DreINT0102974 @ danRer10
Intron Retention
Gene
ENSDARG00000103902 | nde1
Description
nudE neurodevelopment protein 1 [Source:ZFIN;Acc:ZDB-GENE-050913-61]
Coordinates
chr3:36540670-36542530:+
Coord C1 exon
chr3:36540670-36540815
Coord A exon
chr3:36540816-36540917
Coord C2 exon
chr3:36540918-36542530
Length
102 bp
Sequences
Splice sites
5' ss Seq
GGGGTTAGT
5' ss Score
2.75
3' ss Seq
ACTTTGTATCTCCTTTGCAGTAT
3' ss Score
9
Exon sequences
Seq C1 exon
AATCTTGAATCAAAGCTGGCATCATGCAGAGAGCTACACATCCCTGAGAAAACATCAAACCGAGCACTGATAGGCCAGAGTTCACCAAGCATTGCACGAGAAACACCAGAAATCCCATCCAACACAAATGGCTTGTATGATAAGGG
Seq A exon
GTTAGTCTTGACGTTAATTCCAGCACATGTCTATTATTTTTCTATTATAACAGATCTGGCTTGGATTGTTTAAGTATTTCACACTTTGTATCTCCTTTGCAG
Seq C2 exon
TATGGTGAAACGACTGGACTTTGGAACAGGATCCAAGATAATGCTGTGACCAGCGCATCTTCTACAAACGCACAAGCATTCACACATCATCAGGAAAACAGTATTCCTAATCCAGTTATTATAAACAATGCTTTATTTTCAGAAGCTGAAGCAAGTGTTATGACCCAAGTCTTCCACGATCTAAGAAGGGTCTGCTTTTATGCTCATACAATATCAATCCTTCTGGTGTGCCTATATTAACTGTTCACCTGCTCTGTCTGGCCTGTGGACTTAAACTATAACTTTTTGCAGATGTACTAACTCTTTGTTTGTTTGTTTGTTTGTTTTTTATTTACGTTTTCAGGTTCTGGCGATTTATAGCCATTTTGAAATGCATAATCTGCACTGTAATCTTAATTTTTTTGGGTCCATAAATTGGGAGAATGTTGTGGGTGACTGAAAGTAAGTCCATAGATTTGCCTCTGCAACCCCAGTTACCTGGCACTAAACTACTGATCGATGTCTAGTGAATCGTCTACTGTACATGCATACTGTTGGACACAGGACTAGAGCAACGTTAACAGCAGGCTCTTTTTTTTTAATATAGAAATAGCTGATTTTATTTTTTTAGACACTAGCATTTTGATGAAATACGAGTTTGTTACTAACAGAATGTCAAGTCTTTAGCATTCAGAGTTAGAAATTGTTACAAGGAAGTTGGTGAGATGTTATGAGCTGAAGCTGCTGTTCATGTTGTTGGCTCATAGGGGTTGACGGAAGTTACCAGCAGTAGCCAAAATGTTTATGCATGAGGAAAACCCCCTAGTCTGGGGCCTTTTTTTATTTCTAGTAATAACTAACTCCTCTTTTGAATTGTCAGTGCCATCTTTGAATTCAAAGAATTTGTAGATCTCTACAATTCTGGGGAGTAGTTGATGTCATATCATGCACTGAACGTGAATTTAATGTGCCTTAATTTTGTGGCCATTATAAGCTTTGCCTCAAAGTTAACTTGGGTATTGGGGAACTTACTAGCCCGAAGGGAGCTGCAGCTTTTCTCGCTATTCTTCCCAATGTATTAATTCTCTGATATTTCAGGGATTCCAGGATGAGGAGAAATTGAAATTCTGAGTGGAGTTGTCTCGCTTAGTTTCCTACATTTCTTTCATCCATGATTTGAAGATATAGTCCAGTAACAAGCAATATGAATACTTCAGTGAAGGTTACAGATATTTTTATGTTAAAAATAGGAATTTATGGAAGAATTGATGCATTATATTATCCAGTTTTTTTAGAGGTACTAGTGAAAATGATAGAACTAGAGAATACTAGTTGATGGGAAGATTTAGCACACTTGATTGCACCATCTCAGGGCCATCTCAGCAATAACCTCACTAAAGATGTAATTACAGTCCAAATTCTATATGCACAAGGCATGCACAATTGCCAATTATGTAAATGTCAGCATGGGTTTTCTTTGCTATTAATGAACCTAAACATCTGTAATGTCCACGCATTCCTCAGCAAAGGCAATGCTTAGTTTATCCTGTGTCTAAGACCATTTGTTGGTTAATCCATAACCTACAAAATAAATGTCTGCTTGACAGGATTAAATGATTGACTCTTTTTGGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000103902:ENSDART00000159033:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.673 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF048808=NUDE_C=PD(17.8=61.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTTCACCAAGCATTGCACGA
R:
AGATCGTGGAAGACTTGGGTCA
Band lengths:
250-352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]