DreINT0097002 @ danRer10
Intron Retention
Gene
ENSDARG00000035984 | mnx1
Description
motor neuron and pancreas homeobox 1 [Source:ZFIN;Acc:ZDB-GENE-040409-1]
Coordinates
chr7:40367325-40369127:+
Coord C1 exon
chr7:40367325-40367823
Coord A exon
chr7:40367824-40368966
Coord C2 exon
chr7:40368967-40369127
Length
1143 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TTTTAAAATTCTCCATGCAGGCC
3' ss Score
9.3
Exon sequences
Seq C1 exon
ATGGAGAAATCTAAAAACTTTCGGATCGACGCGCTTCTGGCTGTCGATCCACCAAAAGTGCAGACCTCGCCGCTGGCGCTGGTCACCTCCCTGCCCACCTCATCCATATCCTCCTCTTCCGACAGCGTCCAGGCGGTGGAGCTGACCACGAACTCCGACGCACTCCAGACAGAGTCTCCATCGCCACCCAGGATATCGTCTTGCGGCTTGATTCCCAAACCGGGTTTCCTGAACTCTCCACATTCGGGCATGGTCGGACTACACCCTCAGAGCAGTACCGGGATTCCTCCTCAGGCTCTCTACGGTCACCCAATGTACACGTATTCAGCAGCAGCGCTCGGTCAGCACCCGGCGCTCTCGTACTCATACCCGCACGGTTCCCACCATCATCACCATCCCAGCGACCCCCTCAAACTCACAGCCAGCTCCTTTCAGCTCGACCACTGGCTGAGGGTCTCCACCGCCGGAATGATGCTGCCTAAAATGGCAGATTTCAATG
Seq A exon
GTGAGTACCAATTGACTTTCATTAATAATATTTGTTTTTGTTATTATTAATAATAATAATAATATTAGTAGTAGTATATTGACATTTTTATACGCTACAAGTTTCCATTTTATTTGTGCTTAAAAAGTGTATTTTTGAACACTAATTTTGAACAATTAACATTTAACAATTGGCCTACTGATTTATGCTGCTGTATCATGATGTAAATAAAAATAATCATATTAGATTTGAGCCCCTAAACCATAAATACTGCACTGGGCCTGTTCAGTCAGATCTAGCAAGCGCGTGCAGAGTCAGTAAAGCTGTTCTCTGACTGAGACTGAACGAGCACTCTCTTTCAAAGAGGGGCTAAAATGGACAGATAATGGACAGAGGGAAAGTGGCGGACGAGTGTGAAAACCACAGCCTGCCAACTGTGTACACTGCAGACACAGTCTCTCTGTTCCGCTGCTCGTCTGCAGATTTTCTCAAAGCTCTCCCAAACAAATCAGATAGGGTGGAAATGTTACCAGATGTACTGACAATGCCGTGGCACATAGAGGGTATGTGTGATTGGGAATAGGTCCTTTAAGACTAAAGATTTTAACATTTCTTGCCGTGCCATTATGTTTCTTTAAATTCTTTGTGAGTGTAGTGTAAAATCCACAGTGGTTCAGCAATGTACTGTTACACGGCTGCTAGGCCTATACATAAATAAATTGATAAAAAACGCAGCCTGCATGCATTTACACTGTTTGTGCCATTCTCAAGAAAATATTCCTATATAACATTTCGATATACTGTGGTAATTCACCGAATATATAAATTTTTTTCAGATCAAATGTCCTCTTCCTGTTTTTATTTTTGCTAGGTTTAATCTAGTGCTAGACGTTGCATAGCTATAATTTGCTTCTGAATTTACATTCGTTTACCGAAAGAACTGGTAAGAACTGTACAATAAAAAAAAATCCCTGAACTTAAAATGTTGTAAAATATATCAATTTTGGTTCTAAATAGAATTTGCGGATGGATTCCCTAAAACATTAATAAATAATTTTAAAAAAATTATTTCTTATAGAGGTATGGAAGTCTCAATTTGCTAAACTGGCTAAAGTGTTGTCCTGTGTAAAATGTGCAGTTTTGTTTTTAAAATTCTCCATGCAG
Seq C2 exon
GCCAGGCGCAGTCGAACTTACTCGGCAAGTGCAGAAGACCAAGAACTGCATTCACAAGCCAGCAGCTCCTTGAACTTGAGCATCAGTTTAAGCTGAATAAATATCTATCCAGACCAAAACGCTTTGAAGTGGCCACGTCATTGATGCTAACAGAGACGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000035984:ENSDART00000052236:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.443 A=NA C2=0.167
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=77.8),PF088806=QLQ=WD(100=51.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACCCAGGATATCGTCTTGCG
R:
TTGCCGAGTAAGTTCGACTGC
Band lengths:
343-1486
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]