DreINT0049660 @ danRer10
Intron Retention
Gene
ENSDARG00000055009 | col4a1
Description
collagen, type IV, alpha 1 [Source:ZFIN;Acc:ZDB-GENE-081105-114]
Coordinates
chr9:8660648-8661168:-
Coord C1 exon
chr9:8660991-8661168
Coord A exon
chr9:8660763-8660990
Coord C2 exon
chr9:8660648-8660762
Length
228 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGT
5' ss Score
6.84
3' ss Seq
GTGTCTTTTTTCTGTGGCAGATG
3' ss Score
10.91
Exon sequences
Seq C1 exon
GTACAGCTGGTAGTTGCCTAAGGAAGTTCAGCCCAATGCCGTTCCTCTTCTGTAACATCAACAATGTTTGCAACTTTGCATCTCGTAATGACTATTCCTACTGGCTGACCACTCCAGAGCCCATGCCTATGAGCATGGCCCCCGTCACCGGCGAGAGCATCAAACCCTTCATCAGCAG
Seq A exon
GTCTGTGATATTTATTAATTAAAATTTCTATTGTATTCTATTGACTTTTATTGTGTTTTTATTTAAACTGATTGTTCTAGCTGTCCTGTACGGTAACCTTGAGTGCCAAGAAAGGTGCCTTTAAATAAAATGCATTATTATTGTTATTATGAAAGTTTGATATATCCACGAGTGAGTGTTCTTAGTTCCCATGTACAGTATACAGTATGTGTCTTTTTTCTGTGGCAG
Seq C2 exon
ATGTGCTGTGTGTGAGGCTCCTGCTATGGTTATAGCTGTGCACAGTCAGACCATACAAATTCCAAACTGTCCCGATGGCTGGGCTTCACTCTGGATTGGATACTCTTTCGTTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000055009:ENSDART00000077296:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0141314=C4=FE(53.6=100)
A:
NA
C2:
PF0141314=C4=PD(6.4=17.9),PF0141314=C4=PU(26.3=76.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACAGCTGGTAGTTGCCTAAGGA
R:
CATAACGAAAGAGTATCCAATCCAGA
Band lengths:
292-520
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]