DreINT0104493 @ danRer10
Intron Retention
Gene
ENSDARG00000075707 | nid2a
Description
nidogen 2a (osteonidogen) [Source:ZFIN;Acc:ZDB-GENE-030827-2]
Coordinates
chr17:14800209-14800593:-
Coord C1 exon
chr17:14800424-14800593
Coord A exon
chr17:14800339-14800423
Coord C2 exon
chr17:14800209-14800338
Length
85 bp
Sequences
Splice sites
5' ss Seq
CATGTAAGA
5' ss Score
5.58
3' ss Seq
TCTCCTGGCTACACTATCAGGGC
3' ss Score
5.36
Exon sequences
Seq C1 exon
GTATACCTACTGTGGCCTCGCCTACGGTGCACCCTCTCCCACGCCCAGATGTGACTCCGCCTCCTACGGGCACGTCTCTTCTCTACGCCCAGGGCCAGCAGATTGGAGTTTTGCCTCTCAATGGCACACAGATGGATAAGGAGAGATCGTCAGTGCTGCTCGCTTTACAT
Seq A exon
GTAAGACTTGAACACTTTTAACTATAACACTGAAGTCTTACGCTTTATGAAAAACAAATAAGTTCTCTCCTGGCTACACTATCAG
Seq C2 exon
GGCTCGATAGTGGTTGGCATTGATTACGACTGCAGAGAAAGGAAAGTATACTGGACAGATCTGGCAGGACGGACAATCAATCGAGCCAGCCTGGATCCAGGATCAGAACCAGAGATCATCATCAATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075707:ENSDART00000155857:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.447 A=NA C2=0.114
Domain overlap (PFAM):
C1:
PF0301610=Exostosin=PD(18.3=36.2),PF0008613=Thyroglobulin_1=PD(1.5=1.7)
A:
NA
C2:
PF0005812=Ldl_recept_b=PU(71.4=68.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGCCAGCAGATTGGAGTTTT
R:
CAGGCTGGCTCGATTGATTGT
Band lengths:
172-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]