GgaINT0053523 @ galGal4
Intron Retention
Gene
ENSGALG00000012394 | NID2
Description
nidogen 2 (osteonidogen) [Source:HGNC Symbol;Acc:HGNC:13389]
Coordinates
chr5:57993899-57995407:-
Coord C1 exon
chr5:57995288-57995407
Coord A exon
chr5:57994154-57995287
Coord C2 exon
chr5:57993899-57994153
Length
1134 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
TGGCCTCCCGTGTGCCGGAGGTG
3' ss Score
-1.82
Exon sequences
Seq C1 exon
ATGTGAATGAGTGCACCCTAAACCTGTGTCACCCTGCTGCCATCTGCTACAACACGCCGGGCTCATTCTCCTGCCAGTGCCAGCCCGGTTACGAAGGCGATGGCTTCCAGTGCACGCATG
Seq A exon
GTAAGGCTGCGGTGCGCATCCCCGTGCCTCAGCATGGAGTCCCCATCCTCACTGCTGGTGCTTTGGATTTGCCGGCAGCACAAAGCAGCACGCAGCGGTTGACGCCGTGTGAGCACGAGCAGCTGTACCCACGGACACCGGGACACGTGCCACAGTGTGATGAACAGGGCGGCTACCAGCCCCTGCAGTGCCACAGTGGCAGTGGGCACTGCTGGTGTGTGGACTCCTCGGGGCAGGAGATTGCCGGCACCAGGACAGCAGCGGGCAGCACGCCGCCACGCTGTGGGAACCCAGGTGGGTGCTGTCTTGCTGTGCTCAACGTGGGGAGATAGGGGGTCAGGTCCTTCAGCATCTCTATAGGATCAACTGAGCGGGTGGGGCTTGGATCCTTTGTCATTCTGTTGGCACCAACAGAGAGGATGAAAGCCGTGTCCTTTGGCATTTCATTGGCATTTCTATAGGATTAGCAGAGGGGATGCAGGTTGCATTTTATGGCATTTTGTTGGCATCTCCATTGGATTGATGGAGGGGATGGGGTTTGAGTCCTTTGGCATTTTGTTGACATCTCTATGGGATCGGTAGAGGAAAGGGGGATTGGATCCTTCAGCATTTTCTTGGCAAGTCTATGGAATTGGTGGAGGCAATGAGAGCTGCGTCCTTCGGCATTTCACTGGCATCTCTACGGGATTGGTGTAGATGGTGGGGTTCAGGTCATTTGTCATTTTGTTGGCATCTCTATGGGATCAGTGGAAAAAATGGGAGTCAGGTCCTTTGGCATTTTGTTGGCATCTCTTTTGGATTAGTGGAGGGGATGGGGGTTGATCCTTTGGCATTTTGTTGGCATCTCTGTGGGTTCGGCAGGCACGTAGGTGCTGGGGCAAAGCCTGGCAGCCTGCGTGGTTGTGCTGTGGGACAGAGGGGGCTGAGTCGGGGCTGAGCCCCCTGCTGCCATCATGGCCTTGGCCAGCGGCAGAGTGGGACAGGGCAATTGGAGGGGACCCTTTGCAGGTGCTGCCAAATGGCTGTTTGGGCATCTCAGGAGCTCCCGAGTCATTAGGGCCCCCTGGCCCACAGGGTTATAGCAGCACGGGGTGCCCAGCTCCAAGCCGCCCCCTGGCCTCCCGTGTGCCGGAG
Seq C2 exon
GTGTTTCTCTGCCAGCAGGTTCCTCCCAGCAGCTGACGCCATGTGAGCACGAGCGGCTGTACCCACGGGCAGTGCCACCGGGCCCCTCACCCGTGGGCAACGGACACGTGCCACAGTGTGACGAGCAGGGCAACTATCGGCCCCTGCAGTGCCACGGCAGCACCGGGTATTGCTGGTGCGTGGACGGTGCGGGGCAGGAGATTGCCGGCACCAGGACAGCGCCGGGCAGCACGCCGCTGCGCTGCGGGAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000012394:ENSGALT00000020241:12
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=0.407
Domain overlap (PFAM):
C1:
PF126622=cEGF=PD(15.0=7.3),PF129472=EGF_3=WD(100=82.9)
A:
NA
C2:
PF0008613=Thyroglobulin_1=WD(100=72.1)
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:
TGTGAATGAGTGCACCCTAAACC
R:
GTCCTGGTGCCGGCAATC
Band lengths:
336-1470
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]