GgaINT0090083 @ galGal4
Intron Retention
Gene
ENSGALG00000015908 | COL12A1
Description
collagen alpha-1(XII) chain precursor [Source:RefSeq peptide;Acc:NP_990352]
Coordinates
chr3:80249251-80250257:+
Coord C1 exon
chr3:80249251-80249443
Coord A exon
chr3:80249444-80250135
Coord C2 exon
chr3:80250136-80250257
Length
692 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGG
5' ss Score
7.37
3' ss Seq
AATACACTTAATTATTGCAGGGC
3' ss Score
5.49
Exon sequences
Seq C1 exon
CCTCTCCCTTTAAGCCGCCTAGAAATTTGAGAACTTCTGATTCAACTATGTCCAGTTTCCGAGTAACCTGGGAGCCGGCCCCTGGGCGAGTGAAGGGGTACAAAGTTACTTTCCACCCTACTGAAGATGACAGGAATCTTGGAGAATTAATTGTGGGACCCTATGACAGCACTGTGGTTTTGGAGGAACTTAG
Seq A exon
GTATGGATGATGATAACAATAATAATTAATAATAGCTTAGGGTTTTGCTTAATTGAGTTCTGGGATTGTAATACCTGTTAAAATCTACTGTAAACTAGGAAGTATTTCTGTCAATGTGCTATCAAGATTTGGTAGTGCAGTTTTTGAAAAGAAACTGACAGGGCAGGTTCTCAGATTATTCACATCACTTTTGGTGTTCTCACAGTAACTGAAAAAGGCAAAGATGTGGGCAGAAGTGTTATTATACATTTCACATATGAGTGTTAATGGGATGTTGGAGAAGACATCTGGGATTTCTAAAGTTTCTCCAAAAGGTCATTATCTCATGTTAAAAAGAGCTTAGTTTAGTTCTTGATTCATTTTATCAGTGGCCAGAATTTATAAAGTAGGCTTCAGAGCATGTCGAAGTCTGTTACGACTTGTTTGCAAGTTAGACTTGTATGCACATTAAAAATAGGATCATTAAAATAGTCTTAAATTACTTGAACAAAGAAAGCTATTAATGTAAGTATAGAATCTTCAATCAGCTCTGAGATAGTGAATATTTGCCTGTCTTGTTAAAGAACTAGTCTTTGGGCTTCACATTTTAGCACTTTCTTTTCTGTGTAGTAAACTGGTAAAAATTTCTTAAATGCAGTATCAGCATTTAGCCAGCCAAGTATCTTCAGTTACAATACACTTAATTATTGCAG
Seq C2 exon
GGCAGGAACTACCTATAAGGTAAATGTTTTTGGAATGTTTGATGGAGGAGAAAGCAACCCCCTGGTTGGACAAGAGATGACCACTCTTTCAGACACTACCACGGAGCCATTTTTATCTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000015908:ENSGALT00000025640:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.385 A=NA C2=0.286
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(74.1=92.3)
A:
NA
C2:
PF0004116=fn3=PD(24.7=47.6)
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:
CCTCTCCCTTTAAGCCGCCTA
R:
AGATAAAAATGGCTCCGTGGT
Band lengths:
311-1003
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]