DreINT0165547 @ danRer10
Intron Retention
Gene
ENSDARG00000021948 | tnc
Description
tenascin C [Source:ZFIN;Acc:ZDB-GENE-980526-104]
Coordinates
chr5:27967872-27968237:-
Coord C1 exon
chr5:27968107-27968237
Coord A exon
chr5:27968005-27968106
Coord C2 exon
chr5:27967872-27968004
Length
102 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CTTTATTTTTCATTGCTCAGGAG
3' ss Score
6.57
Exon sequences
Seq C1 exon
ATGTTGATGCCCCTCAGAATCTGGCCGCCAGTAACATTCAAACAGAGACCGCCATGTTGACGTGGAAGCCGCCAAGAGCAGACATCAGTGGGTACATCCTTAGCTTTGAGTCCGCTGATGGTGTAGTCAAG
Seq A exon
GTGAGAAGACAAGATCAAATTAATGGCCAAGCATAATTTACAGATGTTTATTTGACCCTATTATACTGGAGTTTGCTCATTTCTTTATTTTTCATTGCTCAG
Seq C2 exon
GAGGTGGTCCTCAGCCCCACAGCAACATTTTACAGCATGTCCCAGCTCACCGCCTCCACCGAGTACACAGTAAAACTGCAGGCCATCGCTGGACCAAAGAGAAGCAGAGTCATTTCTACAGTCTTCCTCACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021948:ENSDART00000131729:17
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:
PF0004116=fn3=PU(52.6=93.2)
A:
NA
C2:
PF0004116=fn3=PD(44.9=77.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTGATGCCCCTCAGAATCTG
R:
TGACTCTGCTTCTCTTTGGTCC
Band lengths:
242-344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]