HsaINT0077272 @ hg19
Intron Retention
Gene
ENSG00000105991 | HOXA1
Description
homeobox A1 [Source:HGNC Symbol;Acc:5099]
Coordinates
chr7:27134880-27135625:-
Coord C1 exon
chr7:27135178-27135625
Coord A exon
chr7:27134975-27135177
Coord C2 exon
chr7:27134880-27134974
Length
203 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGT
5' ss Score
10.93
3' ss Seq
TTGTCCCCTCTCCACGCCAGCCA
3' ss Score
4.82
Exon sequences
Seq C1 exon
ATTCATATCATTTTTCTTCTCCGGCCCCATGGAGGAAGTGAGAAAGTTGGCACAGTCACGCCGGGCTTCGCAGGACCAGGTCACTCAGTGACAGATGGACAATGCAAGAATGAACTCCTTCCTGGAATACCCCATACTTAGCAGTGGCGACTCGGGGACCTGCTCAGCCCGAGCCTACCCCTCGGACCATAGGATTACAACTTTCCAGTCGTGCGCGGTCAGCGCCAACAGTTGCGGCGGCGACGACCGCTTCCTAGTGGGCAGGGGGGTGCAGATCGGTTCGCCCCACCACCACCACCACCACCACCATCGCCACCCCCAGCCGGCTACCTACCAGACTTCCGGGAACCTGGGGGTGTCCTACTCCCACTCAAGTTGTGGTCCAAGCTATGGCTCACAGAACTTCAGTGCGCCTTACAGCCCCTACGCGTTAAATCAGGAAGCAGAC
Seq A exon
GTAAGTGGTGGGTACCCCCAGTGCGCTCCCGCTGTTTACTCTGGAAATCTCTCATCTCCCATGGTCCAGCATCACCACCACCACCAGGGTTATGCTGGGGGCGCGGTGGGCTCGCCTCAATACATTCACCACTCATATGGACAGGAGCACCAGAGCCTGGCCCTGGCTACGTATAATAACTCCTTGTCCCCTCTCCACGCCAG
Seq C2 exon
CCACCAAGAAGCCTGTCGCTCCCCCGCATCGGAGACATCTTCTCCAGCGCAGACTTTTGACTGGATGAAAGTCAAAAGAAACCCTCCCAAAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000105991-HOXA1:NM_153620:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.297 A=NA C2=0.407
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACAACTTTCCAGTCGTGCGC
R:
GTCTGCGCTGGAGAAGATGTC
Band lengths:
307-510
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)