GgaINT0097683 @ galGal4
Intron Retention
Gene
ENSGALG00000009641 | COL1A2
Description
collagen alpha-2(I) chain precursor [Source:RefSeq peptide;Acc:NP_001073182]
Coordinates
chr2:23729443-23729655:+
Coord C1 exon
chr2:23729443-23729496
Coord A exon
chr2:23729497-23729601
Coord C2 exon
chr2:23729602-23729655
Length
105 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGA
5' ss Score
4.07
3' ss Seq
CCTCATTGTCTTCTCTTTAGGGT
3' ss Score
10.28
Exon sequences
Seq C1 exon
GGTGAAGGAGGTCCTGCTGGTCCCGCTGGTCCTGCTGGTGCCCGTGGTATTCCT
Seq A exon
GTAAGAAGCAATTCCTTCAATTATTTCATCGTGTCAAAGACATGATATTCAGAAAAATGCCCTTTTAAAGCCAATTCCAACTAGTCCTCATTGTCTTCTCTTTAG
Seq C2 exon
GGTGAACGTGGTGAGCCTGGTCCTGTAGGTCCTAGTGGATTTGCTGGACCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009641:ENSGALT00000015703:35
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(1.5=5.6),PF0139113=Collagen=FE(19.5=100)
A:
NA
C2:
PF0139113=Collagen=FE(19.5=100),PF0139113=Collagen=PU(9.1=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:
GGAGGTCCTGCTGGTCCC
R:
AGGAGGTCCAGCAAATCCACT
Band lengths:
102-207
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]