HsaINT0092599 @ hg19
Intron Retention
Gene
ENSG00000136944 | LMX1B
Description
LIM homeobox transcription factor 1, beta [Source:HGNC Symbol;Acc:6654]
Coordinates
chr9:129458118-129463311:+
Coord C1 exon
chr9:129458118-129458282
Coord A exon
chr9:129458283-129458572
Coord C2 exon
chr9:129458573-129463311
Length
290 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
ACACCCCTTCTGCCCCCCAGGGA
3' ss Score
9.25
Exon sequences
Seq C1 exon
AGGTCCTGTCCAGCCGCATGGAGGGCATGATGGCTTCCTACACGCCGCTGGCCCCACCACAGCAGCAGATCGTGGCCATGGAACAGAGCCCCTACGGCAGCAGCGACCCCTTCCAGCAGGGCCTCACGCCGCCCCAAATGCCAGGTGACCACATGAACCCCTATG
Seq A exon
GTAAGCCGCCCTACCCCCACCCGCCCGCCCCAGCACAGCCCCTGCCCCCTGCCAGGCCAGGCAGGCCTGGGGCCAGGACAGCCACCTGCTGCCCTAGGGCTCAGGCAGCATGGCCAGCACAGCCCTCCTGCCCCTGCTGACAGGAAGGGCCCCAGTCCTTCTTGGCCGGCACTAGTCAGCAGGCCATCCTGTCTCTCCCTGGCCTCCAGTCACACAGCCTACAGGGCAAACAGGGGGCCCCCAGGAGCCCCAGCCTGTACCCCGGTCCTGACACCCCTTCTGCCCCCCAG
Seq C2 exon
GGAACGACTCCATCTTCCATGACATCGACAGCGATACCTCCTTAACCAGCCTCAGCGACTGCTTCCTCGGCTCCTCAGACGTGGGCTCCCTGCAGGCCCGCGTGGGGAACCCCATCGACCGGCTCTACTCCATGCAGAGTTCCTACTTCGCCTCCTGAGAGCCAGCCAGGCGCACGGACGCTTGGGCAGGGGCCTGGGGGGGACTGCCAGCCTCTGCGGCCAGCCTGGCCACCCCCGCCCTGCTCTCCGCACAGACTACAGACAGCCATACGGTGCCCTCCCCTCGGCCAGCTGGGCCTGACCACTGTGCCCGTTGGGTACAGCCAGACCGGTAGATGGGCACAGCCTGGGCAGGGGCTGTGTCCTGCCCACAGAGACCTTGTCATCCCCAGGGACCCAGAGCTCTCGGACGGCCACTCGCCTCCCAGCCCCACCTCGGCCTCCATCGCCTCCTCCCCATCTCTTTTTTGGGAAGCTTAAATTCTCTCTATTTTTTTAAATGTCCTCTCTGTGTCCATGGCCCTCCATGCAAGCCCCAGGACAATGGTGTCATGAGGCGGTGACCTGAGAAGCGTGTGTACCTGTGCCCCAGCAAGGGCAGGGGTGGCCTCTGGGGGCAGGCCCACTGCCTGGAACCGCACACCCCTCAGCCTGAGTCTGGAGCAGCAGTGGAGAGGGGCCTGAGGGGAGGCACTGTCAGGAGGCGGGCTCGGAGCCTGAGCCTGGGCAGGCGCAAAGGGACAGAGAGGCACGTGCAGACACATGCACACTTGCAGACAAACCCACGCAAACACACACACAGCTGTATGGGGACACCAGAAGGGACAGGGATGCTCAGCGGGTCTGTCCTGCCTTGTCAGAAAGAGAAAAGGAGGCCAGGCAGGGGACCCCCCAGTTCTTAAGAGCGATTGGAAAGGGAGGAAGGGGAGAGGAAGAGGCGAACTTGAAGCATCGGACCCAGTTGTATCCCAGCCTGGGCCCAAATGGGGGCAGCCTGGGCAGGGAGGGCAGCCCCAGGCCCCACCAACTCTAGAGGCAGATGGAGCCCCCAGAACCAGGTAGCATCAGACCAGACAACAGAGCCTCCAGGGGTCAGGGACTTCAGAAGCACCTGCTGGGCACCCCATCTGCAATGTGGTCCTCTCCCCAGCCACCTCTGCCTCCCCTCACATACCTCCAGTGACAAGGAGCTCACTAGGTCAGCGAGCCCACAGCAGCTGTGCTGTCCTGCATCCCAGAGCCAGGCTTCCCCAGCTCTCCCTCTTAACACTGTCCCCCAGCAGGCCTCCGGCTGTCCCTCTAAAGGTGTGGGGCAGGTATCACTTCACCTTCCCACTGATGTCAGCCGGCCAGAAGTGAGCAGGCACATCACCTCTCCTGCTGTGGCACCCTTCCTCTGTTAATTTGGCCCAAAAGACAATGATTTGGCCACATGACCTTAGAGATTCACCCTGCCCTGCTGTAGCTAAATCCCTGGGCCCCACACGCAAGTGACAGCTAAGCCACATCTGTTTTCTGTGTATATGCAGGATGGGGGCACCTACTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTGAGACGGAGTTTCGCTCTTGTTGCCCAGGCTGGAGTGCAATGGCGCGATCTCGGCTCACCACAACCTCCGCCTCCCAGGTTCAAGTGATTCTGATGCCTCAGCCTCCCTAGTAGCTGAGATTACAGGCATGCGCCACCACACCCAGCTAATTTTGTATTTTTAGTAGCAACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCCAACCCCCGACCTCAGGTGATCCGCCTGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCCAGTCTGCACTTACTGTTTAGACTGAATGAGGGACCGTGACCTCTTTCCTTTTCCATTCCTTCTTACTCGATTCATTCCAGCCTGTGGAATTTCTCTGCACCCTGATTCAGTGACCACTGCTCTCCTCTCTCCCAGCACATCTGCCCAGTGAGGAGTTGGCCCTGGGTCTCACCTGAGGTGTGTGGACCGGGCTGGCCTCTCCCTGTTTGACATTGGCCCATTAATGCATCCTCTTTGGGGGACACATTCCAATTGCATTTCCTGCCCCCTTCTCCCAGGGCAATTGCAGAAGATTGTGTCAGGCGCCCTGCTGGAAGTCAGGTGCACTAGATCCATCCCCAGCCCCAGTCTGCTCAACTCTATCCCTGTCAGAGCAAGGAGGCTGGGCTGCTGGGGCCTGACTGGTGAGCCCACCCTGTCCCCTGGTGATCACTGTGTCCCCTTGTTCAGGTGCTCACAACCCTACCTTTAACTCTGAGGTCAAGCCCTAGGCCACCACCCTAAAGTCTGCCTGGTCCAACCTTTGAGCAAGTAAGGATAATGAATGTCCCTTTTCCACCTTTGGGGCCCTCTGCCTGGATCTCTGGAATCCTCTAAGTTCAACCTGTTCTGTGGTTTTGCTCCCGTTTGCTGGGAAATTCAGTCCCCCCAGAATGTCCTGGGCCAACCTCCTTGCCTGACATGTGGCCTCGTGTCACCCATTGGGCCCCAGCAGCCAGCTAGCCCTTCTGCAGCTCTTCTTACAAACAGAGCCTCTCCAAGGACCTCAGTTGATGTTCTGGTCCTTCTGCCGCCTCAGCCCACCAGGGTCCGTGCCACCATGGGTCTCTTGAGCAGCAGCTGCACTGGCTTCTGGAGAGACACCCCTCTTTCTCCTTTTGCACATGCACCATCTGAATCGTGCCAGGGACATCCTGGGCAGATTCAGGGGCAGATGCCCTATCCCCCAGGAGACCTGGCCCTTCTCTCTCAGACCCAATAAGTTGGAAGGGACGTCAGAAGCGGTCATCTCATCTGCCCCTTATTTTATAGTTGGAAACCCTGAGGCAAGAGAGGGAAAGAGGCCTGTCCAAGGTCCGGGTTAGTGACAGAGCTGAGCTGAGAACAGGGACGTTGTGCCCCACTGTCCCCTGTGGTTTGTGAATGACCTCCAGGTCAGGGGGTCACAACTTGTTCTTAGTAAACTTGCCAGCTGTTGGGGTCACATATTCCCATTCTGGGGCCTCACAAACCCCCGAATCCAGCCGGGACCCCATGCCAGGAGCTGGTCTAGGGACAGCATGCTTGTGACCCACAGACTGTTAAAGCCAGAAGGGACCTCAGAGAGTCCCTTATGCTGGAGGCGCCCTGTCAGCCGTGGCTAGGGGCCCCTTGCTCTATGCTGTGCCTTGCTGCCCACAGGCTCCCAGACACCAGTGCCCACTCTGCCCAGCCCCGGACTGGGTGTGGCTCGCAGATGAACAAGATGCAGGGCCTGCCTTGAGGGGTGTCTCCTAGAAGGAAAGCCAGACTCTCCGGCCCAGCCAGAGAGTCCAGACATGGCAGGGACCCGTTTCTCAGATGAGGAGCCTGAGGCTCAGAGAAGGGAGGCGATGTGTTCAGGGCCACCCAGCAGAAGCCTGTGGGGCTGGGCAACCTTCTCCCACTTTATGGGAGGAGCTGCAGCCTTGGCTGGGAGCTGGGCGGGGAGTAGCCAGGACCACCCCTTGCCCGTGCCGTGACATGGAACCTTCATCACTAAGGGGGCTGGAGTGGGAAGAGGGAGATAACTGTGTGGTCTCCAGAGCAAAAGAGAATGAGAGGTGGGCAGGGGGAGTCTTGGCAAAAGACCAAGTTCCACTTCCCTGCTGGGGAAGTCAAGGCTCAGAAAGAGGAAATAATTGCCCCAGGTAACACAGGGCAGAGGAGGGACAAAAAGCTGGGCATGGCCCCAGCCAGAGCCTCATCTGCCTACTCCGTGAAGCCTCCCAGGTACTCTGCTATCCTGGGAAACGCACAGGGAGGCCACACAGAGACACTGCTCACAAGAGTCAGACCAAGGTGCCAGCACAGCCTGGAAAGAGCTCAGAAAGGGGGTTGGTGCACGTGGCTGGGCATCTTAGGAGGCTTCCTGAGGGTGGGTAAAGGTGGGAAGGCCCTGGCGCTGCATCAGATGAGCAGGGCCTGGCAGGGACAAGCCTCTTCTCCTTTGGGAAGCCCTGCAGCCTCCTAGCAAGAGGCTGATTCCCCACTCTGCCCCCATCTGAATGTCCTTTTCATGTTGCACGCAGGGAACCTCAGGAAGGAGGATTGCCTGATGCCTGCCTGGCTCCATCCTTGAGCTCTGGGCACCACCTAGGGTGAGGGAGAGCCTGCAGCTCTGGGGCTAAGTCTGCCCTGGGGGGAAAGGGCTCCACGCTCACACGCACGCGCTCGCACACACACACTCACACCTGGACGCACACGGAGGCTTGCGGACCCATACTCACAGGCACATGTGGCCTGGGGACTGGGGGAGCAGGAAAGACCCCTCCAACATTTGGCCCTTGGAAGGCACCATTGCCAATGAGCCTCTTTGCTGGTTCCCCCGACCCCACCTGGGGGTCCCATGGGAGCCCAGCCCAGCCAGGTGTGGGGATGGGCCACCGGCCATTCCTGTTTTCCTTGTACAGACAGATTCTCACTACCCACCCGCCATCCCCAGACACATTTTATTTAATAACTTGTCATTGTTAAATTATTTATTAGCGTTTACCACACCACCACCCCCACCCTGCCCTCCACTCTCACCTTCCACCTCTTCCCACAACAGCAGAAAATGGAAACAACAACAAAAAAAGATGAGACATCAGTATATTTGTAAATAAACCGACCTGTACACTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136944-LMX1B:NM_001174147:7
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.979 A=NA C2=0.242
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGCATGATGGCTTCCTACAC
R:
AGGCGAAGTAGGAACTCTGCA
Band lengths:
296-586
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)