GgaINT0053527 @ galGal4
Intron Retention
Gene
ENSGALG00000012394 | NID2
Description
nidogen 2 (osteonidogen) [Source:HGNC Symbol;Acc:HGNC:13389]
Coordinates
chr5:57992316-57992754:-
Coord C1 exon
chr5:57992625-57992754
Coord A exon
chr5:57992488-57992624
Coord C2 exon
chr5:57992316-57992487
Length
137 bp
Sequences
Splice sites
5' ss Seq
CGGGTGTGT
5' ss Score
5.31
3' ss Seq
GCACCTCACCCCTCCCGCAGGGC
3' ss Score
10.03
Exon sequences
Seq C1 exon
GGCTCCATCGTGGTAGGGATTGATTACGACTGCCGGGAGAAGACAATCTATTGGACTGACGTGGCGGGCCGAACCATCAGCAGGGCAAGCCTGGAGCCAGGCGCTGAGCCAGAGACCATTATCAACTCGG
Seq A exon
GTGTGTGCCCGCTACCCGCTCCGGGCCACCTCTGCTGGGTCCGTCCCAGACTGTCCCCACTGGGACTCTGGCTACGGGGCCGGCAGCGGACCAGGATCCGCGTGTCCCCATCACTGAGCACCTCACCCCTCCCGCAG
Seq C2 exon
GGCTCATCAGCCCCGAGGGGCTGGCAGTGGACCACCTCCGCAGAGCCATGTTCTGGACTGACAGCGGCCTGGATAAGATCGAGCGAGCGCAGCTGGACGGCTCGGAGCGACGGGTGCTCTTCGACACCGACCTCGTCAACCCTCGGGCCATCACCGTGGACCCCGTCCGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012394:ENSGALT00000020241:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.205 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
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTACGACTGCCGGGAGAAGA
R:
TTGACGAGGTCGGTGTCGA
Band lengths:
247-384
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]