GgaINT0097679 @ galGal4
Intron Retention
Gene
ENSGALG00000009641 | COL1A2
Description
collagen alpha-2(I) chain precursor [Source:RefSeq peptide;Acc:NP_001073182]
Coordinates
chr2:23725972-23726870:+
Coord C1 exon
chr2:23725972-23726070
Coord A exon
chr2:23726071-23726762
Coord C2 exon
chr2:23726763-23726870
Length
692 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
CAATAACCTGTTGTTGCTAGGGT
3' ss Score
3.29
Exon sequences
Seq C1 exon
GGCGAGCGTGGTCTTCCTGGTGAAAGCGGTGCTGTTGGTCCTGCTGGTCCTATTGGAAGCCGTGGTCCATCTGGCCCACCAGGCCCTGATGGTAACAAG
Seq A exon
GTATGTTAAATTCTCAGTGGGACATAATTACGTATGTCTGCTCCAGCTACTACTGCCTCACTGTTGAATTGCTGGTGAGGGCAGTCAGAAACCTTCTTTACTCAGTATAAATGGTTGCTGCCAACAGGTAACCTACACACATCATAGGTACTGGGCCCTTTCTTCAAGTAGTAAATCTGCATAACAGCTAGTCCATACTAATATAGATTTTTGTTGTTGTTGTTGTTTATCACTGATGAGAATGGAAGAGGAGCTTCAGTTTATTCTAAACTTGGATACTGCTTCTTAGCTGGGAATGCTGTTACTCTGAGATTTTGGCTAAAATTCATGCTAGCCTGTTTATACCCACCTGGGGAAAGAAGTTCTTGTGTCCAGTAAGCAATATTTTCCCAAAAACATTAGTATGGTCTGCCAAAATAAGTGTGGGGCTCAACTTTCAAGATCTTCATATGTAGTCTTTCCACAAAGGTTTAGTTTGGAATATGGGACCACAGAATCGGAGAGAGTTCATGTCCAGCATATTCACTAGCTGAAAAACTACAAATGCACAATAGCTAGAGACCAAATACTACTACTCAGTATATTTACAAGCCAGCAGAATATGGGCTTATAGGTAATGACAAAATTTTGTTCCATATTGCAATATTGTTCCATATTTCACCTTGTCTTACACAATAACCTGTTGTTGCTAG
Seq C2 exon
GGTGAGCCTGGTAATGTCGGTCCTGCTGGTGCTCCTGGTCCCGCTGGGCCTGGTGGAATCCCAGGAGAGAGAGGTGTTGCAGGTGTTCCAGGAGGCAAGGGTGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009641:ENSGALT00000015703:31
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:
NO
A:
NA
C2:
PF0139113=Collagen=PU(42.6=80.6)
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:
GCGAGCGTGGTCTTCCTG
R:
CTTCTCACCCTTGCCTCCTGG
Band lengths:
206-898
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]