HsaINT0138558 @ hg19
Intron Retention
Gene
ENSG00000184898 | RBM43
Description
RNA binding motif protein 43 [Source:HGNC Symbol;Acc:24790]
Coordinates
chr2:152104728-152109369:-
Coord C1 exon
chr2:152109269-152109369
Coord A exon
chr2:152108179-152109268
Coord C2 exon
chr2:152104728-152108178
Length
1090 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TTCTCTCTTTTTAATTTCAGATC
3' ss Score
10.97
Exon sequences
Seq C1 exon
TTGCAGAGAATGTCATCAGACAAAAGAAACACTGGCTAGCAAGGAAGACTAGACATGCTGAACTCACAGTCTCTCTCAGAGTCTCTCATTTTGGTGACAAG
Seq A exon
GTAAGGTGTGATGCTGTAGGTGTACTGATAGTCCTGTATCCCATTTCTTTTTTGAAGTTTTTCTTATGGCAGGCGACACAAAGTGCTCTCACTCCATGACTTCTAGGAAGGAAAATGCAAACTCCCTGAGTCAGTGTTAAAGGCCAACCCTGGCCCTTGAAATTTTGGTTATCACCTCATCTATTTTTATCTTTCTATGTGTGTCACTTAATGTTTTATTTTACAAAGTGTATATTTTTTGAGAAAAGGTCTTGCTCCGTCACCCAGGCAGTGGCATAATCTTGGCTCACTCTAAACTCTGCCTCTTGGGCTCAGGTGATTCTCCTGCCTCAACCTCCCGAGTAGCTGGGACTATAGGTGTGTACCACCAGGCCTGGCTAATTTTTGTAGTTTTTGTAGAGACAGGGTGTCCCTATGTTGCCCAAGCTGGTCTCAAACTCCTGGACTCAAGCAGTCCTCCCACCTCAGCCCCCCAAAGTGCTGGGATTACAGGGGTGAGCCACCACGCCCAGCCTCACTTAATGCTTTTAAAGTGATGGTAAACGCTTATACTGTCATGGATGATGCCAGGTACCAACCTAAAGGCTTATTTTGGGAAAAAACAATTAGAATGAACATTAAAAAGAAGCTTTGAAGAGACAGAAAGTAAGAAAAAGAGGAAAAAGTTAAAATCCAAAGCAATGGTTTACCAACTTGATTCTGTAAGACACTCAGAGTTGTATGCAGCCATCTGATGAACTTGACTGGGGGCAGGAATGACTCCTGGGGGAACCCTATCCAAGCAGAACCAGAACAGTTTGTATGTATTGGTTCTGCATAAAACTGTTTCAAAAAAGAATTCTGCCTCTAAAAATTATTTGAGCCTGTCTGTTTTGGGGTATGTGGTGAGGGAGTGTGAATCCCAAATTGAACAAAATGGGATAACTTTGATGGGCTGCCCTGGTGCAAGAAGTCAGGAAGTCTGGGGCAGGCAACTGGGGCCTGGTTTATTGCAATTTCTGCAGAGAAAAGAAAGTGGCAGAAAAGAACATGTTTATGTAGTCTTTCCCACTAGGCAGTACTGTTTTCATTTCTCTCTTTTTAATTTCAG
Seq C2 exon
ATCTTCAGCTCTGTAAATGCCATCCTTGATCTTTCTGTTTTTGGAAAAGAAGTTACTCTAGAAACTCTGGTAAAAGACCTGAAAAAAAAAATCCCGAGTTTAAGCTTCAGTCCTTTGAAACCCAATGGAAGAATCTCCGTGGAAGGATCATTTCTGGCTGTCAAGAGGCTCAGAGAATCTTTGCTAGCAAGAGCATGTTCTCTCTTAGAAAAAGACAGAAATTTTACCAGTGAGGAGAGAAAGTGGAATAGACAAAATCCCCAGAGGAATCTACAGAGAAGTAATAACTCTTTGGCATCAGTCAGGACCTTAGTACCTGAGACTGCTAGAAGTGGAGAAATGCTTGTGCTTGACACAGATGTTTTTCTTTACCTGAAACACAAGTGTGGATCTTATGAAAGCACACTGAAAAAATTCCACATTCTGAGTCAGGAGAAAGTGGATGGTGAAATCACCACAATTTGTCTAAAAAGCATTCAAGTTGGTTCTCAGCCAAACAATGCAAAACATGTAAAAGAGCTCATTGAGGAATGGTCACATGCTCTTTACTTAAAGCTTAGAAAAGAGACATTTATTTTGGAAGGAAAGGAAAATAGAGAGAAAAGAATGATCAAAAGGGCATGTGAACAATTAAGTTCGAGATACCTTGAAGTCCTGATTAACCTTTATAGGACACACATTGACATTATAGGATCTTCTTCTGACACTTACCTGTTTAAAAAAGGGGTCATGAAATTAATAGGGCAAAAGGTTAGTTAATAAAATCTCAGCAATATAGTCATAAGGGCTGCTTTCTCTTGCTGAGCAGTGACCATTGCCATGAATGAGGCTAGCTTTACACACCGTATCTCATGAATCCTTATAGTCATCCTTCTTTGTCAGTGTTGACTATCCTCATGTTACAGCGGAAGAAACTAGGATTTGGAGAAGTTAAAACACTTTTCTGAAGTTATCCAGTTGACAAAGAATGAGGCTGTGGCTTAGCCCAGTCTATCTGATTACACAGATAATATCTAAGGAATAAAACTTTGAAAAAAACTCACCAAACTTTTTTTTTTTTTTTTTTGAGATGGAGTCTCGCTCTGTTGTCