DreINT0170277 @ danRer10
Intron Retention
Gene
ENSDARG00000052170 | uap1
Description
UDP-N-acetylglucosamine pyrophosphorylase 1 [Source:ZFIN;Acc:ZDB-GENE-030131-1233]
Coordinates
chr6:35063741-35065781:-
Coord C1 exon
chr6:35065577-35065781
Coord A exon
chr6:35063917-35065576
Coord C2 exon
chr6:35063741-35063916
Length
1660 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGG
5' ss Score
8.92
3' ss Seq
TCAATGTTTTGTTTCACCAGGTA
3' ss Score
9.69
Exon sequences
Seq C1 exon
GCTTGCGCTGTATAGCGGAGAACAAAGTAGCAGTTCTTCTCTTGGCTGGAGGTCAAGGGACACGGTTGGGGGTATCATTTCCAAAAGGCATGTATGATGTGGGCCTGCCTTCCCACAAAACCCTCTTTCAGATCCAAGCAGAGCGCATCCGAAAACTGGAACAACTTGCAGAAAAGCAGCACTCAAGGAAATGTTGCATTCCTTG
Seq A exon
GTAAGGTGATCATTAAGCTCAATTCAGGCATATTCAATTACAATAGGAGTAGTAGATAATAAAAAAGCACATTTTCAGCTTCGCACTAAAGCAGTTTGAGTCAATGATTGTTCAATTTAATTACTTGGATTACCAAACTTGTCCTGATCTTGAGGAAGTTTCTTTCACTGACCGTAATGCTAGTAACCTCCCTGCTATGAATGTCAAAAGATGGTTTAGTCCGTGTGTAATCGTGTTGACACAGCACCTGCATGTCGTCCTGGGGAACTAGGTCAGACCTCAGGAGAAAATAAGTTTCCGAGCCATTCTCTATCCAGCTGAATTGACCATTGACGCAATACATACAATGCATTTCCTAATTACAGCTCTAATCTCATTAGAGCAACAGAATGATAGTTTAAAAACTGGTCGTAAGATTTACTTTTTTAAAAATTATAATATTTAGTGTGGTTTGAATAAGTAGTCTCCAAAATAGACAATGACAACAAAACCTGGTGAAATCATGACCTAATGAATTAAAAGAATGATCACAGACCATAAATATGTACATAAAAAATATAAAACATATCAAAAATTTGTAATGTAATATAAGAAAAATATAAGATAAGAATAATATAAGAAAATTAATATAAGAAAAATATGTACATATCAAATAAGCAATGCTATTTTTAACTATCAAAGAATTATAAAGAAACTGAATACCACTGGGCATAAATGATTGCAAAATGTAATACTCATTTATGCATCAGTTCAAGAAACAAAGAACTTCATATAGAGCAAATTACATTTTTAAAACAATATTATTTGTATTTTCTATTTCCAAATAAAGCACACATTTGTGCATCTTTGAACAACACTTTTGAGTTTCATCCACGAATGAATCTGTTTTTACCAAGTCAAGGAGTTAATTACAAATTTATAAAGACATAATCAGAAATTGCTTACTGAGAAGTAGTTTTTTACTGTCATGTTACTTATGGTGTTAGTTGTGGTGCTTCACTTTCATTCAGAATGTGTGGCCTCATATGATAAGGCATCCATCAAATGTGCTCCTGTACTGCAACAGTAGTTCACCAACTTTATGAATACTCAGAATTCAATCATACTACTTGCCTCACAAATTGCTTTTTTTGCCTCCTATAGAGAAATGGAAACAAATATATTCCATCACAGGGAGACACTTGAATCATTTAAAAAAAAAAGGTTGTTTTGAACAAATCATCTGGATGTTAGATTCAGTGAATCACTTAGTAGGATGGGGCCTTGCCTCACCTACTGGTAGTTTTAGTGTCATATCTATGTATGCATGACAGGACTAAATCAGTCAAGATATCAACACTAAAGAACATTAAACACTGTTTATTGTTTTTTTCTAATCCCTAAAATATGAAGATATTATTTTATTGTTAAAGCCCTGTCTGTTGAAAACAAAGGAGATATTTTTAAGAATGCTGGACCCCATTAGCCATTGACTTCCATATTAGGTAAGGGCATACTTTGGAAGTCAATGAGCAAAGGTATCAGTTCACATTCTTCAAGATGCTTTCCCTTAGTTTAGAACAATTTAAGGTTGAGTAAGTTGAGTAATTATGCTCTTAGGTAAAATTCTGTAAACGTCTAGCCTTGCAATTGTTCAATGTTCAATGTTTTGTTTCACCAG
Seq C2 exon
GTACATTATGACAAGTGGCAGAACAATGGACATGACCAAAGATTTTTTCATTCAGCACAAATACTTCGGATTAAAGGAAGAGAATGTGGTTTTCTTTCAGCAAGGCATGCTTCCAGCCATGGACTTTAATGGCAAAATCATTCTGGAGGGCAAATGCAAACTAGCCATGGCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000052170:ENSDART00000073970:3
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:
PF111663=DUF2951=PD(36.3=47.8),PF0170413=UDPGP=FE(29.1=100)
A:
NA
C2:
PF0170413=UDPGP=FE(13.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCAGTTCTTCTCTTGGCTGG
R:
TGGCTAGTTTGCATTTGCCCT
Band lengths:
344-2004
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]