HsaINT0091938 @ hg19
Intron Retention
Gene
ENSG00000050405 | LIMA1
Description
LIM domain and actin binding 1 [Source:HGNC Symbol;Acc:24636]
Coordinates
chr12:50594560-50598483:-
Coord C1 exon
chr12:50598335-50598483
Coord A exon
chr12:50594668-50598334
Coord C2 exon
chr12:50594560-50594667
Length
3667 bp
Sequences
Splice sites
5' ss Seq
ACAGTATGT
5' ss Score
6.05
3' ss Seq
CAGTTATTTTTATTTTGTAGAAT
3' ss Score
7.66
Exon sequences
Seq C1 exon
GTCAGTTGTCATCTTCTACATTTGACTCGGAGAAAAATGAGAGTAGACGAAATCTGGAACTTCCACGCCTCTCAGAAACCTCTATAAAGGATCGAATGGCCAAGTACCAGGCAGCTGTGTCCAAACAAAGCAGCTCAACCAACTATACA
Seq A exon
GTATGTGTTCTGCATCATTCATTCATTCATTCATTCCATCATCCAGCAGATGGTCACTGAGTACTGGAATTAGGAAATGTCACCAGACCCTTGTATCTGAGCCCTGGTCCCCTAGCTGTTCTCTTTTCACATGAACCCTACCCTCGCTGGATTTGCAGTTCTTACCATGGTCTAATCCTGACTTTGCTTTCTTAGTCCTGGTTCCCACCCCACTCACTTTTTTTGTGATGTTACCAGTGAGTATCATTGAGAGTTTCCCTGGCTCTTCTACTTAATCTTTGTGTTGTTAAAGAAGTAGTATTTTATTAGTTTTAATATAACTCTTATTTTATCTTGGTTGTTGAGGGAAGAAGGAAGAAGACTGAAGAGCTTATTTTGGCTTTTGAGGGAAGAAAGAAGAAGACTGGAGAGAAATATCAGCTGTGTTCATTAACGAGGGTTTTTTTTGTGATTTTTTACTGAGATATAACTCACATAATATAAAATCACCATTTTAAAGTATACAATCTTGTGATACTTAGCATATTCACAAGGTTGTACAACCATTACCACTGTTTAATTCCAGAACCTTTCCATCACCCTGAAAAGAAACTTCATACCTGTGTAGTCACTCCCAACTTCCCCTGCTCTCATCCCCTGGCAACCACTTAGCTACTTCCTGTCTTTATGTATCTGCCTATTTTGGAAATTTCATATGAAGGAGTCATACAGTAGATCTTCTACTTAATCTTTAATCCTTACGATGTACTGTTTTCCTAAAGAAGTAGAATAGTAGATAAGGAAAAGGGAGAGATCACAAGAAGGTGACGTGCTCAGTAAGCATGAAAATTTTGATATTCAGCTGGGTGTGATGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGTGGGCAGATTGCCTGAGGTCAGGAGTTCAAGACCAGCTTGGCTAACGTGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCAGCATGGTGGCAGGCACCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTGGAACCCAGGAGGCAGAGGTTGCAGTGAGGCAAGATTGCGCCACTACACTCCAGCCTGGGCGACACAGCAAGACTCCGTCTCCAGGAAAAAAAAAAAAGATTGGTATTCAAAATACAATGGAGGGTCCTTCCCCTTTACGTTGTCCTGTGCTTAACGGGTAAGCTGATGCTACAGAACTGCTAAATTGAAGTTACCTTATAGCCAGGCGCAGGAGCTCACACCGTAATCCCAACACTTTGGGAGCCTGAGGTGGGTGGGTCATTTGAAGTCAGGAGTTCAGAACCAGCCTGGCCAACATGGTGAAATCCCGTCTCTACTAAAAATACAAAAAAAAAATTAGCCAGGTGTAGTGGCACACACCTGTAATCCCAGCTACTAGGGAGGCTGAGGCAGGAGAATCACTTGAACCTAGGAGATGGAGGTTACAGTGAGCTGAGATCACACCACTGTACTCCAGCCTGGGTGACAGGGTGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAGGAAGTTACCTTTCAAATGCCATTTATTCACATATATATGTATACACACACATAGATACAAATGTACACACACATATTTTTGTATCCTTCAAGCATTTGTTCTAAGATTTCAAATTACAAACCATTAATCTCTTGATGTCCTAATTGTCTAACAAAATCAAAAAGAACAATATTGAATTTTATTTGTTCTTAGGCAGATCGAAATTGGTGCATATTGGAAACCATAATGAGTATTCTGGGAGTTAAGCCTTCTCTTCCCCACATTATTAAGTATACATTCTCTAATAATATTTGGTGGACTAATTCTCTGGGCAATGAATAATTTCATCTTGGTTTTTTAACTGTAATTTTAACAACTTTATGTTTTAAGAAGAGATGATGTGTGTAAATCAATTAGCAAAGTGGAGTATCACAGGCTGATTATGCACCGTGAATGTGAAAAGCGAGCAAATTTAGACTTCCCTTAGAAGGCAGGTCAGGAGATACAGCAAATTGGGATCTGCGAAGCTGAACTTCCTCTTGTTACCAGATTTTACTGCTTCTCAGTGCCCTCCTGCTGTAAACATTCCCACCAGGTGACTCCCTATGTGGGGAAACCTGTTGAGTAACTTTTTTTTTTTAACTCCTAACCATTTCTGCATTACAGTTCTCCTGCTCTGGAGATTTTAAGAGTTGAAAACTCTTTGGGAATTCTTGTAAAAAGTACATTTTGTCTCATCCCCAAAGAATTTCCCAGGCCCCTTACAGAATATGGTTGTAACAAGGCACATACATACTCTCTGGCAGCAGTTCTGGAGGTGGGGCTTTGAGATGGGGTCAGGAATGAGTTGTTGGGCTATATAATGTTCTGCAGTGCTAGCTGCCAGCTCCTCCTCACAGATGCACCTCCGGTGCTGTGGGTCGTAATCTAGAATACCATCACTAGGTGACTAAGTCATACTCACATTCCTTTCATTGACCTGGTGGCCATAAATTGTTTCCTCCCATGCCTAAAGATTCACAGAGAACAGAAAAGTACTAGATTACTACATTATTAGCAGACTAATGGTGGGAAATGTCTATAGTCATCGACCTCTATGTTTATTTTATTTTATTTTATTTTTTTATTTTGAGATGGAGTTTCACTCTTGTTCCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTGCAACCTCTGCCTCCCTGATTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAACTGGGATTACAAGTGTGCACCACCACACGTGGCTAATTTTTTGTATTTTTAGTAGAGACAGGATTTCACCATGTTCGCCAGGCTGGTCTTGAACTCCTGACCTCAGGCGATCCACCCGCCTCAGCTTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCACCCAGGTTCTATGTTGATTTTAGATGTAATAGATGAGTTAATTGTAATATTCACCCCAGTGTCCTTTGCAAGGAAAAAAATGCAATTATCCTTATTCCTTATGACAATAAAATGCATGTTCTTTTATGTTGAGGCTCTGTTTTGAGAAGTAAAATAAATTATGTCTTTAGTACAATATATGAATTGTATATGGAAAAACATGCTTTTTGAAAGTCCCACCAAAAAGGTTTCTTTATGGTATCATTAAATATAATTTCAGTTTTTATATGTATACATCATCCCTGTCTCTCTTTCCAGGCCGGGCATTTATATATGTATGGTCAGTATATTTTCTATTATTGGCACTTGGCATCTCCTTTCCCCTGCTCCAGAATGGTCTTTTCTGATAAAACTCACAAGCTTTGCATTACCACAAGCTCTGCTGCTAGAAGAGTGAATCACAAGAATGTTGTATGCTTGGGGTGTTCTGTGTGCCTGTGTTGATGTGTCTGTATTCTAATGAGCAATCCAGTTTTACACTAGCATACAGATATTTAACTCTGAGGTATGTGTCCACAAAGCTGCTTTTGTCATTTCACTAGTCAGTGGGTTTTGCTTGTGAGAGTTAGGGGGTTGATTTGACCCGAGGCTTCTTAGAAGAATTTTTTAACATTCCAAGTTTATCTAATAGATGTGCTATGAAGAGAACAGAATGATGGGACTTTAAAAAAATTTTTACAGTTATTTTTATTTTGTAG
Seq C2 exon
AATGAGCTGAAAGCCAGTGGTGGCGAAATCAAAATTCATAAAATGGAGCAAAAGGAGAATGTGCCCCCAGGTCCTGAGGTCTGCATCACCCATCAGGAAGGGGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050405-LIMA1:NM_001113546:6
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.950 A=NA C2=0.963
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
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]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)