GgaINT0125317 @ galGal4
Intron Retention
Gene
ENSGALG00000002546 | COL5A1
Description
collagen alpha-1(V) chain precursor [Source:RefSeq peptide;Acc:NP_990121]
Coordinates
chr17:7552674-7553298:+
Coord C1 exon
chr17:7552674-7552727
Coord A exon
chr17:7552728-7553039
Coord C2 exon
chr17:7553040-7553298
Length
312 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
CTTCTTTCCCCATCCATCAGGGT
3' ss Score
8.29
Exon sequences
Seq C1 exon
GGTCCAACGGGTCCAAAGGGTGAATCGGGTCTTCCTGGGCCTCCAGGGCCTCCT
Seq A exon
GTAAGTACAGTCCGTTACACAAACTTAATGGGTGTTGTCATGTGGATTTCCAGAGTCCTCACAATGGAGTGACATCCGTTAGGGATGCCAGGGAAGAAAGCAGAAGGTGAAGGGAGGAATTAGTAATGAGAGGAGAACAAGAAGGAACCAATGTTGGTGGCTGGGGTTTTTCTCGGTGCCACCATGGGTGTTTTAGATGTCTAATGTATATCTTGTGATGCTGTTCTTCAGCACTGGTGGATGCTTTGGCTGTTTCTTCTGTCTCGTCCCCACTTCCACTGAGAAGCTGCATCTTCTTTCCCCATCCATCAG
Seq C2 exon
GGTCCTCCTGGAGAAGTCATCCAGCCTCTGCCCATCCAGTCTTCCAAGAGGACCAGGCGAAACATCGACGCCAGCCAGCTGGTGGACGATGGAAACGCTGACAACTACATGGACTATGCAGATGGCATGGAGGAAATCTTTGGCTCACTGAATTCCTTGAAACTGGAAATTGAACAAATGAAGCATCCATTGGGCACTCAACATAACCCAGCTCGTACCTGCAAGGATCTCCAGCTCTGTCACCCTGATTTCCCAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002546:ENSGALT00000004020:60
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=0.759
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(27.0=100)
A:
NA
C2:
PF0139113=Collagen=PD(12.7=9.2),PF0141013=COLFI=PU(12.7=31.0)
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:
GTCCAACGGGTCCAAAGGGT
R:
TCTGGGAAATCAGGGTGACAGA
Band lengths:
310-622
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]