GgaINT0097666 @ galGal4
Intron Retention
Gene
ENSGALG00000009641 | COL1A2
Description
collagen alpha-2(I) chain precursor [Source:RefSeq peptide;Acc:NP_001073182]
Coordinates
chr2:23718575-23718856:+
Coord C1 exon
chr2:23718575-23718619
Coord A exon
chr2:23718620-23718757
Coord C2 exon
chr2:23718758-23718856
Length
138 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
ACTTTCTCTGTTTGGAACAGGGT
3' ss Score
8.46
Exon sequences
Seq C1 exon
GGCAACCCTGGTGCTAATGGTCTTCCTGGGGCTAAAGGTGCAGCT
Seq A exon
GTAAGTATAGCCATATGCCAATGCAAAGGATTATTTGCTTTAAGATTAAAAAAAAAAACAAAAAACAACACACCACATTTCAGTTAATGGATCACAAAAGATAATGAACTTACAGTAGACTTTCTCTGTTTGGAACAG
Seq C2 exon
GGTCTTCCTGGTGTTGCTGGTGCTCCTGGTCTGCCTGGGCCCCGTGGTATTCCTGGTCCTCCTGGCCCTGCTGGTCCAAGTGGTGCTAGGGGACTTGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009641:ENSGALT00000015703:18
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(16.9=100),PF0139113=Collagen=PU(10.4=53.3)
A:
NA
C2:
PF0139113=Collagen=PD(15.7=39.4),PF0139113=Collagen=FE(41.6=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:
GCAACCCTGGTGCTAATGGTC
R:
ACAAGTCCCCTAGCACCACTT
Band lengths:
142-280
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]