DreINT0104500 @ danRer10
Intron Retention
Gene
ENSDARG00000075707 | nid2a
Description
nidogen 2a (osteonidogen) [Source:ZFIN;Acc:ZDB-GENE-030827-2]
Coordinates
chr17:14849617-14851825:-
Coord C1 exon
chr17:14851584-14851825
Coord A exon
chr17:14850099-14851583
Coord C2 exon
chr17:14849617-14850098
Length
1485 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGC
5' ss Score
5.34
3' ss Seq
ATCATTTTATCTCTCCTCAGAAA
3' ss Score
9.46
Exon sequences
Seq C1 exon
GTAAACACGTTCCAAGTGGTGCTTGCGTACAATGAGAAGGACACTTATGCGCTCTTCCTATACCCTGAGGATGGCCTGCAGTTTTTCGGGACACGGCCCAAAGAATCTTACAATGTTGAAATTGAGCTTCCAGCTCGTGTGGGATTTTCCAGAGGAGAGATTTCCTACTTGATTTTTTCTCGAACAGAAGGGCCGTATTATAGCCTCACCAGCAATGAGCAGTCCGTCAAGAACCTGTACCA
Seq A exon
GTAAGCATTGCGGGAATTACCATTTAAGATCAAGCCACCCTGTTGTTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAATAGACGCACACACACACACACACACAAAGTTAAAGTATACACAGTTGAAGTTTTTCCCAATTTCTGTTTAACGGAGAGAAGAAATTTTCAACACATTTCTAAACATAATAGTTTTAAGAACTCTTCTCCAATAACTGATTTATTTTATCTTTGCAATGATGACAGTACATAAAATTTTACTAGATATTTTTCAAGACACTTCTATACAGCTTAAAGTGACATTTAAAGGCTTAACTAGGTTAATTAGGTTAACTAGACAGGTTAGGTTAATTAGGCAATTTATTGTATAACGATGATTTGTTCTGTAGACTATCGAAAAAACTAATGCTTAAAGGGGTTAATAATATTGACCGTAAAATGGTTTAAAAAATTAAAACTGCTTTTATTTTAGCCCAAAAAAAGACTTTCTCCAGAAGAAAAAATATTATCACTCATACTGTGAAAATTTCTTTGCTCTGTTGAACATCATTTGGGAAATATTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATGTATGTATATATATATATCTGTCATTTCACAATTTAGGTGCTTCATTGGCTTGACAAATAACTACATTCATGTTGCCAAAGCAGTGAAGCATTGCTGCTTACAAGCAAGACAAAAGGGCAATAGTGCAAACAATATGAATATAAAATATAATACAGAGAAAAAACACAGATATAAATAAAAATAGATTAATAAAAAAAATCGATTAATGGTAGTATATAAAATAGGATAAAAGTAACTCTCTCTCATATATATATATATATATATATATATATAAAATGCCTATGCTAGTTGTTTCTATAGCGTTGATGGTACGGGACAGTAAGTGTAACATTGTTCTCTCTTCTGGTTGCTGTTATCAGTCTCTCACAGTTTTTTTCCTCTTTTTTTAAAAGCCATGGAACGTTTTTTTTTTTTTATTATTTAAGTGAATTGTAATGCAAAAAAAAAACGTTTTTTTGATGCTCTTCCATTCATTGCTCTCTGAGATTACTGTGAAGACTTCCACTGCCGGAAATATGAAAAGGGTCTATAAAGTTAAAAAATTACTAGATTGTAAAAAAAATAATAATAATGACAAATAAGTCAAGACAACAAATATTTATATATTCATTTAAATAATTTAAATAAGTTAACCAGGTTTCAGCAGGTTTTTTAACTTAATAATTTTAACTTAATAATAGTTCTTTAACGTAATATTTATTTTTTTCAAGTTGAGATGACTAGAAAAGATTGCAAGATCTTGCTAGATGCAACAATTTTTTAACAGTGTCGGAATAAAATGATTTCATTTTTAATTTATCATTTTATCTCTCCTCAG
Seq C2 exon
AAAGGGAAACATAGGTGAGCCCGGAGTTTGGCTCTTCCATGTTGGAAACCTTTATTCCTTCCAGAATGTGGTTCCTGCTCAGCAAGAGGCCGTTTCAAGCAAATCTCCCACTGTCCAGGACACTGTGTTCACTGATGAAGACTACACAGACGAGGAGGAGTACGATCCCATCGACCCAGACTTCCAGGATCCCACAACAACAGAGTTTCTGGAGCCGGAGCCAGACTCCTCTCTGTTGGAGCGTCTCAACCAGGAGACTCCCCTGGGTCAGTCTCCATTGCAGCCTTCAGTGTCGGGTCCAGAAGATCTTCCTCAGCCGGATCCTCATCATGTCCAGCCTGAGGACAACACTCAGCCCCAGTGGCCCTTACCAAAACATGCCATTCTGCAGGTGTACCCGAACCGCGTGAAGGATGTTCCAACTCACCCTTCTGATGGCCAAGTGTTCAGTGTTGAGGAGAAAGTGGACTTTGACTCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000075707:ENSDART00000155857:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.753
Domain overlap (PFAM):
C1:
PF061199=NIDO=PU(81.6=98.8)
A:
NA
C2:
PF061199=NIDO=PD(17.3=10.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACACGTTCCAAGTGGTGCTT
R:
CCTGGACAGTGGGAGATTTGC
Band lengths:
358-1843
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]