GgaINT0116533 @ galGal4
Intron Retention
Gene
ENSGALG00000016841 | COL4A1
Description
collagen alpha-1(IV) chain precursor [Source:RefSeq peptide;Acc:NP_001155871]
Coordinates
chr1:138180989-138181206:-
Coord C1 exon
chr1:138181144-138181206
Coord A exon
chr1:138181043-138181143
Coord C2 exon
chr1:138180989-138181042
Length
101 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACA
5' ss Score
5.19
3' ss Seq
AATTTCTCTGTTCCCTGTAGGGT
3' ss Score
10.07
Exon sequences
Seq C1 exon
GGCATTCCTGGACAAGATGGCCCTCCTGGTCCACCTGGCATTCCAGGATGTAATGGCACAAAG
Seq A exon
GTGACACTTCCATATGTTTATAACAGTATCTCTGTGTTGAAATAAAAACATCCCTCAAGCATATGTTCTCTAAACAAAACCAATTTCTCTGTTCCCTGTAG
Seq C2 exon
GGTGAAAGAGGTCCAGTAGGTCCCCCAGGTTTACCGGGACTGACTGGAAGCATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016841:ENSGALT00000027197:6
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=PD(23.4=71.4),PF0139113=Collagen=FE(33.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(28.3=100)
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:
GGCATTCCTGGACAAGATGGC
R:
TATGCTTCCAGTCAGTCCCGG
Band lengths:
117-218
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]