DreINT0048967 @ danRer10
Intron Retention
Gene
ENSDARG00000012422 | col11a2
Description
collagen, type XI, alpha 2 [Source:ZFIN;Acc:ZDB-GENE-000208-23]
Coordinates
chr19:7305795-7306265:-
Coord C1 exon
chr19:7306020-7306265
Coord A exon
chr19:7305909-7306019
Coord C2 exon
chr19:7305795-7305908
Length
111 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
GAAACTGTCCCGCCTTGTAGTCA
3' ss Score
5.96
Exon sequences
Seq C1 exon
CACACACACACACACACACGCTCCCCTGCATTTCGTGGGAGAAAGTAAGAAGAGGGAGAGAGAAAGAGAGAGATTGAGAGAGAGTGATTTGAAGCCTCTCTCTGCTCTCTCCGCTTTTCTGTTCTCTCAGACTCAATGGGGCTCTAGCAAAAGGGATTTCAAGCTGTAAAACTACATATTTATTACCCGAACCCTTCTTTCTATTTAAGTTTTGTACATAGCACAGATAACTTATTGAAGAACAAG
Seq A exon
GTGGGTGTGCGTTTACGACGTCTCTAAAGGCTCTCTTAAAGCCGAGTCCACTGAGTTTTTGTGAGAGAAAAGAACCAAAAGGCTAATTTCTGAAACTGTCCCGCCTTGTAG
Seq C2 exon
TCAAACCAAACCCGTCAAAAAACTTGGGAACTATGGATATTCGGAAGAAGCGGAGGCCGTGGTGCATGGAGACCTCGTTTGTGCTCCTCCTGTGCCTTTCTATGGCACAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012422:ENSDART00000104799:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCTCTGCTCTCTCCGCTT
R:
TAGAAAGGCACAGGAGGAGCA
Band lengths:
253-364
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]