DreINT0049453 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41408649-41408954:+
Coord C1 exon
chr19:41408649-41408756
Coord A exon
chr19:41408757-41408900
Coord C2 exon
chr19:41408901-41408954
Length
144 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGT
5' ss Score
9.79
3' ss Seq
TACATTTATCTGATATACAGGGT
3' ss Score
4.54
Exon sequences
Seq C1 exon
GGAGAGCCTGGTGCAGTTGGACCTGCTGGTGCCCCTGGACCACAGGGAGCTGCTGGTATGCCTGGTGAGCGTGGTGCTGCTGGCACCCCTGGAGCTAAGGGAGAGAAG
Seq A exon
GTATGTTCTAAACATTGGTCATGGTTGCCCTGATGTTACTGTTTACATGAAAACAAGAGTTTTTCATGCACACCATTCTATAGTGAGTCTGTTTGCAAATCTATTTGATCCCTTGTGGTCTAAATACATTTATCTGATATACAG
Seq C2 exon
GGTGAGGCTGGATACAGAGGACTGGAGGGCAATGCTGGAAAAGATGGTGCCCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:30
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(29.9=80.6),PF0139113=Collagen=FE(37.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.5=100),PF0139113=Collagen=PU(12.4=61.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGAGCCTGGTGCAGTTGGA
R:
CCATCTTTTCCAGCATTGCCC
Band lengths:
154-298
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]