GgaINT0116534 @ galGal4
Intron Retention
Gene
ENSGALG00000016841 | COL4A1
Description
collagen alpha-1(IV) chain precursor [Source:RefSeq peptide;Acc:NP_001155871]
Coordinates
chr1:138180699-138181042:-
Coord C1 exon
chr1:138180989-138181042
Coord A exon
chr1:138180726-138180988
Coord C2 exon
chr1:138180699-138180725
Length
263 bp
Sequences
Splice sites
5' ss Seq
ATAGTAAGT
5' ss Score
8.65
3' ss Seq
ATGTCTTTTTTTTTTCACAGGGA
3' ss Score
10.98
Exon sequences
Seq C1 exon
GGTGAAAGAGGTCCAGTAGGTCCCCCAGGTTTACCGGGACTGACTGGAAGCATA
Seq A exon
GTAAGTAGATTCTTCGTGCTTCATTCACTTGTTTCAACTTGATTCTTGAAATGTAGATAGTATTCTATGGAATTGTATAGATTATGAAATGTAAAATACACAATACTGAAGAGTAAGTCCCTGAGCAACCTGATCTTGCTGTGGATGTTCCTGTTCATTGCTGAGGAGTTGGGCTGCATTGTCTTCAGAGGTACCTTCCAACTCTAAGGATTCTGTGGTTCTATGAAGCAAATAACATCAAATATGTCTTTTTTTTTTCACAG
Seq C2 exon
GGACCCCCAGGACCTCCTGGAATTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000016841:ENSGALT00000027197:7
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(28.3=100)
A:
NA
C2:
PF0139113=Collagen=FE(13.3=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]