GgaINT0097659 @ galGal4
Intron Retention
Gene
ENSGALG00000009641 | COL1A2
Description
collagen alpha-2(I) chain precursor [Source:RefSeq peptide;Acc:NP_001073182]
Coordinates
chr2:23711794-23712117:+
Coord C1 exon
chr2:23711794-23711847
Coord A exon
chr2:23711848-23712063
Coord C2 exon
chr2:23712064-23712117
Length
216 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
TAATTTTCTACTCCATATAGGGA
3' ss Score
6.37
Exon sequences
Seq C1 exon
GGTGCTCGTGGTTTCCCTGGAACTCCTGGTCTGCCTGGCTTTAAGGGAATTAGG
Seq A exon
GTGAGTATATGTGTACTTCTTCCCTGAGTAGTTAACTGACAGCCCTTCAAGGTACTGAAAACTCCTGAAAATCCCCTCAAAGTTAAAAGTATATATTCTAAATGCATTAATATATTTGAAGTTCTGAATATTTCCTGTCAAAAGAGAATGCGCAGTTTGTGTATGGCATTTAGTGAGAAAGTACGTACTTAACCTTTAATTTTCTACTCCATATAG
Seq C2 exon
GGACACAATGGTCTGGATGGTCAGAAGGGACAACCTGGTACTCCTGGCACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009641:ENSGALT00000015703:11
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(27.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(27.9=100),PF0139113=Collagen=PU(10.3=44.4)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]