DreINT0048975 @ danRer10
Intron Retention
Gene
ENSDARG00000012422 | col11a2
Description
collagen, type XI, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-000208-23]
Coordinates
chr19:7278035-7278310:-
Coord C1 exon
chr19:7278257-7278310
Coord A exon
chr19:7278089-7278256
Coord C2 exon
chr19:7278035-7278088
Length
168 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGA
5' ss Score
6.8
3' ss Seq
TGTGTTTATTTCTGTTTTAGGGT
3' ss Score
12.7
Exon sequences
Seq C1 exon
GGTCGCGCTGGTGCTGATGGAGCCAGAGGGATGCCAGGAGAGTCTGGAATTAAG
Seq A exon
GTCAGATATTTGATTTGTTAAAGTTGTGATTTGTGTGTGATTCATTGTGTTTTTTGTTTTTAAGTTATGTGTATCTTCCATTTCTAAACCTTTACCTCATTGCAGTCATGTTGAATTTAACCAAGTGTTTTATCAATCAGTTTGTGTATGTGTTTATTTCTGTTTTAG
Seq C2 exon
GGTGACCGTGGTTTTGATGGCCTTCCTGGTTTGCCTGGTGACAAGGGTTATCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012422:ENSDART00000104799:17
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(12.9=44.4),PF0139113=Collagen=FE(21.0=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.7=100),PF0139113=Collagen=PU(2.2=11.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCGCGCTGGTGCTGATG
R:
CGATAACCCTTGTCACCAGGC
Band lengths:
106-274
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]