DreINT0165551 @ danRer10
Intron Retention
Gene
ENSDARG00000021948 | tnc
Description
tenascin C [Source:ZFIN;Acc:ZDB-GENE-980526-104]
Coordinates
chr5:27964543-27964931:-
Coord C1 exon
chr5:27964835-27964931
Coord A exon
chr5:27964705-27964834
Coord C2 exon
chr5:27964543-27964704
Length
130 bp
Sequences
Splice sites
5' ss Seq
TTGGTATGT
5' ss Score
7.12
3' ss Seq
CTCATTGTGTGTGTCTGCAGGTC
3' ss Score
11.04
Exon sequences
Seq C1 exon
GTGTTTGTGAGGCGGCAGAGTGGCAAAGTGGAGTTTTTCAGAAACTGGAAGAACTACACGGCAGGCTTCGGTGACCTGAATGATGAATTCTGGCTTG
Seq A exon
GTATGTTTAAATTTCTGCACACATCAAATTGCTATTATTGCTCTAGGAAGCACAGAGGCCTAGAGGTATAGTTGATACGGTGTGATTTTCGCAAATGTTGGTCTATAAATCTCATTGTGTGTGTCTGCAG
Seq C2 exon
GTCTATCTAACCTCCATAAAATCACCTCCTTTGGGCAGTATGAGCTGCGTGTGGACCTCAGAGATAAGGGCGAGTCTGCATACGCGCAATATGACAAGTTTTCAATCTCTGAACCACGTGCTCGCTACAAAGTCCATGTTGGAGGATACAGTGGCACAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021948:ENSDART00000131729:20
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(15.2=100)
A:
NA
C2:
PF0014713=Fibrinogen_C=FE(25.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGAGTGGCAAAGTGGAGTT
R:
CTGCTGTGCCACTGTATCCTC
Band lengths:
245-375
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]