GgaINT0043073 @ galGal4
Intron Retention
Gene
ENSGALG00000004286 | COL13A1
Description
collagen, type XIII, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2190]
Coordinates
chr6:10620380-10621172:+
Coord C1 exon
chr6:10620380-10620532
Coord A exon
chr6:10620533-10621073
Coord C2 exon
chr6:10621074-10621172
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:ENSGALT00000006816:30
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(56.2=80.4),PF0139113=Collagen=PU(8.5=15.7)
A:
NA
C2:
PF0139113=Collagen=PD(38.0=90.9),PF0139113=Collagen=FE(36.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
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]