RnoINT0093368 @ rn6
Intron Retention
Gene
ENSRNOG00000046959 | Mnx1
Description
motor neuron and pancreas homeobox 1 [Source:RGD Symbol;Acc:1588091]
Coordinates
chr4:2376958-2378022:-
Coord C1 exon
chr4:2377862-2378022
Coord A exon
chr4:2377318-2377861
Coord C2 exon
chr4:2376958-2377317
Length
544 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGC
5' ss Score
9.1
3' ss Seq
ACGCCAGATTGTGCCTGCAGGTG
3' ss Score
5.97
Exon sequences
Seq C1 exon
CCCAGGCGCAATCGAACCTCTTGGGGAAGTGCCGAAGGCCTCGCACGGCCTTCACCAGCCAGCAGCTGTTGGAGCTGGAACACCAGTTCAAGCTCAACAAGTACCTGTCGCGACCCAAGCGTTTTGAGGTGGCTACCTCGCTCATGCTCACCGAGACCCAG
Seq A exon
GTGCGCGCCCGACGAACCGGAAGGCGGAAGGCGGGTGCTGATTTGGGGAACTAAGTCCTTAGCTTCTTTATCTTTAGGTTGGGTATTAATTTTCAGCGGGTGAGGTTCTTCGTTGCCCCACAATATCTTTACGAGCTTGGAGGTTTGATTCAGTTAAGTTGGGGAGTAGGCTGAGAATCTGTATTCTGGAGGCGTCCCTCAGGTCACCTCAAGGAGGTTCTTTTTCTACAAAGGTACGGACTTGAGAGTTTAGTGACTTGCCAGCTGCCTTGGCGCCTCGGTAGACCGAGAGCATAAAACGCGGCCAGCTGGGGAGTTAGGGACACCACACCCATGATGTCATTGTTGAATAGGGCAGATTTGGAGGCAAAGGAGTGGAGAAGCTGCTGCCCAGTCAGCTTCTTAGTCCTCTAGCGAAGTAGCGAAGTAGCGAAGCCCCTTCTAGGGTGAGGGTGGATCGAGGGGCAGGGGTCCCGGGTGCTTGCTCCCTCTGGATTGATGGGGATGCAGGTGGCCGGTTTCTCACGCCAGATTGTGCCTGCAG
Seq C2 exon
GTGAAGATTTGGTTCCAGAACCGCCGAATGAAATGGAAACGCAGCAAAAAGGCCAAAGAGCAGGCTGCGCAGGAGGCAGAGAAGCAGAAGGGCAGCGGCGGGGGCGCCGGCAAAGGCGGCACTGAGGAGAAGACGGAGGAGGAGCTGCTGGGACCTCCAGTTTCGGGGGACAAGGCCAGCGGCCGTCGCCTGCGGGACTTGCGGGACAGTGACCCAGATGAGGATGAGGATGATGAAGAAGACCACTTCCCCTACAGCAATGGGGTCGGTGCCCACGCTGCCTCATCCGATTGCTCATCTGAGGACGACTCGCCTCCCCCAAGGCCAGGAGGGCCCGGGCACCAACCTCTGCCCCAGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000046959:ENSRNOT00000072287:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.148 A=NA C2=0.891
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=77.8),PF088806=QLQ=WD(100=51.9),PF090735=BUD22=PU(23.8=66.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=10.8),PF090735=BUD22=PD(74.8=94.2)
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:
CCAAGCGTTTTGAGGTGGCTA
R:
CGTCCTCAGATGAGCAATCGG
Band lengths:
354-898
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]