DreINT0049544 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21171150-21171370:+
Coord C1 exon
chr8:21171150-21171203
Coord A exon
chr8:21171204-21171316
Coord C2 exon
chr8:21171317-21171370
Length
113 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATT
5' ss Score
8.55
3' ss Seq
GTTTCTTTTCTGTATGACAGGGA
3' ss Score
8.47
Exon sequences
Seq C1 exon
GGTGAGGCTGGCAAACCTGGTAAAGCTGGTGAGCGTGGACCCCCAGGACCTCAG
Seq A exon
GTAATTATATAGAAACAAAGACCCACATACAACAGTTTTAGTCACTTATTTAGGTTATTTTTTTTCTATTAAGGCGCAACAGTCATTAAATTTGTTTCTTTTCTGTATGACAG
Seq C2 exon
GGAGCTCGTGGATTCCCTGGGACCCCTGGACTCCCTGGCATCAAGGGACACAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:12
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(6.6=22.2),PF0139113=Collagen=PU(23.3=77.8)
A:
NA
C2:
PF0139113=Collagen=FE(21.8=100)
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:
TGAGGCTGGCAAACCTGGTAA
R:
TCTGTGTCCCTTGATGCCAGG
Band lengths:
106-219
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]