GgaINT0097658 @ galGal4
Intron Retention
Gene
ENSGALG00000009641 | COL1A2
Description
collagen alpha-2(I) chain precursor [Source:RefSeq peptide;Acc:NP_001073182]
Coordinates
chr2:23711256-23711847:+
Coord C1 exon
chr2:23711256-23711309
Coord A exon
chr2:23711310-23711793
Coord C2 exon
chr2:23711794-23711847
Length
484 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
TATGCTCTGCGTGTTTTTAGGGT
3' ss Score
11.02
Exon sequences
Seq C1 exon
GGTCACCCTGGCAAACCTGGAAGACCTGGTGAGAGGGGTGTTGCTGGTCCTCAA
Seq A exon
GTAAGTAGTGATCTACTGTCTATTACATGAAATAGTTCTCATATCAATTAAACCTCTGATGGTATTTCTGAATTGCTCTCCATAGACAATCCATTAATATTCTTTACATGGATTAATCTCAGCATCTGTGTTTCATTTCTTACTTCCAAGGGTATTGTGTAGTTACGATTTTGTTTTGTTCCCTGACCCCTCCCTCCTCACCCCTCTTTACTGGTAATAGAGGTAAAATAGAGTGCTGACATAGCTGTGATGTCACAGGTTAATTAATGAAATTTCTGGGATTCAGAACTGGGAAGTCAAGTTGATTATTGTTAGACCTGGGCCAAGTCTGATCCTGGGAGGTTTGGGATCGGACTGTGTTCCTCACTTGAGTGAGTGAGACCCCAGTCTACTCAATAATGTTAATGAAAGACTTATGTTTTTTCTTTATTTTTTAACTGTACATAACATGAGAGACAATCACTTATGCTCTGCGTGTTTTTAG
Seq C2 exon
GGTGCTCGTGGTTTCCCTGGAACTCCTGGTCTGCCTGGCTTTAAGGGAATTAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009641:ENSGALT00000015703:10
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(15.2=55.6),PF0139113=Collagen=PU(26.2=94.4)
A:
NA
C2:
PF0139113=Collagen=FE(27.9=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:
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]