DreINT0050384 @ danRer10
Intron Retention
Gene
ENSDARG00000021720 | col7a1
Description
collagen, type VII, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-030131-2427]
Coordinates
chr6:40211829-40212212:-
Coord C1 exon
chr6:40212087-40212212
Coord A exon
chr6:40211901-40212086
Coord C2 exon
chr6:40211829-40211900
Length
186 bp
Sequences
Splice sites
5' ss Seq
AGGGTTAGT
5' ss Score
5.02
3' ss Seq
TGCTTTTTATTCTGTTTAAGGGT
3' ss Score
9.79
Exon sequences
Seq C1 exon
GGTGACCCTGGCTTACCAGGTCCTCCGGGCCCTCCTGGGCCACGTGGATTAGATGGGACGCCAGGACTGGCAGGACAGAGAGGGGAAGCAGGTCAGCCAGGACCCCCTGGACTACCAGGAGAAAGG
Seq A exon
GTTAGTAGAGTCACTGCAGACACAAAAACAAATCTAGACTAAAAATGACATACGTTTAGGTAGACTATTACTTCATGTATTCAGTAACATTAAACACATTTCCTAATTTTTTGTTGTGTCCCTCTGCTGCATCTAATGATTGATTGATGATGAGTAATTCTGGTGGTGCTTTTTATTCTGTTTAAG
Seq C2 exon
GGTCTTAACGGAATTATAGGCAAAACAGGAAATCCAGGAACACCAGGAGATGCTGGACCACCTGGACCCACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021720:ENSDART00000154878:93
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(68.4=92.9),PF0139113=Collagen=PU(28.3=40.5)
A:
NA
C2:
PF0139113=Collagen=FE(38.3=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:
GGTGACCCTGGCTTACCA
R:
GGTCCAGGTGGTCCAGCATC
Band lengths:
194-380
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]