DreINT0050278 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40203773-40203982:-
Coord C1 exon
chr6:40203911-40203982
Coord A exon
chr6:40203809-40203910
Coord C2 exon
chr6:40203773-40203808
Length
102 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAA
5' ss Score
4.51
3' ss Seq
TGTTTGCTTATCATTTACAGGGG
3' ss Score
7.79
Exon sequences
Seq C1 exon
GGTCTAAGAGGAGAGCAGGGAGAAAGAGGTTCAACCGGCTTCCAAGGAGCACGCGGCCCTGGTGGCCAGAAG
Seq A exon
GTGAAATAAAAACTCTCCTCGACACATGCATATACATGAATACATTCGAGCATGCCTGCGTCTGAATTTCACACTAATCGGATGTTTGCTTATCATTTACAG
Seq C2 exon
GGGGAAGCAGGGCAGCCAGGTGTCCCAGGAGAAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:102
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(32.8=79.2),PF0139113=Collagen=PU(31.1=95.8)
A:
NA
C2:
PF0139113=Collagen=FE(15.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCTAAGAGGAGAGCAGGGA
R:
TGCTTCTCCTGGGACACCTG
Band lengths:
108-210
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]