GgaINT0097670 @ galGal4
Intron Retention
Gene
ENSGALG00000009641 | COL1A2
Description
collagen alpha-2(I) chain precursor [Source:RefSeq peptide;Acc:NP_001073182]
Coordinates
chr2:23720519-23720779:+
Coord C1 exon
chr2:23720519-23720572
Coord A exon
chr2:23720573-23720680
Coord C2 exon
chr2:23720681-23720779
Length
108 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
TTTATTTCTTTTGTTGTTAGGGA
3' ss Score
7.26
Exon sequences
Seq C1 exon
GGCGTGCCTGGATCTCGTGGTCTCCCTGGAGCTGATGGCAGAGCTGGTGTCATG
Seq A exon
GTAAGGCTTGTCTCTGAGTCATTATTTCTAAACCATCTTCTTTTATATACAAATGTGTGATGCTTTTTGCTACCTATTCCTAATTTTATTTATTTCTTTTGTTGTTAG
Seq C2 exon
GGACCTGCTGGTAACCGTGGTGCTAGTGGTCCTGTTGGTGCTAAGGGTCCTAATGGTGATGCTGGCCGTCCTGGTGAGCCTGGTCTTATGGGTCCAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009641:ENSGALT00000015703:22
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(18.7=100),PF0139113=Collagen=PU(16.2=66.7)
A:
NA
C2:
PF0139113=Collagen=PD(19.8=54.5),PF0139113=Collagen=FE(43.2=100),PF0139113=Collagen=PU(13.2=36.4)
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:
TGCCTGGATCTCGTGGTCTC
R:
TTGGACCCATAAGACCAGGCT
Band lengths:
147-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]