GgaINT0043073 @ galGal3
Intron Retention
Gene
ENSGALG00000004286 | COL13A1
Description
NA
Coordinates
chr6:12133309-12134101:+
Coord C1 exon
chr6:12133309-12133461
Coord A exon
chr6:12133462-12134002
Coord C2 exon
chr6:12134003-12134101
Length
541 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
AAATCTTTCTTGATTCATAGGGT
3' ss Score
7.17
Exon sequences
Seq C1 exon
GGACCACGAGGCAAGCCAGGAGAAATGGGACCTCCTGGACCTCATGGACTGCCAGGAAGGGATGGACCACCTGGAATAAAGGGAGAGCCAGGCCAGATTGGGGTCGCAGGAGAAAAGGGGGATAAAGGAGAGCCAGGACAAGCAGGCTCACCG
Seq A exon
GTGAGTACATTGGAGCCCCTCAGCAGTGTTCTGTTCTTGTGGCTCTTCAGGTTATGGGCAGAGCTGTGGGATAACTTGGAGCCCCTAAGCAACGGGGGCAGAGTGCCCAATCTCCTAGCTTGAGCCTGTCACAACTTCTGCACCCCAACACTAGTCAAGAGGGTTTTTTGCAGCAAGTTTTTGCCTCTCTGCAGGATTACTAGGATAAAGCTCTTGCAGTAACAACAGCTAGCTGTTGGAGTGATTTCTAGCATGTACCCCAGCAAACTGCCTAACCACAAGCAGAACTTGGAGGCAGGAAAGCAGTCCTCCATTGCCATTCTGGGGAATGGCACATCCACAGTGACAAGAGGGTGTTTCAGGCACGTTACTGTCTGGTTTCAGTACTAGCAAAGCCCTGTCTTTCCCTGTGTACCTGATAGCTGTCTGGGTTTTCCATTGTATTCTTGGAACGCACAGGGCACAACTCATTTCTGGCAATGATATCTGTAATACTGGCAAAAGGTCTTGCAAAAAGCTGCAAATCTTTCTTGATTCATAG
Seq C2 exon
GGTCTTGATGGCCCCACTGGAGAGAAAGGAGAACGAGGTGACCAAGGGATGCCAGGACCACCAGGATTGCCGGGTCCCATTGGACTTCCAGGATTGACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000004286:ENSGALT00000006816:27
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(40.0=47.1),PF0139113=Collagen=PU(68.1=92.2),PF0139113=Collagen=PU(3.6=5.9)
A:
NA
C2:
PF0139113=Collagen=PD(29.0=60.6),PF0139113=Collagen=FE(38.1=100)
Main Inclusion Isoform:
NA
Other Inclusion 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:
CGAGGCAAGCCAGGAGAAATG
R:
TGTCAATCCTGGAAGTCCAATGG
Band lengths:
246-787
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]