GgaINT0046110 @ galGal4
Intron Retention
Gene
ENSGALG00000002552 | COL3A1
Description
Gallus gallus collagen, type III, alpha 1 (COL3A1), mRNA. [Source:RefSeq mRNA;Acc:NM_205380]
Coordinates
chr7:576799-577104:-
Coord C1 exon
chr7:577006-577104
Coord A exon
chr7:576853-577005
Coord C2 exon
chr7:576799-576852
Length
153 bp
Sequences
Splice sites
5' ss Seq
GAGGTTAGT
5' ss Score
7.15
3' ss Seq
TGATCTTTCTCTTTTGTAAGGGT
3' ss Score
6.7
Exon sequences
Seq C1 exon
GGTAATCAGGGTGAACCTGGCCGTTCTGGTCCACCTGGCCCAGCAGGCCCACGTGGTCAGCCAGGTGTAATGGGTTTTCCTGGTCCAAAAGGAAATGAG
Seq A exon
GTTAGTGGGCTGTTTCCACTTCTCCTGTGCTTATGCTTGAGCAGTCATGTGGTAAAATTATATTGCTTCATGGGAGATTCAATGCTGCAGTTGTTAAGTTATTGTGTGTGGACTAGAACAAGTATTTTACATGTGATCTTTCTCTTTTGTAAG
Seq C2 exon
GGTGCACCAGGTAAGAATGGAGAAAGAGGCCCTGGTGGACCACCTGGAACTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002552:ENSGALT00000004032:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GTGAACCTGGCCGTTCTGG
R:
AGGAGTTCCAGGTGGTCCAC
Band lengths:
143-296
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]