DreINT0049892 @ danRer10
Intron Retention
Gene
ENSDARG00000052061 | col4a6
Description
collagen, type IV, alpha 6 [Source:ZFIN;Acc:ZDB-GENE-101001-2]
Coordinates
chr7:50652135-50652496:-
Coord C1 exon
chr7:50652335-50652496
Coord A exon
chr7:50652234-50652334
Coord C2 exon
chr7:50652135-50652233
Length
101 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTC
5' ss Score
6.8
3' ss Seq
TTCTCTCTCTATATTTAAAGGAC
3' ss Score
8.25
Exon sequences
Seq C1 exon
GTCCCTTTGGTCCTCCTGGACTCCCTGGTCCACCAGGCCCTGGAACTGTCCAGGGAGACAGAGGAGACCCTGGGTTTCCTGGTCGTCCAGGAATAATAGGACCACGTGGTGAGCCAGGTGGTTTTGGAGCCCCTGGATTACAAGGCAATCCTGGTTTCAAAG
Seq A exon
GTATTCCCATTGACATTTTGACATGTTTTCTCTTTAACCCTTTTTCTATGTTGTAGTTTGTCAAAAAGTGATTAAACATGTTTCTCTCTCTATATTTAAAG
Seq C2 exon
GACAAAGAGGTGAGCCTGGCTTCAGTGGTGTGCCTGGACGACCAGGGTCTCCTGGAGAACCGGGGGATTATGGCAGAAGTGGACCCAGAGGTCTAAAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052061:ENSDART00000121574:41
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(73.9=92.7),PF0139113=Collagen=PU(31.3=38.2)
A:
NA
C2:
PF0139113=Collagen=FE(49.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCCTTTGGTCCTCCTGGA
R:
CACTTCTGCCATAATCCCCCG
Band lengths:
243-344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]