GgaINT0046087 @ galGal3
Intron Retention
Gene
ENSGALG00000002552 | COL3A1
Description
NA
Coordinates
chr7:601216-601684:-
Coord C1 exon
chr7:601473-601684
Coord A exon
chr7:601308-601472
Coord C2 exon
chr7:601216-601307
Length
165 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
CCCTGAGCTACTTCCCTGAGCAG
3' ss Score
-7.23
Exon sequences
Seq C1 exon
TAGCCCTAGGAGGATGTACCCATCTTGGGCAGGAATATGCTGACAGGGATGTTTGGAAACCAGAGCCATGCCAAATCTGTGTGTGTGACTCTGGATCTGTTCTCTGTGATGACATCATCTGTGATGACCAGGAGTTAGACTGTCCCAACCCAGAGATCCCCTTCGGAGAATGCTGTCCAGTTTGCCCGCAGACAACACCACAGCCTACAAAA
Seq A exon
GTAAGTTCTCAATATGGTTACTTTGGTGTTGCCAACTTTGATTGATTTTCTTTTATATAAAAAATGTGTCACTTTCTGATCCCTGGCAAATACTTGGAATGGGCTGTTTGCATTATGGTAGTGAATTTGTACATCTTCCAGAATTCCCTGAGCTACTTCCCTGAG
Seq C2 exon
CAGGTTGCAATGGTGCAAAGGAGTGGTCCATACAAACATGATGGACATTCAAGCACAGCTTCCTCTCCCTTGAGTCTAGGACCTGCTTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002552:ENSGALT00000004033:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.028 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0009313=VWC=WD(100=80.3)
A:
NA
C2:
PF0139113=Collagen=PU(11.8=19.4)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAACCAGAGCCATGCCAAA
R:
AGCAGGTCCTAGACTCAAGGG
Band lengths:
245-410
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]