DreINT0049677 @ danRer10
Intron Retention
Gene
ENSDARG00000104110 | col4a2
Description
collagen, type IV, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-070725-3]
Coordinates
chr9:8893966-8894353:+
Coord C1 exon
chr9:8893966-8894112
Coord A exon
chr9:8894113-8894245
Coord C2 exon
chr9:8894246-8894353
Length
133 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAA
5' ss Score
7.09
3' ss Seq
TCTGTTTTTAGGATTTGTAGGTC
3' ss Score
0.95
Exon sequences
Seq C1 exon
GTTTTCCTGGATTACCTGGGGCTAAAGGATATCCACCAGTTCCACAGAAACTTCCAGGGGAGCAAGGGCCGCCTGGTCAGATGGGTATTCAGGGACCATCGGGGCGCAATGGAAACCCAGGCCCTGCGGGACCTCCTGGTGATTCAG
Seq A exon
GTACAAAAATTCAAAGTGTCAATCTAGAACTTCTGCAATGAATATGACTTACCTTCTCTTCTTGTCCTGTTGCTGTCCCCCTGATTCCAGCTCCATCATGTAATTGGCTCTTATCTGTTTTTAGGATTTGTAG
Seq C2 exon
GTCCAAGTGGACACAAGGGGATGCCAGGTCTTCCTGGAATACCAGGAAGTCCAGGCTTCCGTGGAGAACCTGGATCAATGGGCCACTCTGGTCTGCAAGGCGAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104110:ENSDART00000160004:18
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(24.6=32.0),PF0139113=Collagen=PU(57.4=70.0),PF0139113=Collagen=PU(4.8=6.0)
A:
NA
C2:
PF0139113=Collagen=PD(41.0=67.6),PF0139113=Collagen=FE(58.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGATTACCTGGGGCTAAAGGA
R:
CTTGTTCGCCTTGCAGACCAG
Band lengths:
248-381
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]