DreINT0166291 @ danRer10
Intron Retention
Gene
ENSDARG00000001760 | tnxb
Description
tenascin XB [Source:ZFIN;Acc:ZDB-GENE-070103-5]
Coordinates
chr16:16717546-16717955:-
Coord C1 exon
chr16:16717859-16717955
Coord A exon
chr16:16717708-16717858
Coord C2 exon
chr16:16717546-16717707
Length
151 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGA
5' ss Score
6.04
3' ss Seq
ACCTCTTCCCCTCTACTCAGGAA
3' ss Score
10.65
Exon sequences
Seq C1 exon
GTTTTCCAGAGAAGAATGGATGGATCCACAGATTTCTTTAGGAGCTGGAGAGACTATAGTAAAGGCTTTGGTCTCTTAAGTGGAGAATTCTGGCTGG
Seq A exon
GTGAGATTCTCCATGGAGATTATATTTTATTTTTTTAAAACCCGACCCCAATTTGTATTTTTTTAAATATCTGAGGTAGTCTCACCTAAAAAAAATATCAGCTTGACATCTTGGGTATTTATTTAAATTACACCTCTTCCCCTCTACTCAG
Seq C2 exon
GAAATGATGTGCTTCACACTCTCACCAGTCTTAAAGCAATGAGCTTGCGGATTGACCTGCGCTCAGGAAATGACACAGCCTTTGCTCAATATATAAACTTTAACATTAGCTCAGAGGCTAATCACTATGCAATTGACCTGTCTGGATACTCTGGCACTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001760:ENSDART00000014439:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0014713=Fibrinogen_C=FE(17.2=100)
A:
NA
C2:
PF0014713=Fibrinogen_C=FE(29.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
TTCCAGAGAAGAATGGATGGATCC
R:
AGCAGTGCCAGAGTATCCAGA
Band lengths:
255-406
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]