DreINT0050347 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40281871-40282303:-
Coord C1 exon
chr6:40282145-40282303
Coord A exon
chr6:40282029-40282144
Coord C2 exon
chr6:40281871-40282028
Length
116 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
CGACCATGTTTCTTCATCAGAAG
3' ss Score
6.56
Exon sequences
Seq C1 exon
GTATAAAGAGTGCAGATCCAGCTGAGCTGAAGCTCATCGCCTCTCCTCCTCAAAGTGAGTTCACCTCTCAGATTGGGAACTTCAGGGCACTCAGCTCTTTACTGCCCCTAGTGTCTCGACGCGTGTGTACAGCAAGTGGAGGCTCCTACTCTAGTGATG
Seq A exon
GTAAGACTGAGTTAGACATACACAGTTCAATTAAAATATGTTTTCATAAATAAAATTGTACAGTTGGAATTTTGTGAAATCAATCAGTTTATGATTCGACCATGTTTCTTCATCAG
Seq C2 exon
AAGCCTACAGTGGTCCATCAGACTTGCAGGTTTTGGGTGAAACCCCTGACTCACTGAGATTTCAATGGACATCTGCAGGAGGGCCTGTAAGTGGCTATGTTGTTCAGTACAGGCCGTTATCTGCCCAGGGTCAGCCAATCACTGCAGAGCTCCGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.226
Domain overlap (PFAM):
C1:
PF0009223=VWA=PD(21.4=68.5)
A:
NA
C2:
PF0004116=fn3=PU(57.0=92.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCATCGCCTCTCCTCCTCAA
R:
AACGGCCTGTACTGAACAACA
Band lengths:
245-361
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]