DreINT0049560 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21175547-21175799:+
Coord C1 exon
chr8:21175547-21175645
Coord A exon
chr8:21175646-21175745
Coord C2 exon
chr8:21175746-21175799
Length
100 bp
Sequences
Splice sites
5' ss Seq
AATGTAAAA
5' ss Score
-0.78
3' ss Seq
TGTATCTCCCTCTCACATAGGGT
3' ss Score
9.1
Exon sequences
Seq C1 exon
GGTGCCCCTGGTGAAGATGGCCGCCCTGGACCACCTGGGCCTCTGGGAGCTCGTGGTCAGCCTGGAGTGATGGGATTCCCTGGACCCAAGGGAGCCAAT
Seq A exon
GTAAAACCATCAGAGCATTTCTGCATTTCAGCTACAATTTGTCTTTGAAAGTGAGTGGCAAGTGTATGTTTTGTGTCTCATGTATCTCCCTCTCACATAG
Seq C2 exon
GGTGAACCTGGAAAACCTGGAGAGAAAGGACTTGTTGGACGCACTGGTCTTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:27
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(26.2=66.7),PF0139113=Collagen=FE(43.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(23.3=100),PF0139113=Collagen=PU(3.1=11.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCCCCTGGTGAAGATGG
R:
AAGACCAGTGCGTCCAACAAG
Band lengths:
149-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]