HsaINT0014187 @ hg19
Intron Retention
Gene
ENSG00000184743 | ATL3
Description
atlastin GTPase 3 [Source:HGNC Symbol;Acc:24526]
Coordinates
chr11:63398512-63400569:-
Coord C1 exon
chr11:63400498-63400569
Coord A exon
chr11:63398944-63400497
Coord C2 exon
chr11:63398512-63398943
Length
1554 bp
Sequences
Splice sites
5' ss Seq
GAGGTACGT
5' ss Score
10.2
3' ss Seq
TGTTTCTTTGTTCTTTTTAGGTT
3' ss Score
12.87
Exon sequences
Seq C1 exon
GCCACTGCTGAAGCCAACAACTTAGCAGCTGCAGCCTCTGCCAAGGACATTTATTATAACAACATGGAAGAG
Seq A exon
GTACGTGGGACATACGCCTTATTCTGAAATATCTATAATCTGGGCATTGTTGCTGACTTCAAAAGCCCAACTTGATCCTACTTAATGTATCTTTAAGTGATGAGGCAATAAACTTATATTCAGGTTGTCCTGGTAACGGGGGCCTTCTAATTATTACCATTTCTTTGTTTGTTTGTTTGTTCTTGTTTTGTTTTGTTTTGTTTTGAATAGCAAATAGTTTATTGGTAAGTACATAGTTTCAATGGGAGTAATAAATTCACATGAGCAGGAGACAATAATCAAGTCAAAAGAATAAATGCTTACTAATCATCAGAAAATCTGTGGCCATTAAGGCTGGCACATAAAAATCCAAAATCACTCAGAGGCCGAATCTTAAAAGAAGATTCGTCCTCTTATTAGTTCATATGGAATAGGTCCATAGTAACTGGAATCTGTAGAATTCTGTAGATTTATCACCTTCTAACCAAACATGACCCACTGGGACATAACTGTAGCTTTTAAAGAAATCTGATGGACTAGTGGTGAGGATTTTGTCTCCTTCCAAACCAGTTACTCTTTTACAAATATTTGATGTTGGATCACTTGGGCTTTTTGCAATCACAATGTCACCTCTTTGGATACTATCAAAATGTCGACTAAGATTTTGTGCAAAGACAGTATCTGAATTTTGAATTGTAGGCTCCATTGATGGTCCAGAACACATGACAACACCACCAACGTATTCAGAAGCACAGTGAGCTATACAGCCATACTGAATAGCATAGCCAACAAGTCAGAAGGTTTCCCCAGAGCACCACGAAGCATAGTTCTATGTAGACTCTGCCACCATTGGTCATAGATCTGTTCTATAATTCATTTAATTTTTAGGGAAGTCGCAGGGCTTCCAGAAAAAAAAAATTAAAGCATGTCTCAAAGCGTATGTGGGTGATCCATGATTTCAGGAATCCTCGGGTCCCAAAGAACCCTGAGGACCCTCAACCAGGACACAGGTGGGCCTTTCTCACCTGGGCCCTGCAGAAGTCGACCGTTTGCTTTTGTTTTTTAGAGACGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGGTTCTCCTGCCTCAGCCTTCTGAGTAGCTGGGATTACAGGTGCCTGCCATCACGCCCGGCTAATTTTTTTTGTGTTAGTAGAGACGGAGTTTCACCATGTTTACCAGGCTGATTTCAAACTCCTGACCTCAAGTGATCTGCCCGCCCTGGCCTCCGAAAGTGCTGGGATTACAGGCGTGAGCCACCGCACCCGTCCCAGTGTCACTGCTCTTTCCAATTGATATTATCACCCTGGTTTTTTAAGTGTGCTTTTCAGAGGAAGTGAAACTAGACTTTATTGGTCTTAGTCATCTTTTAAAAGTTAACTTATTAATACATTGTTAACATCTTAAAACATTCTAATCCTTTCATTATCTTTTCATGTTTTATTTGGCACTTGTTTTTGAAGAGATCTTTTAACATATTGTTTCTTTGTTCTTTTTAG
Seq C2 exon
GTTTGTGGGGGAGAGAAACCTTATTTGTCTCCAGACATTCTAGAGGAGAAGCACTGTGAATTCAAACAACTTGCTCTGGACCATTTTAAGAAGACCAAGAAGATGGGTGGGAAGGATTTCAGCTTTCGTTACCAGCAGGAGCTGGAGGAGGAAATCAAGGAATTATATGAGAACTTCTGCAAGCACAATGGTAGCAAGAACGTCTTCAGCACCTTCCGAACCCCTGCAGTGCTGTTCACGGGCATTGTAGCTTTGTACATAGCCTCAGGCCTCACTGGCTTCATAGGTCTTGAGGTTGTAGCCCAGTTGTTCAACTGTATGGTTGGACTACTGTTAATAGCACTCCTCACCTGGGGCTACATCAGGTATTCTGGTCAATATCGTGAGCTGGGCGGAGCTATTGATTTTGGTGCCGCATATGTGTTGGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184743-ATL3:NM_015459:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF028419=GBP_C=FE(18.1=100)
A:
NA
C2:
PF028419=GBP_C=PD(53.5=47.2)
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:
CAGCCTCTGCCAAGGACATTT
R:
TGGGCTACAACCTCAAGACCT
Band lengths:
346-1900
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)