DreINT0049675 @ danRer10
Intron Retention
Gene
ENSDARG00000104110 | col4a2
Description
collagen, type IV, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-070725-3]
Coordinates
chr9:8891399-8891879:+
Coord C1 exon
chr9:8891399-8891560
Coord A exon
chr9:8891561-8891780
Coord C2 exon
chr9:8891781-8891879
Length
220 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAT
5' ss Score
7.24
3' ss Seq
TTTATTTTACATTTAATTAGGTG
3' ss Score
7.55
Exon sequences
Seq C1 exon
GTTTTCCTGGTACCAGAGGAACCCCAGGGATCCCATCTCCCTTCGGAGCAAAAGGAGATAGAGGAAATGTTGGTGATTTCGGATTATTTGGAGAAAAAGGAGTCCAGGGTGACAGAGGAGAAAAGGGAAGTTCTGGGGAATCTGGAGTGTCAGGAAGAAAAG
Seq A exon
GTAGATGAGATGGAATAGGAATCAGGTGATGCTTACTGCAGCTATACAAAACTGAAACAGCTCACTGTTAATCATAATGAATATGAATACAAAAATACAGAAATAAATTGATCAAATGTTGTCCTTACAATAAAATGACATGATTTAATCCTCACGTTTGTTTTCAATGAACTGAAAAAGAACTGGAGTCATGTGCAATTTTTATTTTACATTTAATTAG
Seq C2 exon
GTGATAAAGGAGAGCCAGGGATGATGGGATTTCCAGGAAGACGTGGTTTTCAAGGTGACAGGGGCCCTTTTGGACCTAAAGGAGATACCGGACCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104110:ENSDART00000160004:16
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(19.7=25.5),PF0139113=Collagen=FE(69.2=100),PF0139113=Collagen=PU(22.7=27.3)
A:
NA
C2:
PF0139113=Collagen=PD(9.0=20.6),PF0139113=Collagen=FE(50.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTTTCCTGGTACCAGAGGAACC
R:
TGGGGGTCCGGTATCTCCTTT
Band lengths:
260-480
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]