RnoINT0085167 @ rn6
Intron Retention
Gene
ENSRNOG00000018427 | Lhx3
Description
LIM homeobox 3 [Source:RGD Symbol;Acc:71078]
Coordinates
chr3:3657541-3661810:-
Coord C1 exon
chr3:3661723-3661810
Coord A exon
chr3:3657713-3661722
Coord C2 exon
chr3:3657541-3657712
Length
4010 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
GCTTATTCTTGTATCCACAGAGA
3' ss Score
8.44
Exon sequences
Seq C1 exon
ATGCTGTTAGAAGCGGAACTCGATTGCCACCGAGAGCAGCCCGGTGCCCCTGGAGCTGCTGCCCTCTGTACCTTCAGCAGGACTCCAG
Seq A exon
GTAAGAGCCATTGCAGTCCAGAGGCCTCCATACCAGGCAGGTAGAAGAGAAGAGACAGAATGCAGAGGGGTGACTAGGAGGAAGTAGCATAGGAATGGTTGCGGAGAAAAAAGTAGAAGGTGATAGCAGGCAGGGAGGCTAGGAAGGCTAAAGGCTACAGGGTCAACAGTGACCAGAAAGGCCTGGGGCAGAATGAGGAGCATAAAGGATCCCAGAGATTGGATGCCCCACAGTTTCCAGAGCTGCTTTGGCTTGCAGCAAGGATCCCCAGGGCAAGCCTCCCACTTGAACTCTGATCCCCAAGGGCCATTCCACTGCCATGGACGTTGGAAAATAATGGAAGCATTGTTGGCGGCAAGCCAGATGCCCAGTAGTGGGAGCCGCCCCTTCCCTAGTCTAGTCACACATGGCCCCCGCCCCACTGCCTCTGCAGCAGCTGACACTCAATGGCTCACATCCTGGTTCACCCAGCACCCATTTCACTCCAACTGATGTCTCCAGACCGTCTCGGAATAACAAATTCAGAGCAACATGACAGGATGGCTATGGGTGGGCAGGCAGGCGCAGGACTCTTTCTGAGGCAGCAGGTGTGCTGGGACCAAGTGGGGAATCCTGCGGCCTTTCATTCGCCCTGCCCTTCGTATTCTGGGCTCTGATCAGTCACAGCCCTAGGGACAAGGACAGAGGCAAAGCAGGGCAAGTAGAGGAACCAGGAAAGTGGCAGCAACCTGCTGATTCTGCAAACACTTATAGGGTGTCCCTGATAGATACCAGGGTGCTACACCCTGCTGGATTCTAGTTCCTACCGGTGACTGCACAGGTCTGGTGCTGTCTCCTGGCTGAATGCTAGGAGCCCTCAGTGAAGGCACATGCAAGAATAGGATGGGTTCTGGTGGGCTCACCTGTTCGGATGGGGATGAGATGTGGAAATCCAGGTACAGGGATTGTTTTAAGGAGTTGGGGTGTGGAAGTGAGGTTGGACCTCAGGGCTTCCGCAGTTCAACCCTTTTTTGACCTAGAGTCTTGGTGTGTTCCTGCAGAGGACACCAGGCCTGAAGTCCTAAGAATCGTTCCTTCTCCCTACACTGGCTCCAGGAGGCAGTTCCAGTAGTGGGGTCCAGAAGTTCAGAGTTGGGGGCCTTCAAATAGAGCTCCTTGCAGTTCTACTGTGGCTTCTTTGCCTCCACGTTCCCTCGGTGGCTATCAGGTTGCCCTTCTGCTGGCCCGGTGTGGTCCCAATGATTTCCAGCTCCGGTTCAGAGGCTAAACGTGAGCAAAGAGAATGCAGTCCCCTCCCTGTCACTTTCCTCAGGACCTCAGCCTTCCGGGAGCCTTAGCGAACTTGCTTGGGGTAGGGGTGAGCATCTGTGGGAAGCCTTGAGTGGTTACCCAGCTGTCTCCGTCCTCGGGAAGTGCAAGTCGGACGGCTTCTAGGCACCTCAATTCTGGCTGAAAGGCGCACAGAGTTTCCAGTGGCATCCAGTGGCCTCCGGAGCGTCTCTGCGACCCCCGTCCCAGCCCCGCCCCGCGGCCCCGCCCCCCGCCGCTCCGCCCTCCGCGGGCCGGAGGCTTGGCGCCCAGAGGCCTCCCGTGGGCACAGCGCCCAGCAGCGACACGAGTCGCTCCGACGCCAGCTCGGAGTCCCTGCAGCGGTGGCCTCGCTGGACCCAGGGGAAGTTCAGGGTCGGAGGGCGGCAGCACCAAGCGCCCGGCCCCATGGAAGCTCGTGGGGAGCTGGACCCGTCCCGGGAATCCGCGGGCGGAGACCTCTTGCTGGCTCTGTTGGCGCGAAGGGCTGACCTGCGCCGAGGTGGGTGCCCGACGGAGAGGCTGCACTGAACAGATCCGGATGTCCTCGGTTTTTTCTGGCCCCTACGCGGAGGCTAGCAGAAGCCAGGGTATTTGGACAAGGGTGTGTCTGAGGGGCTCTGGCATGGCTAAGCAAAGGCGCCTCAACCTCCAAAATGTGTTCTCCGCCTGATGCTGTGTTGTCCTGGCACTGGGAGCCCTTGGTGATTCAGGAATGGTTTAAGGGACCCTTTGCAGGGGCTGAGGCCCCTGGGCTGGAGGGAACATGTGAAGATGTTTCAAGACCCAGGAAGCAGGAGTATCTCCTTAGGAACTGCCTTCACTCAGTCCCTTCCCCGTTTTCAGAGGGATCAGGGCCCCGTCGTGCTGAAACGCGCATCTCCCCTGAGTTGAGTGAGTCTTAGTGTCTGCACCGGCAGTTTACCGCTAAGCTGGTGGTCAAGACTCCATTAGAGGGAAAAGTGGGACTTGTCGGGGCCCCCAGCTTCTTGGTGGTACCAGACTTTTTTTGAAGGGTTTTGGTTCTGGGGAATGAGAGCTCTCTGCGTTTTCAGGCGATAGGAAAAGAATCAGTTAGGCTGGCAGAAGGTCGGTCGAAGCAGGCGGGAAAAGGATTCTATGCAGATTGGGGGTGTTGGATATGAGCTACTTGCTTATTTATTTATTTTCCGATGGTTTATGGGATGGGTTACCCTCAGGGGCTGGGAGGAAAAGGTGGGAGGGGAGGATGAGAAGGGGAGGGAGGAAGGCTTGGTAAGCTAGACTCCAGAATTCTATGAGGCTTGCTAGAGCGCTGGTGGCTTCCGAGGCTCCATTGGGCCCTCCAACTCTGTATAGGAAACTGTACTGAGACTGGAGTTCACCATGCAACGTAAGCAGGAGGAGGTCGAGGGTGGCTTCCCTGGGAGGCTTGACGTTGGCGACAGCTTTTGTAGGAAGCGGGCCCCCTGCTGTGAGCTTCTTGGCCGAAGCGCTGTCCGGGCCTGGGTGCTGAATCTGCAGTGTATGGCCTGTCCAGCCACCCCACTCTCTTCTGCGTATCCTTGCGACCTTAGGACGGCTCTGGTGGTGCTCTGGTACAGTTCTAGTCGATCTCCATGTCCACACCTGGAGATGTGGTTTTGCTCAGTGCGGGACAGCATCTATCGCAGGCTGTGGCCAGTGCTGGAGGGAGGTGGGGCAATCCTTTTCTAATTCCTCCCACCATGGAGGCCAGCCTGGAGCTAGGTGTCTGTAACACGAGATAAAGACACTGGTGTGGTTGTGACATGAGTGGGTCCTGGGTCCTGCACATGGTTCTCCTTTTTCTAGAAACCTTTCCTAAATTACCAGGGACTCTTTGTCATGAACATAAGGAAGAGCCCCTAAATGTTTCCCCTGGCTCTCGAAAGGCACCTTTAGATTTTCCCACCCGGTTTCCGGAGGCCTGCCATCCTGGGGATGAGAACTTAGGTGTTAGAAGAAGTGGCGGTGTACAGAATTGAAGTCACTGCAGCTCACATCTGAACAGGAAAGGAATGGGTCTTTCGTATATACATATGTGTGTATGTATACGTATATGTGTGTATATATCACATTACATACATATGAAAGCATATGTGTGTGCTCAAAAAAAAAAAAAAAACAGCCGTTGCACTCATAAATTCCTGCTGTCATTGAAGCGGGGCCAGCATCCATTTATCCATACCTCAGGTGCTGTGGGCAGGGGCCATGCTGGACAGACTTACTTTGCTGGAACTCTGCAGAGTGGGGCTGAGATGCTCTGTTGATCAAAACCCCAAAGGCAACGAAGTTCCACGTGTGGTCCTTTGCCCTTGCTTGTAAGGACATGTTGTCTATTTTCTGTCCTGGCTTTCCCGATCACCCCAAGGGTGGGGTTTTCATTTGAGATGGACACGACCCGTCTGGCGCTGGAAACACTTTGTAGAGCAGTTATTCAGCTTACAGGACAGCTTGGTCACCTTCTTGCTGCGGACACATTTCTAGACCTACTTCACTTTCCCTTGACTACAGTGAGGCTGAGGATACAGTACGTGAGCACTGCTCTCGCTGGGGAGCCTGTGGCCCTGAAAGCCGCAGGAGAAGGTGGCAGAAAGGCAGATCCTTGCACAGCTCTAAGGCCTGCAGGCTGACTCCAGCTCACGAAAGGACCATGCGCGTCATTTGTGGTTCCATGACCTGGCTTATTCTTGTATCCACAG
Seq C2 exon
AGATCCCCATGTGCGCGGGATGTGACCAGCACATCTTGGACCGTTTCATCCTAAAGGCTCTGGACCGACATTGGCACAGCAAGTGTCTCAAGTGCAGTGACTGCCACGTGCCTCTGGCTGAGCGCTGCTTCAGCCGCGGGGAGAGCGTCTACTGCAAAGACGACTTCTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018427:ENSRNOT00000025047:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(94.6=91.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
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]