DreINT0049569 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21177587-21177783:+
Coord C1 exon
chr8:21177587-21177640
Coord A exon
chr8:21177641-21177729
Coord C2 exon
chr8:21177730-21177783
Length
89 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TTTCTGTCTTTTTTTGCCAGGGT
3' ss Score
9.17
Exon sequences
Seq C1 exon
GGTGACTCTGGAGAGAAGGGACCTGAAGGTGCTCCTGGTAAAGATGGTTCAAGA
Seq A exon
GTAAGTGCTATAAAGACAGCAACTGTCAGCAAATTGCTTGCTTTTTATAGCTGATCAAAAGTAATGATCTTTCTGTCTTTTTTTGCCAG
Seq C2 exon
GGTTTGACTGGTCCAATTGGCCCACCTGGTCCTTCTGGTCCCAATGGCGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:35
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(23.9=100),PF0139113=Collagen=PU(0.1=0.0)
A:
NA
C2:
PF0139113=Collagen=PD(24.6=88.9),PF0139113=Collagen=PU(20.0=77.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGACTCTGGAGAGAAGGGA
R:
CGCCATTGGGACCAGAAGGA
Band lengths:
103-192
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]