GgaINT0039336 @ galGal4
Intron Retention
Gene
ENSGALG00000005180 | COL11A1
Description
collagen, type XI, alpha 1 [Source:HGNC Symbol;Acc:HGNC:2186]
Coordinates
chr8:10248094-10248516:+
Coord C1 exon
chr8:10248094-10248183
Coord A exon
chr8:10248184-10248462
Coord C2 exon
chr8:10248463-10248516
Length
279 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAA
5' ss Score
7.09
3' ss Seq
ACACTTTTTTCATCTTTTAGGGT
3' ss Score
11.63
Exon sequences
Seq C1 exon
GGTGACCCAGGTCCTCAAGGTATTCCTGGGAAAGATGGACCAGCAGGTCTTCGTGGTTTCCCTGGAGAGAGAGGCCTTCCAGGAGCGCAG
Seq A exon
GTACAATATTAAGCACTACAAACATTTGACATGGTTTCTAAATAAATGAAAAAAATAGATTAATCCTCTTAATTCATAGAACCTTCAGTTGTGTTTAAAAATGAATGTAGCAGGTGAACACACATCAAGTATCCATCATTAAGTACCACTGGCCGTATAACCAGAAAGTAATTTCTTCAGTTGTTTGTCTCTGGATTTTTATGTTCTTCCTGTTACACGTGTTGCAAAAATAACCAGAATTTTCCATTGTAAGAGATAAACACTTTTTTCATCTTTTAG
Seq C2 exon
GGTCCCGCTGGTCTAAAAGGAGGGGAAGGCCCACAAGGTCCACCTGGCCCTGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005180:ENSGALT00000008321:40
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(34.1=100),PF0139113=Collagen=PU(11.6=26.7)
A:
NA
C2:
PF0139113=Collagen=PD(7.1=33.3),PF0139113=Collagen=FE(24.6=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:
GTGACCCAGGTCCTCAAGGTA
R:
CAGGTGGACCTTGTGGGC
Band lengths:
135-414
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]