DreINT0104494 @ danRer10
Intron Retention
Gene
ENSDARG00000075707 | nid2a
Description
nidogen 2a (osteonidogen) [Source:ZFIN;Acc:ZDB-GENE-030827-2]
Coordinates
chr17:14799689-14800338:-
Coord C1 exon
chr17:14800209-14800338
Coord A exon
chr17:14799861-14800208
Coord C2 exon
chr17:14799689-14799860
Length
348 bp
Sequences
Splice sites
5' ss Seq
CAGGTATAT
5' ss Score
7.88
3' ss Seq
TTTATATGAATGTTTTGCAGCTC
3' ss Score
8.27
Exon sequences
Seq C1 exon
GGCTCGATAGTGGTTGGCATTGATTACGACTGCAGAGAAAGGAAAGTATACTGGACAGATCTGGCAGGACGGACAATCAATCGAGCCAGCCTGGATCCAGGATCAGAACCAGAGATCATCATCAATACAG
Seq A exon
GTATATTTATTTTAAAGAAACAGACACACAGCATTAGTTAGGGTTTAAATCAGTGAATCAATGGGAAGAGCTAAATAGGCTGTGATGTATAAGTGGCTGTTGATCTTTTGTGGAGGCGGAGCTTAGCCACTCTATTACATAATAAAGAGTCACATTCACAACCTTTCATCTTATCAGATTTGCTTCAATATAAGCCATTTTCAGGCTAACCAGACTGTTTTGAGTTTTGAAACGTACAGGATGTTTTTATAGCACAATGACCTCTTCTAATTCAAAAGATCAGGAGAAATGTGATTTTTTAGATCATGCCCCCTTTATTAGTTGATCATTTATATGAATGTTTTGCAG
Seq C2 exon
CTCTGACGAGTCCTGAAGGTCTGGCTGTGGATGTGGCCCGAAGGAGATTGTTTTGGGTGGATAGCACACTGGACAAGATCGAAACGGCCAATCTCGATGGAAGTGACAGACATGTTCTGTTCGCCACAGATTTAGTAAATCCCAGAGCGATGATCGTGGACTCGTCTACAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075707:ENSDART00000155857:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.114 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005812=Ldl_recept_b=PU(71.4=68.2)
A:
NA
C2:
PF0005812=Ldl_recept_b=PD(26.2=19.0),PF0005812=Ldl_recept_b=WD(100=70.7),PF0005812=Ldl_recept_b=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTCGATAGTGGTTGGCATT
R:
CCTGTAGACGAGTCCACGATCA
Band lengths:
302-650
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]