RnoINT0085887 @ rn6
Intron Retention
Gene
ENSRNOG00000004642 | Lmx1a
Description
LIM homeobox transcription factor 1 alpha [Source:RGD Symbol;Acc:1304784]
Coordinates
chr13:86057217-86061176:+
Coord C1 exon
chr13:86057217-86057387
Coord A exon
chr13:86057388-86059126
Coord C2 exon
chr13:86059127-86061176
Length
1739 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
ATGTCCCATCTTCCTTTCAGGTG
3' ss Score
11.75
Exon sequences
Seq C1 exon
CTCAGACAAATGGTAGTGGCAATGCTGGCATGGAAGGCATCATGAACCCCTATACAACGTTGCCCACCCCACAGCAACTGCTGGCCATTGAACAGAGCGTCTACAACTCTGATCCCTTCCGACAGGGTCTCACCCCACCCCAGATGCCTGGAGATCACATGCACCCCTACG
Seq A exon
GTAAGAGGGACTCAACCCTCAGAGGTCCCTCTCGGTCTGCTCGTGTGAGCTTCCCATCTTTCTTAAGCACATCTACGCAATTCCCAGAGACTTTCTCAATTACCAAATAGGAATGTGTCCCACAAAATATTGCTGACACCATCTACCTGATGATGTGCAGAGGATTCCTGAGCACATTCTTTGGTGACATTTCCATGTGTCATCAGTTTCGAGGCTTCGTTGTTGAGCCTTTCCTTGTCCACCTTGCCAGTTAGAGCAATGCTCAAGGGATGTGTCCTGGAGACTCTAGTGGGATGGGTGAATGAGTGTAGGGTCCCAAGGTCATTTCATGTTTACATTAAGAAAGGAAGTGTGTGACTTACACTCTATGTGACTTAATATGTGATACGGCATGCCCTAAGTCATCCTGATGATTATACAATAAAGTTTGGTTCAGCGTCTTGTAAAATTTAGTAGCAGAGATATAAGGTGTTCACTCTGCCAACTTCTGTCCTTTAGTTAATATTTCTTGTTGGTCAGGAGTGGGACCAATTGGTAAAATGCTTCTAACACATACATGAGGACAAAAGTTCAGATACCCAGCATCCATGTTAAAATTAGACATGGCTACAAATATCTGTAGCCCCGTGCTTGAGGAGAGTGCAGAGGCAGGCACATTGATGGAGTTTGCTGGCCAGCCAGTCTTACCAAACTTGTGGCATTCAAGAATGAGGAGGAGACCAGCTGAGGAAGATATCTGACATTAGCTTTTGTCCTCTACATGCACACACTCAAACATGTAACCAACACACACACACACACACACACACACACACACACACACACACACACACCACAAATTTGTTGTTAAAGTCACCTTTACTTTGGTTTATCCCAGCTTCAGCAAACACCATGGTGTTTGTGGACCCTCACTGTCCAACCTCAGGAACACATACATTCTAGGTTTGTACCTGTGTGCATCCCATTGATGCCCTTCCCTTTCCTCTTTAGAAGACACGTGTCACACTCAAACCATCTTCACTCTGCTACATCGGAAACCAGGGCAGATGCAGTTTTGTTGTTCATTTTGCAAATCATTATGTCTATGACCTTTAACAAAATGAACAACTAAATCTCAGTGATAAGTTTTGGGCACTTGCTTCTGCTTCTCCAGGTGAATTGAAGTGCAGGTACACCCTGCCAGGTTCAATTGTAATGGTACCTCAGCTGTGGTACAGTGTGAGCTCCTGGCCTCTAACCAGGGTACAGTTGAGGTCAGGTGCCTAACCTTCCTTTGTCGTGAGGTGGAAATCTAGGAGACAGAAAAACCTTGGTACTTCCCTGCTTTTTGAAATGACTGATGTTACCAGCAAGATCAGAACTTGAAGAATCCATGTTCATTTCTTACCATCTGTCCTTGAGGTGCCTTTTGTGAGGCCAAGGACATTCAGGATCCCTGTCTAAGTCCCTCCAGCCTTTGGTGATGAGCCTACCCCGTGTTCTCTGTGTAGATACCCTCACTGTTCATAACTTAGCTCACATGGCTTAATGCTTTTCCAACCTTGGGCATGAACTCTCAACGAGACTCTGGACCCAGCATTGTAACCTTTACACTTTTGTGTGTAGTTGTTCCCCATGCTTCAACACTTAGTAGGTTCTCATCCCTGGGATGTATTCAAACACTTGTTCAGCTAATTTCCTAACACACAAGAGTGTTATTTCTTCCAGACCCTCATGCCCATGTCCCATCTTCCTTTCAG
Seq C2 exon
