DreINT0104498 @ danRer10
Intron Retention
Gene
ENSDARG00000075707 | nid2a
Description
nidogen 2a (osteonidogen) [Source:ZFIN;Acc:ZDB-GENE-030827-2]
Coordinates
chr17:14790508-14792035:-
Coord C1 exon
chr17:14791912-14792035
Coord A exon
chr17:14790618-14791911
Coord C2 exon
chr17:14790508-14790617
Length
1294 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAG
5' ss Score
8.27
3' ss Seq
TCTCGTCTGTGTTGTTTCAGGGA
3' ss Score
11.45
Exon sequences
Seq C1 exon
GAACCAAGCGTCTGGAGTGTATTTCACCAAACGGGACAGGCAGACGCGTGATCCAGAGTAACCTGAACTACCCTTTCAGCATGGTGTACTTCGCCAATCACTACTACTACACTGACTGGAGGAG
Seq A exon
GTAAAGAAGCACAACACCAGTAATAACTATATTTAAAGCAGGTCCCACAGTTCAGTCGTATGTCATTTAAACAATGCAAACATTAGAGCAACAGGATTTAGGGTGTACTTACACTATGTACAGTTGCAATGAACCGGGCCAAAGCACGCTTGTCCCCACTCCTGTCTCCCCCGATGACTCGCACTCACATTGCATTCGATTGAGCGTGCTTACGTCATTGATGATGCGCTGTTCAGTAAGAAGTGCTCTCGCTCAGCACAGCGGAGATTTCTTCAGTTATATGGTTTTAGTCGTTTGATATGCAGTGACGCAGTCAAATATTTCACTGAACAGATCAGCCACTTTTGACGCTCATAAACAATCATTAAGTACTCGTGCTGCAGGAATTAGGAGGTTTGCTAAAGGTGCATCTGTTGTACAGTAAGGGGTTTGCGTCTTTAATAATCTCTGACAGTTTGTGTTCATTGAACAGTAAGAATGATTTATAGATCCATATGAAACAGTCCCTTAAAAGTCACGTCTCGTCTTCAGTTTCAGTACAGCGTCAAAGCCCAAGTGAACCGCGCTCTGGCACACCTCTTCCAACCTGGCCAGGGCCGGCCAAGTGAACCACGTCTGTGCCCAATTCAGAGCACTCACACTTGTCAAACGATCCAGGAATTTTTTCGTTTGTCACGGGGGGCATGCATGAAATGTTCGTGAATGAAAGTGAAAGTGCCAAACTGCAGTTAAAGTCAACAAATCAAAAATGAAAGACCTGAAATAACATGAAACTCCGGAGGAAATGTGGATAGCGCGGTGAAGCAATGACGTTAATCGAATTATGTGCTATAACATTAAAGGGATCATAAAAGGAACATTCAAAAAGTAACTCATGTAAACATCTTAATCACATTATTGTCTTATTCACATTAAGGCAAATAATTTAATTACCAATGTCCATGTAAATGAAGTTAATGGCTCAGATGATTTGTTCAACAACAGATTGGTTTATGATGAAAGCACTACAGTGTTGGTCTAAAATGCACAGTTATTCCATCCTGGCTTTGTTTGTAACCATTTTAGTTCTAAAAACCCAGAAATAAACAATGCAACTCATGTAATATTAGCTTGTTGAACTGTATAAACTCCTATAAAAACATCATGATGGCCTTAATTAAAATTACGTTCATGTGTGATATTGCTATAAGCGGTACTCTTGCTTGTGTGATATTTGTCGAATATATCGGCCTGCCTAATTGAGTGTTCATCAGTGAAATGACCTGATATTATATTCTCGTCTGTGTTGTTTCAG
Seq C2 exon
GGACGGAGTCATCTCTCTAGGTCGAGATAACCAGTTAACAGATGAGTACTTACCTGATCAGAGGTCTCATTTGTATGGTATCACAGTCGCCCCTCCACAATGTTTATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075707:ENSDART00000155857:22
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=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACCAAGCGTCTGGAGTGTA
R:
TAAACATTGTGGAGGGGCGAC
Band lengths:
230-1524
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]