RnoINT0085194 @ rn6
Intron Retention
Gene
ENSRNOG00000028348 | Lhx8
Description
LIM homeobox 8 [Source:RGD Symbol;Acc:1308749]
Coordinates
chr2:260584296-260589992:-
Coord C1 exon
chr2:260589889-260589992
Coord A exon
chr2:260584392-260589888
Coord C2 exon
chr2:260584296-260584391
Length
5497 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGAC
5' ss Score
6.89
3' ss Seq
CTTTTAAAAAATAATCACAGGTT
3' ss Score
3.55
Exon sequences
Seq C1 exon
GTAATGGGATTAGTGTGGAAGGAGCCCTTCTCACAGAACAAGACGTCAATCATCCAAAGCCAGCCAAAAGAGCTCGGACCAGCTTCACAGCCGATCAGCTCCAG
Seq A exon
GTAGACATGGCAATGCATTTCTGATTTTTGACACCCTTTCCCCACAAAAGAAAACAAACCTAAAGAAAAATTAAAAAGTAACCTCCATGCTGCCTGAGAATATTGTTTCCTAAATAGTTGTCCTATACATTTTTAAGAGACCGAACTCCATGAGTGTTGATGTATACTCACTGCCTTGAAGGGTCATGGTGTGCAGAAGCTAGTCAGTAGTTTGGTGTCCTTCGGGTCTTTTGATATTAACGTCAAACCGGGGCACAGTGTTGGTCTGTTATGGCTTCCGTGAGCATCAGTCTAAGGCAGACGACGTTTTTAGTTTCATATAACGACAGCAGAAGATGACCGTGTGGAGGCTTAGCTGAAAAAGGCAGCACTCAGGGCTGTGGGGCTCCAGTGTGCTGTCATTTAAGTAAATGACGTGTTGTTTAATGTATAGAATCGCACACATTTTGTCTAGGGAAGAACAGAACCTGCCCAGCCACAGACGGGAATCCACGGTTGACACCAATCATAAAGGGATCGAGGCAGCAATTCCATTCTCTATGCTGAGGTTGGCTCTGCCCTTGAAAGTAAAGGGACTTCCTTAGCATAGCTGTCCTGGGTGTGCGCACTGGCTCATGTGTGAAAACTGTCTAGAAAAATACCCCCTGCTTTGGATTTAAGTCGACATATGCTGTGTCTTTCTGGCATTTTTTTTTTTTTTGGATCATATTTTCTAGAAGATCAGTGTGGCTGAGGTATTTGTTTTGTGTTAAGATAAATAATTTACTGCACCTCCTCCAGGGGCTGCTTAGTGTGGTGTTATATTTAGCATCGACTTGGGCTCAGAACTGAAAGCAATTGTGTCTTGTTAACAAATAAAGGAAAACGCACTTAAGTAGTCAGAGACTGGCCAGCACTTCAGACCTCTCTAGTAAAAATGTTTCAGGAGTGGTATTTTAAAGAACAATTAGACGGGTAACCTGGATGTAGCCAGTGTTCTGAGAGAATTTGGCAGTGGACCAGATTCGGAGTATTAAAATCTAGATCCATTAAGGAAAGGCCTTCCAAGAACACAATTGCTTTTATTGATTCGATATTAAGTCTTTGACTAATGAGTAATACGGGGAAAATAAGAGAATTGAGAGATTTGGTTTCACTTGAGTGTTGCTGGTCTGATGCTCCCTGGAGTGTTGGAGAAAATCACACACATCCTGGGTTTGAAGTGAGTTCTTATCCAAGCTTTGCAGCAACAGTCAGTCTGAGCAGTGGGCTGGGTTAGACATAGTCGCTAATAGACAACCATCGGACTGAAACTTCCTCAGAGACTTGGCCGTGACTTTGACAACTATAGGCTTCATAATTTGGATGTGAAAATCCCTTATTAAAATTATAACTGTGGAAGTTTGAAGTCATGGCAGGTATCTAGCTATACAGTCTCCTGTGGGAAGATAATTATAGAAAAAAGTATGGTGATCATTTGTGGAAGTTTATACAGACCAAGCCCTGTCTATATCATCTTCGACTCTTCACCCATTCCAACAAGTCCTCAGTGTAGTCAGCCTCTCCAAGGGCACAGGAAAGACCCATGAGGTAATCAGCCACTCAAGGAATAGCAGAGAAAAGGCTCAGACAGACTTGCCCAACCTCTGAGCTTTTCATGTGGTTTTGCCTCCCAGGAGACCATGTGCTTCATCGGAACCCAGCAATACAGAGAAGAGAAATCCTGAATTTTGCAGACAGGCTTATAATAACAACCTACAATGTTCACAAAAACTTAAACTATGCATTGCTACGTAAGAACATGATTCCAATCATAAACTATAAATTGATAAGAGTGAGTTCTGAAAGTTAAAACACCATCTAGTCGGCATTCAGTTGCATCGATCCTACACCTGAGACTGTCAAAACAAGTGAGGTGCAAGGCTGAGCTGTTCTAAGGAACAAGAAAGACGGAATAGCCACAGATAAAAACGAAACAAAACAAACAAACAAAAAACCCCAGAAAACAAAAAAACAGAAACCCAAAACAAACAAAACCCATATCATGTAGTTTTGCCAGATCATCTGATATATAGGTATGATAGTCACCTTGTCGAATTGTCTTAATTTTGAGAAAACTGAATGTATTCAAGTATTGACTTCAACAAAATAATAATAAAAATCATCCATGAAAACCGAGCTAAAACTGTCCATGTGGTTCTTGCTTTGGACAGAGGAGTGTTAGCATGGGATGACTAAAGAAATTCCCAGAGTTCCACTTCAGAGTCTCATAGGAGGAAGAGTTTCCGGATCAGAGGGGCATGGCTACAGATGTATGTCAAACTGGTATACAGATGTATGTCAAGCATTAGGAGGACACTTAAATTCCTGCTCCTGCCATGGTTCATTCCCAACAGCCAGCCATGTGGGCATCAAACATGCCAAGGTTGGCTCCTCCTTGGAGCTACTTCTGATATATTATTCAGATGCTACTACACACACTTCTGGCTTTTTAGAATCTTGATTGATTTGGGTTTTGTTTGTTTTTGATTTTTGTTTTCTGGGTTTTTGTTGTTTTTGTTTTTGATTTTTGTTTTTGTTTTGTTTTTATAATGCCATAGAACTTTGCCTTGATCACCCCCAAAGAGCTCCCAATAGAACTAGGAATGGTTTGCAGTGGTTTAAACATATGCCAAATAGGGGAGCTAAATAGAATTTAAAGGTTTTGTCATCTTTTCTGTTTTTTTCTTTCTCTCTTTCTCTCTTTCTGTCCCTCTCTCCTTCCTTCTCCTTCCTTCCTTTCTTTGATCACATACTTGCACTAACTAAAAGAATAGAAAGTGCCCTATTTTCCCTAGAATATTTTATTTTTAAGATTTATTTCTTTATGTATGTGAGTATACTATATCTTTCTTCAGGCACACCACAAGAGGGCATTGGATTCCATTACTTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGCCAGTGCTCTTAACCACTGAGCCATCTTTCCAGCCCAGAATATTATACTTCCTAATGACCAGGGTAGACTTAAGTTCAATTTTCCTTCCCTAATGAACTATCTTTACTAAATGTATGTTGGTTCTATGATTACACTTTTACATATAGAGGTTTTTTTTTTTTTTTTGTCTTTTCTTTTCTTCTTTTTAAACCAGCTCATCAGGAACCTTAGAAATGAATCCCCAAATAACTGTTCTGCTTTGTCTTTTGAGAAAGTAAAGACATGACCCATTCACTTGCCATTTGTCTNNNNNNNNNNNNNNNNNNNNNNNNNTAAAAATGTATAGGACAACTATTTAGGAAACAATATTCTCAGGCAGCATGGAGGTTACTTTTTAATTTTTCTTTAGGTTTGTTTTCTTTTGTGGGGAAAGGGTGTCAAAAATCAGAAATGCATTGCCATGTCTACCTGGAGCTGATCGGCTGTGAAGCTGGTCCGAGCTCTTTTGGCTGGCTTTGGATGATTGACGTCTTGTTCTGTGAGAAGGGCTCCTTCCACACTAATCCCATTACCTGCGTTTTGAAAACAAACCATCTAGTTGGTAACTCAGATGGGTCTATACTTCTGTACAAGCCAGTCTCCTCGCACACCTTGGCTTTTTGCAACTCATCTGCCTCTTCTAAATTGGTAACTTTTTTTTCTAAACCTTCTTGCAAATAGACTGAGAAAGATAATATTCATAGCCTTCCACACTCTGAATGAAATGCAGTAAGTTAAGAGTATATATCTAAGGCCCATCTTATGAAGGCAAACGCACAGAAAATAAAGGCTAAACCCAAACTCCAAGCTGCTTGTATTAAAGAAGGGAAAAAAGAAGGCTTTGTGGAGTCCATTTTGCCACGTTTAAAACAAGAGTAAGTTATGTTCCTTTTACCGTGGACCTATTGATGCAGCATTAGGTGGGAAGCTAGGAGCACCTGATTCTAGAAGAGTCCTAACCAAGGGCATCTTAACTGAAAGGGCCATTCACAGCCTCAAAATGTTTCTGGTCTTTCTCTCCATGCCCTGGAGACTTTTCTCATACTGTCAAGGTTCCTCGTCACCAACTCTGAAGTGCACATCACATTACAGGCAAGCAGAGAATGCAGTCTCCCTCCCCACAAGGAGGGTAATGCAAAAGGGTGCTTTCCCCTAAAGGGGAAAAAGGAGCTTCTACTGCTTCAGAGTGAGGGACTTTGCAAAGTAAGCTGTTGGGGCTTCTTCTGACAAGAGAAGAGGCAGAAAGACAGCACGGGCAGGAGCAGGCCAAGACAAAGTTCACACTTCCCTGGGGGAGAGGGAGGGCCAATTCAAACTGCTTAGGGCACGGGTGGGGCGGCCAACACAGTGAGGGATGCAGGTGCTCACAGACAAGCACAGCCTACTGAATGCCTGAATGCCCTTACTTTTTGTCAATTACCTTTATCTCATACTCTCCTCAGCTGACTGACTTTAAAAAATTTAAAACTTTATAAAATTCAAAACTGCTCGATGAGTCTCAGGAGTCCCTCTTCCAAGAACCCAAAAGCCTTGACCATGACTTGTATTACCTTTAATTAGAAATGATTATTGGCATTTCAATACTTTTCTTATAGGAGCTTAAGACCCCTACCCCCACCATGTATGAGTATATACATGCCACAGCACTTGTCATAGTAGTACCAACCCAAAATGTCATCTCTGAGTCGCTGGACTCTGCTTGTCACCTGGACTAAGGGAGGGGTCTCCTTTCTAGATCTCAAGAGGTTGTGCCATATGGAGCAAACGCCCTACCCCCACCCCCACAAACACCAGTGACATCACTGCAGTATGCTGTAATCCGTCTCTGCAGCAAATACTGTTTGTAAATCAACAAAAACTAACGTGAGAGCCCTTGAGGTTGTTCAGACCCTCAGAGGCTAGAGATAGCTGGGGTGGGGTTTGAGCATTTTGCTCACTTACAGTGCCAGGGATATTTCACAAATGGGAAGCCAAGGGAGGGAGAGTCAGAGTCCGTGGGTTTTGAGAGTTCTGAGACTGGATGGAGAAAGGGTAGTGTCTCTAATGGCATGGCTGAGGGGCAGAGTTTTACCTTCTGGTAGGTTAGTTTTTTAAAGATCTCTCAGAAGAAGAGTTTGGGTAAATTTACAAAGTATGCCTTCCTTCCATTTGTGTTGGCTGCATTCATTTCTCTTTTTTTGTTGTTGTTGTATTTATTTATTTTATGTATGTGAGTACACTGTAGCTGTCTTCAAACACACTAGAAGAGGGCACTGGATTCCATTATTTACAGATGGTTGTGAGCCATCATGTGGTTGCTGGGAATTAAACTCAGGACCTCTGGAAGAGCAGCCAGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCAACATTCATTTTTAATACCAAAGTACACATTGCATCATTTTCTTTGTGTGCCTTTATCTGTTCTCTACCATCAAAATGCAAAAGTTCAAGCTTTTAACTATTTTCTCCCAACATCTGTCTTTTAAAAAATAATCACAG
Seq C2 exon
GTTATGCAAGCACAGTTTGCTCAGGACAACAACCCAGACGCACAGACCCTCCAGAAACTGGCAGAAAGGACAGGCTTAAGCCGGCGAGTCATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028348:ENSRNOT00000009370:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.429 A=NA C2=0.406
Domain overlap (PFAM):
C1:
PF099434=DUF2175=FE(34.3=100),PF0004624=Homeobox=PU(21.1=34.3)
A:
NA
C2:
PF099434=DUF2175=PD(19.2=59.4),PF0004624=Homeobox=FE(54.4=100)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]