GgaINT0011659 @ galGal3
Intron Retention
Gene
ENSGALG00000005797 | COL20A1
Description
NA
Coordinates
chr20:8829897-8830564:+
Coord C1 exon
chr20:8829897-8830020
Coord A exon
chr20:8830021-8830424
Coord C2 exon
chr20:8830425-8830564
Length
404 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
TGTCACTCACTGTGTTGCAGTGG
3' ss Score
6.93
Exon sequences
Seq C1 exon
ATTAAGGTGGCTGAGCCCGAGGTCCTGCTGGACGGGCTGTCACCCAGCACTGAGTACTCCATTGCAGTGTATGCGTTGTATGGGGAAGATGCCAGTGATCCAGCCAGCATCCAGGAAACCACCT
Seq A exon
GTAAGTGCTGCTGCTGGTTGTTTTTAAACACTTAATGTGGGAGAGATTAGGTAAGTTAGGGGTTTCTTGTATTGTGGCTTGTAAATCCTGTCTTTTCTTAATACTGGTCCCTAAGGAGATCTCTAATCACCTGGTGTGCTGTGAAACAGTGATTCTCCCCCGGTAAAGGAGGACTCCTGAAGGGATTGCTCCTTAAGATCTTTTTGTTTGGGGAGAAAGGAGGAATTGCTTGGCCATTTCTTCACCTAAAGCACAGATGGGATTCCATGACATCCCACAGAACGGGAATTGTTTTGAGTCTTTTAGTTTGAGATGGAGTCACCCATGAGCAGCAGGAGGCAACCAGTGGCATTGCTTTGGTGCAGCCTTTCAAACCCTGAGTGCTGTCACTCACTGTGTTGCAG
Seq C2 exon
TGGCCTTGAGCCCTCCCAGGTACCTGAGCTTCTCAGAGCTCAGCCACTCATCCGTGCGGGTCAGCTGGGAGCCAGCATCACCGGCAGTGAAAGGTCATCGCGTCACCTACATGTCTAGCAGAGGGAGCAACACCGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005797:ENSGALT00000009312:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.277
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(42.0=81.0)
A:
NA
C2:
PF0004116=fn3=PU(53.8=91.5)
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:
CTGAGCCCGAGGTCCTGC
R:
CTCCCCGGTGTTGCTCCC
Band lengths:
254-658
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]