HsaINT0012410 @ hg19
Intron Retention
Gene
ENSG00000162980 | ARL5A
Description
ADP-ribosylation factor-like 5A [Source:HGNC Symbol;Acc:696]
Coordinates
chr2:152668871-152670830:-
Coord C1 exon
chr2:152670683-152670830
Coord A exon
chr2:152668955-152670682
Coord C2 exon
chr2:152668871-152668954
Length
1728 bp
Sequences
Splice sites
5' ss Seq
GAGGTAATG
5' ss Score
8.73
3' ss Seq
TTTTTTTGTAATTATTTTAGTTT
3' ss Score
8.16
Exon sequences
Seq C1 exon
TTCTATGAATGAAGTTGTACATACATCTCCTACAATAGGAAGTAATGTAGAAGAGATAGTGATTAATAATACACGTTTCCTAATGTGGGATATTGGTGGCCAAGAATCTCTTCGTTCTTCCTGGAACACTTACTATACTAACACAGAG
Seq A exon
GTAATGTTTCTTACAATATTTAAAATTCTATAAACAGAATGCTTGGAAAACATCTAGATTTGAGTCCTTATAGTTAATCTTTTTGAAATATCACAGTATGTTAATACATAGAGAGTTTAAGCAGAGTAAAATCTGATTTCCTATTCCAAGGTCATTGTTCAATATGTCCACTATCATTGAACCTCTATAGGGAGAATTGGTGGTTAATTATGTTCTGATTGTGTATTGATCTCAGAACTTGTCTTTAATAGTTTTTTTTAATGACTTCCATCTCATAGTTTATAATTTCATTTCTCTCTATTTATGTTTGACTGAGTTTAGCTCACCAAATGAGAGGGTTTTGATGGTTTGAATCCTAGCCAGTTTTACTATTTTCTTTTACAAAACACAATTGCACATTAAATAATTGTTTTTCTTTTGATTATAAGGCATTTTAGACATAGTCATATCTTTTTATTTACACATTATTTCCCAAAGGAAATTTCAGACCTTTGACATTTGAGTGCTTCATTGCATAGACCTGTGAATTAAAAGACTGACCGTTGTTTTTGTAGTGTTCATTATTACAAGTTAATAAAGCATGGTTTATAAGTATATAAAGCTGACTTTTAAGTCATTAAGAAACCATTAAGTGTATCTGACAACTTGATTTCCTAACACTGCATTAGGCATTTAATCATTTTTTAATAAGGGAAGTTATGTATGATTATAAAGGTATATATGCTACTGTATACATATGCTATAGGTTTCAAATTCATGCCAACAGCCTGAAAATTAACAGTTTTATTAAAATACCTTGGAATAAAATGGGCCTTACAGTGATAAAGCCACCTATCAGTAAGCTGTCAAGTGAGAGGAGAGGTAAAGTAGCAGTTCTCTCATACATCTGCCTTTTGGTTGATGAAGTCTGAATAATTGAAAAGATCCAGAAAATCATAATAATTTATTTAAAAATTAAGATCTAGGTCCCAAAAATAAATAGTGCATGTTACTAATAGGCAGTCAGAACCAACTTGGGCATCATAAATGTTATCATAAAGTAAGTAAGTTAAATCTCCATCTGTTCCTGCTGATCTCTTGCTTTTGGGTGCTCACGGAGTTGAGGAAGAGCTGGGGTGGAGCTCAGTCCTGCACAACAATCACAAGTCTTTCATCGCACCTTCTGATACCAGTCTCATCATCAGTTTATGAAGGGGTTGTGCTTGCAGGTAGCAGGCGATACTTATGTAAGGAAGAGAGCTTGTTTTTAGATAGAGATTTATTCTTTCAGTTGGTTGAATTTTTTTTTAATTGATTTCTTTATCTTGTCACATTACTTTACTCCCATACCCGTGCCCTTTTAGGTGTTCAGATTGATATTAATAAATAATATCTACCTGGAAGTAATAAATTCAGGATCATATTGCATGTTTTTCTTGTTGATTTGTAGTGCAAATAGATAGATATAGGTCCATTAGCATTCAAGATACTAGTTTAGAAAACAGACATGCGTTATATATATTAGTTAGAATGTTAATATCATATTCTCTTTTCTCTTAAAAATTAGTAAATATATTAAAATCGATCAGACCTTTTGGCTTCACAATGTATAGGTAGCTCTGATTTTCCAACAATACCATAAGATTCCAATTTCTTGATATTAATAGCCTGTATGTCAAATAAACACATTATAAATTTTACAGATACCAAATTGTATAATCACTAATAATTTTTTTGTAATTATTTTAG
Seq C2 exon
TTTGTAATAGTTGTTGTGGACAGTACAGACAGAGAGAGGATTTCTGTAACTAGAGAAGAACTCTATAAAATGTTAGCGCATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162980-ARL5A:NM_177985:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.007 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002516=Arf=PU(33.8=97.9)
A:
NA
C2:
PF0002516=Arf=FE(15.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAGTTGTACATACATCTCCTACA
R:
CTCATGCGCTAACATTTTATAGAGT
Band lengths:
223-1951
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)