DreINT0050351 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40230553-40230780:-
Coord C1 exon
chr6:40230709-40230780
Coord A exon
chr6:40230598-40230708
Coord C2 exon
chr6:40230553-40230597
Length
111 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
AATATTTTGCTTTATTTCAGGGT
3' ss Score
9.48
Exon sequences
Seq C1 exon
GGATTGGCAGGATTAAGAGGCCCTCAGGGTCCCCCAGGGCCGCCTGGGCCCCCAGGAGCTGATGGCACACCT
Seq A exon
GTGAGTTATAACTTAGTTTGTGTTGTGAAAAATCAAACCCAACACAAATTCCTTTGCTGAGTCATAAGCATGTGCTTTATCATATCAAAACAATATTTTGCTTTATTTCAG
Seq C2 exon
GGTAAAGCAGGGGAGGACGGCAAATCAGGACTGCCTGGAAAGACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:63
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(6.9=20.8),PF0139113=Collagen=FE(28.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.1=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:
TTGGCAGGATTAAGAGGCCCT
R:
AGTCTTTCCAGGCAGTCCT
Band lengths:
114-225
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]