DreINT0104491 @ danRer10
Intron Retention
Gene
ENSDARG00000075707 | nid2a
Description
nidogen 2a (osteonidogen) [Source:ZFIN;Acc:ZDB-GENE-030827-2]
Coordinates
chr17:14811007-14812292:-
Coord C1 exon
chr17:14812065-14812292
Coord A exon
chr17:14811235-14812064
Coord C2 exon
chr17:14811007-14811234
Length
830 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TATTTTTCATGTGCCTCCAGTTC
3' ss Score
8.05
Exon sequences
Seq C1 exon
TTCGTCCCAAGACCCACTGTGAGCAGCACAGAGACAGTCTTCAGAGTGAAAACGGGGGCGTTCCTGTGGTTGGAGCCTTCATCCCTCAGTGTGATGAGGAGGGTCAGTACAGGCCGCAGCAGTGCCACGGCTCCACTGGACACTGCTGGTGTGTGGACAATAGAGGGCAGGAGAGAGCAGGAACCAGAACTCCACCCGGATCACCCAGAGTAAACTGTGATCAACCTG
Seq A exon
GTAAGAAATGGGATCCTGAAAAATACATAACATTTACATAAGAGCAGATTTTGGGAGGATATCTTCGAACTGTACAGTACTCAACATTTGAAGAGAATCAAAAGTGTTTTTCAAAATTGCCATAAGACACGAATGAATGTTGTTCAGTATTTTAGGACTATCTTGATGAAAGAATTTGATCAATTTAAATGTTGACTGCTGTATGTTGCACTTCACCAGTGTTTTATAGGTGTTATTTATTTACATTTAAAGAGAACAAACTTCACAAGTTCAACATCTCAATTGAAACCCAAACAATCCATTAAATGCCTCAATCTTGTTAAAGCACCATCTGTGTTTGTCACCTTGCTGTGTCTCTGCATATTTTGGCAAGTCTTAGATTTTTGGCTTTCACTTCTGTAAATGAATGTGAATTAGTTTGCCCTGTAATGTATCAACTGTGATTCCACACTGATCAAACACCCTCGGGTTTAGCCAGATGCTACACTAGCAATGCCCTGAACTCTCGCTTTTGGTCAAGCTGCAATGTGATTGACAGATTTTAGTGGACCGCTCTCAGTGTTTTGATGGTTCCTGGAGGCTCAATGTTGCACTTTGTGGAAAATAAACCCCTATGAATGAGAAACATTGATGAAATCAATGACAACTGTGCGCTGGATCGAGATCATTTTTACATCTTTATGAATAACAACACTGTTCCTCTCTGAATATTTTAGGTAGCATCATCAAAATCACCAGCAAGATTATCTTTGCTAGACTTTACTTGATTTTTGTACTGAGGGGTTTGATGGGAGTTTAACAAACTTCTTTTATTTTTCATGTGCCTCCAG
Seq C2 exon
TTCATCTCAGGACCCGCTGTGAGCAGCACAGAGACAGTCTTCAGAGTGGAGACGGTGGCGTTCCTGCAGTCGGAGCCTTCATCCCTCAGTGTGATGAGGAGGGTCAGTACAGGCCGCAGCAGTGCCACGGCTCCACTGGACACTGCTGGTGTGTGGACAATAGAGGGCAGGAGAGAGCAGGAACCAGAACTCCACCCGGATCACCCAGAGTAAACTGTGATCAACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075707:ENSDART00000155857:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.468 A=NA C2=0.515
Domain overlap (PFAM):
C1:
PF0008613=Thyroglobulin_1=WD(100=89.6)
A:
NA
C2:
PF0008613=Thyroglobulin_1=WD(100=88.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTGGTTGGAGCCTTCATCC
R:
TCTGGTTCCTGCTCTCTCCTG
Band lengths:
353-1183
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]