGAATATTTGCCCAAAGTGGAGCGGAAGACAGAAAACGAATTCACAGTGCAGTGGTTATAAGTGGTGGTCATGTCACCGCAGGGGTCCTGCTTGTCTCATCCTCAGGGACGGGATGTCCTTGGCCCCATACATGGGGGTGCTCAGCCTGTGGCTCCCCGCCCTGGATGAGCTCCAGCTCTCCCTGACTTCTGACTCCAGGCTGGGTGCTGCAGGAAGGGCACCGTGTCCTCGTGGGGAAGCAGCATCCGGGTGCAACCTTAGCTTGTGCCCATCTGCCTGCTTTTAGCTTAGCTCCCAGCTGTTTGCCCAGCCGGTGCTGGAGGTTTCTCATTCCTCCCCTGCCAGGGAGCAATGGGCATCCCAGGAACGTGGGGAATCCTCACACCGAGCACGCCTGAGGCTTTCCCCATGTGTGGGCTGGGGAGCTCCATTTTCAGCCCTAAGGGTGATGAGATCAGAAATGCATCCATCCCCACATTTAAAGGCTTGTGCACCTTTCTTACTCAGACGATTTTAGGGAGCTGCTTTGCCTCCCTCCCTTTGCTTTGTTCCAGTGGTCCGAAGTTTCTCCATACCACCCTCTGTAACAGAGACACGGTGCAGTATTTGGCTGTGGTTTTGCAGAACTACCTTGCTTTATCTGCTCCTTGCTGTGCGGAGGACAGCCTCTCTTAGGGAGAGATGAGGCTTGCAGAGGGAACACAGAAAGAACAGCTGCATTAAGTACAGTGAGTCCCAAGGGCCAGGACAGAACACTGGAGATACTGGAGCGCTTCCTCACCTTGTCACAAATGACCTCAAGGACATCACTTGGTTGGATGTTTCCATAAGTGGTGTTTGCCCAACCTTCACCCTCTGGGAACTGACCTTTCTGTCAGCAGCTCTTTGAGAAGTCAGTGGGAGTTGAACTAGAGCTAGGTGGGAGCTGGTTTTCCATTTGGAGCACGTATCAGGGCTGTTTAAAAGACTTTCTCAGCTCTGAAAACAGAAATCCACAGAATTAAAAATTAAATTAGAATTGATTGAGGTCCCCAGACAGACATTCTCTGCATTTCGGTGGTACTTCTGCTATTGTCAGCTTAAATGTAAGCTCTAACAGTTTCTGAACTGTGGCTTCATCCCACCTCAG
Seq C2 exon
GGGACTCGGAGCAAGAAGTCATGCTGAAAACAAAGACTCCCAAAGCCACGGTGGGGGGGCTGAGCCCTACCAAGGAATACACGCTGCAGGTCTACGTGCTCAATGGCTCCCAGGAAGCCTTATTTGCCAAGAGGAAATTTGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.103 A=NA C2=0.388
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(48.1=94.9)
A:
NA
C2:
PF0004116=fn3=PD(50.6=79.6)
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:
GTCATCAGGCCGGCTGAAAC
R:
ACAAATTTCCTCTTGGCAAATAAGGC
Band lengths:
255-1486
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]