DreINT0049551 @ danRer10
Intron Retention
Gene
ENSDARG00000069093 | col2a1a
Description
collagen, type II, alpha 1a [Source:ZFIN;Acc:ZDB-GENE-980526-192]
Coordinates
chr8:21174060-21174288:+
Coord C1 exon
chr8:21174060-21174158
Coord A exon
chr8:21174159-21174243
Coord C2 exon
chr8:21174244-21174288
Length
85 bp
Sequences
Splice sites
5' ss Seq
TCCGTGAGT
5' ss Score
8.93
3' ss Seq
TAAATGCTCACATTCTGCAGGGT
3' ss Score
6.19
Exon sequences
Seq C1 exon
GGTGAAGCTGGTCCCACTGGGGCTCGTGGACCTGAGGGCGCACAGGGACCTCGTGGAGAGGCTGGTACACCTGGATCACCTGGACCCGCCGGTGCATCC
Seq A exon
GTGAGTATATGATGAAGCAAAACATCTTTTGATTTTCTATATCAGTACATTCAATGTGTTGAACTTAAATGCTCACATTCTGCAG
Seq C2 exon
GGTAACCCTGGTACTGATGGTATTCCTGGAGCTAAAGGATCTGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000069093:ENSDART00000100234:19
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(3.0=6.1),PF0139113=Collagen=FE(41.0=100),PF0139113=Collagen=PU(5.4=15.2)
A:
NA
C2:
PF0139113=Collagen=FE(17.9=100),PF0139113=Collagen=FE(15.2=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:
GTGAAGCTGGTCCCACTGG
R:
AGCAGATCCTTTAGCTCCAGGA
Band lengths:
143-228
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]