DreINT0049561 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21175746-21175995:+
Coord C1 exon
chr8:21175746-21175799
Coord A exon
chr8:21175800-21175941
Coord C2 exon
chr8:21175942-21175995
Length
142 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
TTTGTTTTTACTTTTATTAGGGT
3' ss Score
7.8
Exon sequences
Seq C1 exon
GGTGAACCTGGAAAACCTGGAGAGAAAGGACTTGTTGGACGCACTGGTCTTAGA
Seq A exon
GTAAGTCCTGTTCTTACGCCAGTCGATATCCAGACAGATCTCCAAGCTATAGTTACTAATGAAATAAGTAATAATGCATCAGCATCCCACATCAAACAGATTTTTGCCTTATTTTTTCTCTCTTTGTTTTTACTTTTATTAG
Seq C2 exon
GGTTTGCCTGGTAAAGATGGAGAGACTGGACCTTCTGGTCCTCCTGGCCCTGTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:28
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(23.3=100),PF0139113=Collagen=PU(3.1=11.1)
A:
NA
C2:
PF0139113=Collagen=PD(16.4=66.7),PF0139113=Collagen=FE(26.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGAACCTGGAAAACCTGGA
R:
GGCCAGGAGGACCAGAAGG
Band lengths:
103-245
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]