GgaINT0090087 @ galGal4
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
collagen alpha-1(XII) chain precursor [Source:RefSeq peptide;Acc:NP_990352]
Coordinates
chr3:80253857-80254356:+
Coord C1 exon
chr3:80253857-80254021
Coord A exon
chr3:80254022-80254209
Coord C2 exon
chr3:80254210-80254356
Length
188 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
TTTCATGTCTTCTCTGTAAGGTA
3' ss Score
7.31
Exon sequences
Seq C1 exon
GAATGGCCTTGGATTTCATCTTAAAAAACAACTTTAAACAAGAAGCAGGCTTGAGGCCCAGAGCTCGCAAAATTGGTGTTCTCATTACTGATGGTAAATCACAAGACGACGTAGTGACCCCTTCAAGAAGACTCAGAGATGAGGGAGTAGAACTTTATGCAATTG
Seq A exon
GTAAGTATTACATGAAGAGGTGGCCTGTTGCAGCTCCCTCTCACCCTTCTGCTAAATGTATAGGGAAGTGGAAACAAATAAGTATTTAGAAGGGAATTTAATGAATGTGTTTAGGAACTCATGTTTATGGTGCTACATTTCACATCTGTCATTTCTAACAAGTTTTGTTTTCATGTCTTCTCTGTAAG
Seq C2 exon
GTATTAAAAACGCAGATGAAAATGAATTGAAGCAAATTGCAACAGATCCAGATGACATCCATGCCTACAATGTTGCAGATTTCTCCTTTCTGGCTAGCATTGTTGAAGATGTAACCACAAATTTGTGTAATAGCGTGAAAGGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015908:ENSGALT00000025640:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.089 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(31.8=100)
A:
NA
C2:
PF0009223=VWA=PD(21.4=74.0)
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:
CCCAGAGCTCGCAAAATTGGT
R:
TGGACCTTTCACGCTATTACACA
Band lengths:
255-443
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]