DreINT0049557 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21175015-21175253:+
Coord C1 exon
chr8:21175015-21175068
Coord A exon
chr8:21175069-21175154
Coord C2 exon
chr8:21175155-21175253
Length
86 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGT
5' ss Score
8.46
3' ss Seq
CATATTCTGTACTATCATAGGGT
3' ss Score
6.41
Exon sequences
Seq C1 exon
GGAGCTCCAGGTAACCGTGGATTCCCTGGCCAGGATGGACTTGCAGGAGCAAAG
Seq A exon
GTTGGTGGGACTCACAGTTGTGTTCTCAACTAATCAGCAAATGTATTTTCTTATGATTTCTGTACTCATATTCTGTACTATCATAG
Seq C2 exon
GGTGCTCCTGGTGATCGTGGTGTTCCAGGTTTGAGTGGACCGAAAGGAGGCACTGGAGATCCTGGTCGCCCTGGTGAACCTGGTCTTCCTGGAGCCAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:24
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(24.3=100),PF0139113=Collagen=PU(10.7=50.0)
A:
NA
C2:
PF0139113=Collagen=PD(12.9=27.3),PF0139113=Collagen=FE(38.1=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:
GGAGCTCCAGGTAACCGTGG
R:
TCTGGCTCCAGGAAGACCAG
Band lengths:
153-239
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]