RnoINT0101367 @ rn6
Intron Retention
Gene
ENSRNOG00000016656 | Nkx2-3
Description
NK2 homeobox 3 [Source:RGD Symbol;Acc:1308521]
Coordinates
chr1:263367266-263370219:+
Coord C1 exon
chr1:263367266-263367615
Coord A exon
chr1:263367616-263369097
Coord C2 exon
chr1:263369098-263370219
Length
1482 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
ATGTCTTGCTTCTTCCTTAGAAA
3' ss Score
8.84
Exon sequences
Seq C1 exon
GATGATGATACCAAGCCCGGTCACCTCCACCCCTTTCTCAGTCAAAGACATTTTGAATCTGGAACAGCAGCGGCACTTCCACGGAGCACACTTGCAGGCGGAATTGGAGCAGCACTTACACTCGGCGCCCTGCATGCTGGCAGCTGCTGAAGGGACGCAGTTTTCTGATGCAGGGGAGGAGGACGAGGAAGAAGAGGGAGAGAAATTGTCCTATTTGAACTCACTAGCGGCCGCCGAGGGCCACGGAGTTTCGGGTCTCTGTCCTCAGAGCTATGTCCATACAGTCCTTCGAGACTCTTGCAGCGGGCCCAAGGAGCAAGAAGAGGAGGTTGTGAGCGAACGGAGCCAAA
Seq A exon
GTGAGTACAGGGGGAAAGAAACGCGTCCGTACACCTGGGGCACTGGCTCAACGCCCATAAACAACCCATAAACCTTGCCAGCATGGCCACCCGCCCCTTTCACATTCGACTAGGGTCATGCCTACGCCAGGTTCACGGACAGCTCTGCAAAGCACAGGTACCTGAGATGGGGCTGGGGCAGGGGAAAAAAAAACGAGAAGGTGATTCTGAGAACTACTCTTCCCCGGAGCAGGGAGCGGGAGCAGTCCCCGAAGGAAGGAAAGAGATGACTGCGATCCTGCTTCCTTGAGCAATGAGTGACGGGGGCCCAGAGGCAGGGAGTTAACTTCTCCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTCTTTCGCACACCCCTCTTCTAAAAAAAAAAAAAAAAAAAAAGAGGGTCAGTTGTCTGCCATTTTCTCTGTCTTTCTTCTAATGTGAGGTGAGTTCAGTGAGGCCAGCACAGTCACCCCGGCTCTTCCGAAAAGGCAGTGCAGGCAGATTGTGTTTTGACCGCCCTTTCGGACAAGAAACCTTGATAGACAGCACCTTTCTTCTGAGCTTGCAGCTCTCCCTTCTCACACGCGCAGGACTCGGCGGAGGAGAGGGGGTGGTTGATGTGTGGGAGCGCGATCTATATTAGATGACCACTCCAAGTCACACCCATGAGGTGAAGGCCTCTAAAAAAATATCCCAGTGCTCGCTTTGTGTCTTATGCTGCTGATGGAGTAGAATGGGTAAAGTTTCTAATTTAGTTGGGGATTCTGGCCGCTCAGCAGATCAGAGGTGAGTTAGGTAGGAAAATCGGATAACCGAATCAATCCATAAGAAAATATCCGAAAGGGAGAATCAAACAATCTCTTCTCCAAGTGGAGATTCAATCAGGCTGAGACCAAGATCTTTTCTCTGACAGCTCGCCAGGCCTAACACAGGCATGAACCTGTCTAAATCGGTCCATCCAACTTTTTTTTTCCTCTGTAAGGTAATATACAAATATTGTCACAGACACATTCTCAGTAGTTTTGAGAATTAAAAAAAAATTCTTAAGCTGCACATACGCCTTTCACTTAGATATTAAAATTTTTCTGCAATCAACCCATGCATCCAGGCCGCCTGCCCCCAATACCAACAAGTTTCACACCTTCGGGAGAGCGGAAAGCAAACGAATTTGCAAATATTGTGTTCCTTGATCGCCTGAAAATTGTCATTAGCCCCTGGACCCGCACACTTAATCTCTTTTCTTGCTAATGCTCAAATTTAATAAATACAGTCTAACTATTCCCCACAGAACGAACATGCCTTCTCCCGGTTAGGGGGTCCGCCTGATGCGGGAGCCCTTGGGCACCAGGAACCATAAACTTTCTCCAAATCTAGCATTTACTACGGGGTGTTCTGTGCCTCTAGGGCTTAGGGGTGGTATCCTGGGAACTAGAAAGGCTAATGTCTTGCTTCTTCCTTAG
Seq C2 exon
AAAGCTGCCAGTTGAAGAAGTCTCTCGAAGCGGCGGGAGACTGTAAAGCGAGCGAGGACGGCGAGAGGCCGAAGCCTCGCAGCCGCCGGAAGCCCCGGGTGCTCTTCTCGCAAGCTCAGGTCTTTGAGCTGGAGCGCAGGTTCAAGCAGCAGCGGTACCTGTCGGCGCCCGAGCGCGAGCATCTTGCCAGCAGCCTGAAGCTCACGTCCACACAGGTGAAGATCTGGTTCCAGAATCGCAGGTACAAGTGCAAGAGACAGCGACAGGACAAGTCCCTGGAGCTGGGGACCCACGCGCCGCCGCCGCCGCCCCGCCGCGTGGCAGTGCCGGTGCTCGTGCGGGACGGCAAACCGTGCGTCACTCCCAGCGCGCAAGCCTACGGCTCGCCCTACGGCGTGGGTGCCGGCGCCTACTCCTACAACAGCTTCCCCGCCTACGGCTACGGGAACTCGGCGGCCGCAGCCGCTGCAGCAGCAGCAGCCGCAGCCGCAGCCGCGGCTTACAGCGGCAGCTACGGCTGCGCCTACCCGACAGGCGGCGGCGGCGGTGGTGGCGGCGCAGCCTCCGCCGCGACCACCGCAATGCAACCCGCCTGCAGCGCCACCGGCGGCGGATCTTTTGTGAACGTGGGCAACCTGGGAGGCTTCGGCAGCGGCGGCGGCGCGCAACCCTTGCATCAAGGTGCCGCAGCTGGAGCCGCGTGCGCGCAGGGGACCTTGCAGGGCATCAGGGCTTGGTAAGGTCTGGGCAGGACACGCGGCTGGCGTCCTACCGCAAGCTGGGCGCCGCGGGAACGAGACACGAGAAAGGACAGACCCAAGGGCCATGTCCCCTCGTTAAAATAAAATACAGACGTATCGCTCCTTCCAAGGGGCCAGGGTCGCAGCACACTCCAGGCCTGGGAAAGGGCTCAGCGGAGAAAAGATGCCCTGGTCCAGTCGTCGTCAAGACTGTTTGAGACAGAAACACCGGCCGGGCGCCAGGGAGCAGGTGGCCTCCCCACCCTGGCTCTGTGGGGAGTGCGGGAGGCTGTCGCTTGCTCTCCGGAGGAGGAGGGGGTGCTTTTCTCTTGCCTTCCCTTGGCCTTCTCGTAGTGTGGTCAGGGAACCGGACCGAACAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016656:ENSRNOT00000054714:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.487 A=NA C2=0.203
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=23.1)
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:
ATTTGAACTCACTAGCGGCCG
R:
CTGTGTGGACGTGAGCTTCAG
Band lengths:
353-1835
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]