GTGCTGAACCTCTTTTCCATGACCTGGATAGTGACGACACATCTCTCAGTAACCTGGGCGACTGCTTCCTGGCAACCTCAGAAGCTGGACCCCTACAGTCCAGAGTGGGAAACCCCATCGACCATCTGTATTCCATGCAGAATTCCTATTTCACCTCTTGAGTCTTCTCCTAGAGTGTTGTGGCTGGGCTCCCATGTGGAAGAACCATACTGTGTGAGGGATTGCTGACTTTAGGATGGGGAGGCCAGAGAAGAGGTGGGCTGGGGAGGGAGGTTTGTTGGGGATGCTGTCGTTTAATTATATGGTGTAGCACAGCATTTCCAAAGACTGAATACATTATGGATCGCATAGTTTAATGTTTCTAATAAGAATCTTAGTGTTAGATATGAAGATGTGTTTATCATTAAGGACAGGGTCTTTTAATATAGATATTCTCAAGCAAACTAGATATCTAGGGACTCCCAACAGCTTCCCGCCATCCCGGAGAAGTGCTTGTCAAGAGGTGCCGTATGTCTATTCATCTACACACCAATAGACAGACAGATAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAAAACCTTTCATACTTTATCATCAAAGTTTATTCCTAATTATAACAGACACCAACTGTACAGCAAAAGTAACTTTATTTTCAGTGTGAACTATATTTAAGGAAATGCTTGATGCACTTAAGTTATAAAATGAGATAATTTACTTTTATAAACTTTATTTTTAGTTGGGAGGGACTCATCGGCAGGGCAGAGAGGGCTACTCCACCTGGCCCCAAAGCTTTGAGTGCTTGAGTTCGTTCCGTGATCCTAGCCTCATTGAGGGCTAGAATGTAACGCCCGATGGCAGGCAGCATGCTATAACGAACTCATGCTCACTCTGGTGTCAAGTCACCGGGCCTGAACGCAATTGTAAGCTTATTGGTATGGTACTGTTGGGTAGCATCTGCAAGGTTGTCTCGACCCCCCAGATTCAGCCTCGATGAGTGTGGAAGAAGTTGATAGCCACACCTACCTCCCTCTCTATGAGTGTGGATGAGGTGGATGCCACACCTACCTCCCTGGGGACACTAAGGCTCCATACCAGGACATGACTGAGGGTGAAACAAAAATAAATCTGATATGATTTAAAGTATAACTGGATCATGTGCCTGATGGTAGAGGATACCTGGGGTCACAGAGCGGGAAGTTCCGGTACCCCAAGTCCTATCTCTCTGCACAGCCCACATAGCCACATGACAGAGACACAACTCCGAGGGGGTGGAGACAACACTCCATCTGAGAAGGTGGGAGAGGCATGGTAGATGGAATTCTAGAGCAAGTGTTGACTTGCACATATGTTTTTTATTATTATTTTGTTTTGTTCTTTTTAAAAAGTCGTTTAAAAATGACTGTACGTACCCCAAAATCCGGAATTACTTGTGATCTCTGTTTGTCTCTTTCTTGAGGGCCCATAGTCTACAGGGCCTGCTCATAAACAACCTCATGGAGTTCATAGAAGCAGAGGGGACCAGGCAGGTACCCAGGGCTCTTCCTTTCATCTCCTTTTGCTGACCCTGAGCACAGGAAGACCCAGCAGCCATTGTACACAGGGACAATTCCGTGCCCCAATCTCCAATTATGGTGCTAGGATGGGATCTTCTGTGTTAGAATTCTCCGGGGAAGCAGAATGAGTAGGGGGAAGACAGAAGGACTCCACTGAGAGGGGCTGTGACAGGCATGCCTGGGGACGTCATCAGAGCCACGAACATGCCCACCTATCCACGTCATTCTCTGCAAGGCCAGAGGAAGCATGTCCCTTAGTCGTAGAGTGTGTGTTGTGTGATTTTTGTGCTCTTCTTTATAATTTATACAAACCATCGGGAAACCCGAACCAGTCTGTTGACTGAGAATGAGGCAGGCACAGGTGGCACGGACGGTGTCTGTGTGGCTGATTGGTTGGAGAATGTAGCAGATATTATGTGAATGAAAGCAAACAGAGATCCTTAATTCTACTCTCTAATGATATACCGAGATGAAATTAAAAGCCTCTTACGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004642:ENSRNOT00000006163:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.793 A=NA C2=0.623
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGCTGGCCATTGAACAGAG
R:
TCTGGCCTCCCCATCCTAAAG
Band lengths:
344-2083
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]