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCACTGCAACGTCCACCTCCTGGGTTCACACCATTCTCCTGCCTCAACCTCTGGAGTAGCTGGGACTACAGGTGCCCACCACCACGCCCGGCTAATCTTTTTGTATTTTTTTAGTAGAGATGGGGTTTCACCGTGTTAGTCAGGATGGTCTCCATCTCCTGACCTTGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGCCCAGCAAACTCACCAAACTTTGAAGGAATCTTACTTTCTCTGTAACTCCAAATTATTAGAGAATAATAATTATTAAGAAGTAGCCTTAACATATGAGAAATTTGAAAGGTGATTATTATGCCATGGGCAATTTCTTAACATTTACAGTTTGTGTTTACTCCGTGTAGAATTAGAATACTGGCAAAAATCACTGGGGAAACTACTTAGATGGAAAGCATATCTTATGCAGGTAATCATTATTTGACTAAATTCTATTGTTTCAAGGCTGCTGGCCACATAGGATGTTTTTACTATTTTTTTAGCCTAAGTGCTTACATAAAATGGTGATTCTTTTATAATTGTGCAAGTTGATAATATTAATTGAGTCATTCTTGTCACATCCAACTAAAACAGACTCAAGAAGCTAGGGGGAAAAAGTACTTGGGACACATAATATTGCTCCAAGAATGTAATTCTCTGTGAGCCTGGCTACTGAAACTGCTTGCTGTAACCTGAGACCAGTTTTGTCTATAGCTGCTGAGATAACTTGCTGTAACTCTAGGACTAATTTTACCTATGGCCATTGCCCACCAGTTGGAGCTTGCCAGCTCCCCAGGGCTTTACTAATACCAATGAACTTTCTCTTAAGATCACAAGTTGGCCGGGCGTGGTGACTCATACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACAAGGTCAGGAGATTGAGACCATCCTGGCTAACATGGTAAAACCCCATCTCTACTAAAAATACAAAAATTAGCCGGGCATGGTGGTGGGCGCCTGTAGTCCCACCTACTCGGGAGGCTAGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGTGGAGCTTGCAGTGAGCCAAGACTGCACTACTGCACTCCAGCCTGGGTGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAGAAAGACCACAAGTAACATTCTTAGTTTTAAATAAAACCCTCAACCTTCTCTTTGTTTGTTGGACATACTAAAGATCACCTAGAATTGAAATTCTTTCTTCTCAAAACATTAAATTTAGTTTTGTGTCTACATTTTCATTTTGACTTTGACATGCATGGTGTCAGAAGTGGGATACAAAGCTGACTCACCTCATGGAGAATCATTGGCCTTTGGAGTTATGGCATGAGGTACCCATGTTGGGGCCCTTTGAACCCCCTACACCCCCACCACTTTCACAGGTAATCCTTTCTCCCTCCAGTAAGTATCTCTTGGACAGAACTCTCAGATATGGTTCGAGTTCTGTTTTATTTGGGATATGATTAGGGAGAGGTCTTTCCCCCTCTTGTTTGGTAGATCTGTTGGGTAGAATTATTTTCCCCCTGTTGACCTCAGCTGCGAGGTTTGGACCTTGAGGCTTGGATGAGGGAATTTTTCCCTTTCTTTGGAGAAGGCTTATCATTCTTACTGGTAAGCATGTATTTTATTTTCTGTCCTGTCTTGTATTTATTTGGCCTTTGTGTATTCAGTGCTTGCATTTACTTGGCTTTTGCATAGTTGACATTAAATCAGAGCACCCACGAAATGAGCTCTCAAAGTTCAAAGGCATGCCAGAATATTTTCTGGAACTCCAGCTAGTAACATATTCAAACATTACAGGGATCATTTAGTCTGTTTTTCTTAAAACTGAACTAAAAGATGGAGGCTATAAAATCATACACTCCAAATAAGATATGCATATTTCATTGATATCTTGAGGCTAAAAAAAAATAAAAACAAAAACAAAACACATTCAGGATACAAATATTGCCTTGTTAAAAAATACTGTCTCAAAGGTGGCTGAAACTTTCTTTTCTAGACCTTTCCCCTCCCCTTCTTACAGTATCCCCTCTTTATCCTTCTCTAAACAGCTATTCTAACATACTACTTAAATAAAAACACTTGAAAACCAGCAGATATAAAACAAAGTCATTTTGACCTTCCTACTGTTTTTTTTTTAAAGCAAAGATTAAATTCCCATGTAAAACCTTCCTCCCTATACAAAAAAGAATAGCAGCATTTTTATCTTCAATGACAAAGAATTGAGTCCAAGAAAATACTGTATAAACCTTGTTAAAAATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184898-RBM43:NM_198557:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.063
Domain overlap (PFAM):
C1:
PF142591=RRM_6=PD(24.3=52.9)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGAACTCACAGTCTCTCTCA
R:
GGTCCTGACTGATGCCAAAGA
Band lengths:
355-1445
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)