GgaINT0039315 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10222230-10222448:+
Coord C1 exon
chr8:10222230-10222283
Coord A exon
chr8:10222284-10222403
Coord C2 exon
chr8:10222404-10222448
Length
120 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGC
5' ss Score
6.31
3' ss Seq
TTTCCTTTGTACAAAAACAGGGA
3' ss Score
5.77
Exon sequences
Seq C1 exon
GGAGATCGTGGCCCACAGGGACCTCCTGGTTTACCTGGTGAAGATGGATCAAGA
Seq A exon
GTAAGCTGCTATTTACTTCGAATTCACAGTAAAACTGGGAGTGAATCCCATGTAATGGAAATAGAGTCATAATATCTGCTCTTTTTTTCTAAAACTCGTATTTCCTTTGTACAAAAACAG
Seq C2 exon
GGAGAAGATGGGGAAGTTGGACCAAGAGGTCTCCCAGGTGAAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:19
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=FE(22.1=100),PF0139113=Collagen=PU(19.5=94.4)
A:
NA
C2:
PF0139113=Collagen=PD(13.0=66.7),PF0139113=Collagen=FE(16.1=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:
GGAGATCGTGGCCCACAGG
R:
CCTCTTGGTCCAACTTCCCCA
Band lengths:
83-203
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]