DreINT0049437 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41403165-41403394:+
Coord C1 exon
chr19:41403165-41403263
Coord A exon
chr19:41403264-41403349
Coord C2 exon
chr19:41403350-41403394
Length
86 bp
Sequences
Splice sites
5' ss Seq
CCTGTAAGT
5' ss Score
7.52
3' ss Seq
CTGTCTTTGTATTTTTACAGGGT
3' ss Score
10.59
Exon sequences
Seq C1 exon
GGAGAACTTGGACCCGCTGGTCCCACTGGACCATCTGGAGCTCAGGGACAAAGAGGAGAGCCAGGCCCGAACGGTGCCGTTGGCCCCGTTGGACCCCCT
Seq A exon
GTAAGTGCATTTCAAATCATTTGCAGATAAATTGATTTGATTATCAAGCAGAAGAAAAAGTAACATCTGTCTTTGTATTTTTACAG
Seq C2 exon
GGTAACCCTGGTGCTAATGGTATCAATGGTGCTAAAGGAGCAGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:15
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(14.1=33.3),PF0139113=Collagen=FE(42.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.7=100),PF0139113=Collagen=PU(9.1=40.0)
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:
GAGAACTTGGACCCGCTGG
R:
CTCCTTTAGCACCATTGATACCA
Band lengths:
138-224
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]