DreINT0049445 @ danRer10
Intron Retention
Gene
ENSDARG00000020007 | col1a2
Description
collagen, type I, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-030131-8415]
Coordinates
chr19:41406862-41407089:+
Coord C1 exon
chr19:41406862-41406960
Coord A exon
chr19:41406961-41407035
Coord C2 exon
chr19:41407036-41407089
Length
75 bp
Sequences
Splice sites
5' ss Seq
TCTGTAAGT
5' ss Score
7.96
3' ss Seq
ATCAATTAACCTCCTTGCAGGGC
3' ss Score
7.89
Exon sequences
Seq C1 exon
GGTGCCGCTGGTCAAGATGGTCGCACCGGACCCCCTGGCCCAACTGGACCCAGAGGCCAGCCTGGTAACATTGGATTCCCTGGTCCCAAAGGACCTTCT
Seq A exon
GTAAGTATTTTGTGCAAGTATTTAGAGATTCAAATAGCAATAATTCAATGATCTTATCAATTAACCTCCTTGCAG
Seq C2 exon
GGCGAGGCTGGCAAGCCTGGTGAGAAGGGACCTGTTGGCCCTACTGGACTGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000020007:ENSDART00000144544:23
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(7.8=15.2),PF0139113=Collagen=PU(49.2=97.0),PF0139113=Collagen=PU(6.6=18.2)
A:
NA
C2:
PF0139113=Collagen=FE(26.2=100),PF0139113=Collagen=FE(18.7=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:
GTGCCGCTGGTCAAGATGG
R:
TCTCAGTCCAGTAGGGCCAAC
Band lengths:
152-227
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]