GgaINT0125296 @ galGal4
Intron Retention
Gene
ENSGALG00000002546 | COL5A1
Description
collagen alpha-1(V) chain precursor [Source:RefSeq peptide;Acc:NP_990121]
Coordinates
chr17:7541254-7541473:+
Coord C1 exon
chr17:7541254-7541343
Coord A exon
chr17:7541344-7541419
Coord C2 exon
chr17:7541420-7541473
Length
76 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGT
5' ss Score
8.54
3' ss Seq
CTATTTTTCCCATCTTCCAGGGT
3' ss Score
10.46
Exon sequences
Seq C1 exon
GGGGACCCCGGTCCTGCTGGCCTCCCAGGGAAGGATGGTCCCCCAGGCTTGCGAGGCTTCCCTGGAGAAAGAGGTCTGCCTGGCCCCATT
Seq A exon
GTAAGTATCAACAACAGGATGCCCAGGCAGCGCAGCACACAGCTCCCCAAATGACTCTATTTTTCCCATCTTCCAG
Seq C2 exon
GGTTCTCCAGGGCTGAAAGGCAACGAAGGTCCCCCAGGCCCCCCTGGTCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002546:ENSGALT00000004020:39
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(43.9=100),PF0139113=Collagen=PU(32.2=96.7)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(18.9=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:
CCTCCCAGGGAAGGATGGTC
R:
GGGACCTTCGTTGCCTTTCAG
Band lengths:
103-179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]