DreINT0050286 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40273603-40274027:-
Coord C1 exon
chr6:40273908-40274027
Coord A exon
chr6:40273753-40273907
Coord C2 exon
chr6:40273603-40273752
Length
155 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTAG
5' ss Score
1.01
3' ss Seq
TTTGCCTGTGCCCCTTTCAGGAA
3' ss Score
11.64
Exon sequences
Seq C1 exon
TGCCATTAGAGGGAGTGCAGCAGCTCTCAGTTGAAACCATCTCAACAAGCAGCGTTCGAGTTCGCTGGACAGGAGTGACAGGAGCCAGAGCCTATAGAGTCGTGTGGGGCCCTTTCACAG
Seq A exon
GTCTAGCATCCATACTCATTTTTTTATATTACATTATTTATTAACATTCTTAAACAATACATCACTCAACAATAAGGATTTTATAGTAGAAGCTAAATTGTTTTTAATAGATTTCACTTCTTTAATAGAGTTTTTTTTGCCTGTGCCCCTTTCAG
Seq C2 exon
GAAATGATGTAGAGACTGTAGAGCTGAGAGGCGACAGTGAATCTCATACTCTGGGGAATGTGAGACCAGACACAGAGTACATTGTTACAGTCATCGCTCTTTACAATGGAGAAGCTGAAGGACCTGCAGCCACTACACGTTTTAAGATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.333
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(45.7=90.2)
A:
NA
C2:
PF0004116=fn3=PD(53.1=84.3)
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:
CATTAGAGGGAGTGCAGCAGC
R:
CTGCAGGTCCTTCAGCTTCTC
Band lengths:
246-401
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]