GgaINT0090095 @ galGal4
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
collagen alpha-1(XII) chain precursor [Source:RefSeq peptide;Acc:NP_990352]
Coordinates
chr3:80261292-80261808:+
Coord C1 exon
chr3:80261292-80261431
Coord A exon
chr3:80261432-80261675
Coord C2 exon
chr3:80261676-80261808
Length
244 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
TTTTTTTATTCCCCCACAAGAGT
3' ss Score
2.99
Exon sequences
Seq C1 exon
AGCCTGTGCCATCACCAGTCAATCTGAGAATCACAGAGATAACCAAGAATAGTTTTAGAGGAACTTGGGATCATGGAGCTCCAGATGTTTCTCTCTATAGAATAACCTGGGGACCATATGGTAGATCCGAAAAAGCAGAG
Seq A exon
GTAAGAGTAATCACAGTAAGATTTTGGGGGCAGTCTCTTAGAGGGCATATTTTAAGAATCAGAAATGTAAATAATAAATGGCCTATATCTTGCAAGCCCTCCTGTTGTGCCTAATTGCAATTCAATATAGAAAACGCATTCACAGCCATCTATAGTAATGTTACTGTGTAAAAAGTCACTCAGATTCCTCTCTTTGTCTTTTTTCTCTTTTTTATTTCTTGTATTTTTTTTATTCCCCCACAAG
Seq C2 exon
AGTATTGTAAATGGAGATGTCAACAGTCTGCTCTTTGAAAATCTGAACCCAGATACATTGTATGAAGTCTCGGTTACTGCCATTTATCCTGATGAATCAGAAAGTGATGACTTGATTGGCAGTGAACGAACAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015908:ENSGALT00000025640:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.289
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(54.4=91.5)
A:
NA
C2:
PF0004116=fn3=PD(43.0=75.6)
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:
CCTGTGCCATCACCAGTCAAT
R:
TTCGTTCACTGCCAATCAAGTCA
Band lengths:
268-512
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]