GgaINT0090088 @ galGal4
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
collagen alpha-1(XII) chain precursor [Source:RefSeq peptide;Acc:NP_990352]
Coordinates
chr3:80254210-80255150:+
Coord C1 exon
chr3:80254210-80254356
Coord A exon
chr3:80254357-80255010
Coord C2 exon
chr3:80255011-80255150
Length
654 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAT
5' ss Score
7.79
3' ss Seq
TTACTTGTTTCCACTTGTAGGTG
3' ss Score
11.34
Exon sequences
Seq C1 exon
GTATTAAAAACGCAGATGAAAATGAATTGAAGCAAATTGCAACAGATCCAGATGACATCCATGCCTACAATGTTGCAGATTTCTCCTTTCTGGCTAGCATTGTTGAAGATGTAACCACAAATTTGTGTAATAGCGTGAAAGGTCCAG
Seq A exon
GTACATCCGATTTTCAATCTAGTTTGTCCTTTTTCCATTTATATGCTTGAGCTATTAATTCTTTTATATTACATGGGACGCTGTGTGGCCCTGGGCTGTTTTTTCAGCTGTTAGCGCGAGGAATTTGTTCAGACCACCTAGACTACCCTGTAGGGGTTCTTCCTTTTCTCTTAACAATGACTGTCAAACCTAACACAGCATGACATGACTGGAAATGCCTGCTTTTTCCCATTGTCAGGAATTATGTTGCTAAGTGTGGCAAGGTCTTTGAAGATACTCATCCAATAACAAAAATTCCAGCAACTCTTTTTAAGTATCAGTGTATGGCAGCTCAAAAGCAAAGGCTAGCATGGAAGAACAGTAACACTGGCTGATGGTTGTCTGGTGAAACACTGGTGTTGAAGGTGGGATAAGAAGGACAGAGAGCTTGTTTGGTTTGCTGAGAGTGTGATGATGAGCTATTTCTTTACAGAGCTGTTTTAAGTGTTCCTGAGCAAATAGAGAAGTAAGCAAATGTCCAAAGCACTGTGGGTTGTTGTTTTTTGTTGTTGTTGTTTCATAAGCAATATATTTTTAGGTCTTATTATACCTTGTGTTTCAATTCCCGATGACATAAGATAAATTAATACATTTTTTACTTGTTTCCACTTGTAG
Seq C2 exon
GTGATTTGCCACCTCCTTCTAACCTAGTTATTTCAGAGGTAACACCTCATTCTTTCAGACTGAGATGGAGTCCACCTCCAGAAAGTGTTGACAGATATCGAGTTGAATATTACCCTACCACTGGAGGTCCCCCTAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015908:ENSGALT00000025640:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.200 A=NA C2=0.277
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=74.0)
A:
NA
C2:
PF0004116=fn3=PU(53.8=91.5)
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:
AACGCAGATGAAAATGAATTGAAGCA
R:
GGGACCTCCAGTGGTAGGGTA
Band lengths:
270-924
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]