HsaINT0003175 @ hg19
Intron Retention
Gene
ENSG00000072110 | ACTN1
Description
actinin, alpha 1 [Source:HGNC Symbol;Acc:163]
Coordinates
chr14:69358770-69360464:-
Coord C1 exon
chr14:69360372-69360464
Coord A exon
chr14:69359001-69360371
Coord C2 exon
chr14:69358770-69359000
Length
1371 bp
Sequences
Splice sites
5' ss Seq
GATGTGGGT
5' ss Score
2.02
3' ss Seq
CCACCGCCTTCCCACCCTAGCTG
3' ss Score
8.21
Exon sequences
Seq C1 exon
GCGGAGACAGCAGCCAATCGCATCTGCAAGGTGTTGGCCGTCAACCAGGAGAACGAGCAGCTTATGGAAGACTACGAGAAGCTGGCCAGTGAT
Seq A exon
GTGGGTACCCCCGGGTTCACCTGGCCTGACTCTAGCAAGAGTCAGTCCCCTAGAACGTGTACCTCCAAGTCTTTCCTTGGAGCATAGTCTCAGGCTTGTATAGTCTCTGATCCCAATACTGCTAGTCCAGGGCAGCCTGAGCTCTGTTGTGGCTCTCCCAGAAAGTAGTGAGGTGGGGGCAGAGGCCAGTCCCTGAGTTATCATGAGCCTAGGATATCCCTTTGCCTCTCAGAGTCTTCTTGTTTTTTTCACTTGTCAAGTGAGAGTTGAGCCAGGGGATGTCAAAGCCTTTCCAGCCTAGTGTACTCTTAGTCTGTGAGTTTTGCTTCAGTGAGAAAAGGAGCACATCTGGTTCTAAGAGGGTGAGGGTAGGGTTTTCGGTAAATTAGTGCCGGCTCAGGCTAGCATAACAGCTACCAAAAGTAGCGGCTGTCCCCTACTGTTCAGGGAACAGGATGGCACAGTGCTGGGTTTCCTGTTCTGCCATTGGCTACATTTAGGTTAAGCCTCCTCTTCTTGAAAGAATTCAGCCCGTTGAGCTGCTCAGCCCAGCCTCTTGGTGGATCTGCTGCCCAGCATAGTAAGAACGCAGGTTCTGGAGCCCAAGTGCCTGGGTTTAAATTTCTGCCATTCCAGCCAGGTCACCTTGGCAAGTTACAGGACCTGGTAGGGCCTCGGTTGTCTCCTCTGTAACATGCAGGTGATCACAGCCCTTAGCTTTGTAGTGTTTCTGTGGTGATTCAGATGAGTCCATGTGTGTGATGTGCCTGGCCCCCTGCAGGTGTTCAGTGTATTCCTATTGTCATGTGCACCCCTCCACCTTCTCCACCACCATCACCTTGGCCCAAGGAAAACAGTCCAGGCCGTGCCTGCTTGTGCTCCAGGCCAGCTCTCTGCCCAGAAGCCAGCCTCTTCCCTTTTAAGTCAGAGACCCACATTCTAGATTCTTAGGAAGTCAGATGGCAAGAACTTCTGGAAATAGCTGTTAACCCCCTCCATGGTATAGATGAGGAAACTGAGGCCCAGCCAGTTAGAACCTGGTACTAAAACCCAGGCTTCCTTCCTGCCTTTTAGTTGCACTAACTTCACACCAGGTCTATGGGTCTTCCCTTAGCAAAGCAGGGAGGTTGAGTGACGTGACTGTGAGTCGATGTACCCTAGTAGCCAGGCTTCACGAAGCCTGTGGTTCTCAGAGGGAACACCCTGGAAGCTGACTTCATGGCCTGGGAATGTCAGTGGTTGGGAAGGAGTGTGCTATTAGGAGAGACCCCTTCCCCATGTGGGAGGGCTGTTGGGAGGAAAGGGAGGCTGGCCCTAGCACACTCCCTCCCCGCCTCCTCACCTCCTGCCCCCACCGCCTTCCCACCCTAG
Seq C2 exon
CTGTTGGAGTGGATCCGCCGCACAATCCCGTGGCTGGAGAACCGGGTGCCCGAGAACACCATGCATGCCATGCAACAGAAGCTGGAGGACTTCCGGGACTACCGGCGCCTGCACAAGCCGCCCAAGGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGCTGCGGCTCAGCAACCGGCCTGCCTTCATGCCCTCTGAGGGCAGGATGGTCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000072110-ACTN1:NM_001130005:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.172 A=NA C2=0.064
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=PU(9.9=35.5)
A:
NA
C2:
PF0043516=Spectrin=FE(68.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGACAGCAGCCAATCGCATC
R:
GAGACCATCCTGCCCTCAGAG
Band lengths:
320-1691
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)