HsaINT1015830 @ hg38
Intron Retention
Gene
ENSG00000253552 | HOXA-AS2
Description
HOXA cluster antisense RNA 2 [Source:HGNC Symbol;Acc:HGNC:43745]
Coordinates
chr7:27121917-27122666:+
Coord C1 exon
chr7:27121917-27122026
Coord A exon
chr7:27122027-27122466
Coord C2 exon
chr7:27122467-27122666
Length
440 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGA
5' ss Score
6.12
3' ss Seq
ACCAGAACCTCTTTCAACAGGCC
3' ss Score
6.43
Exon sequences
Seq C1 exon
AGGAAAAGGAAACGCCAAGACATAGAAAACCACGCTTTTCCCGTAGGAAGAACCGATGATGAGCCCTGATGAAAGAAGGAAGAAGACCCGCTGTCTGCGAAGGCCTAAAG
Seq A exon
GTTAGAAATACAGCAATTTTTCTCATGCCGAAGGAAAGGCAAAATGGTCTAAGAAACTGCAAGAGTGTGATACAAGTTTTCCTCAACAGCGAGCTGGGACTGGCGACAATTTCTTAACTCACAGCCTCCGCAGTCGCCTTAGTCGACAAAGAGAGCAGCCCACGCAGCGGCCGCCGCGCCCGTGCCCGTGGCCTTTACTTGCTTTTGCCCTGAAGTTCAGTGTAGTGGTTTGTTTGGGGCTTGCAGGAAGAAACAAACACACTCCCTCTGACTCTCCACAACCCATCTTTGCCTTCTGCAACCGCTTCTCCTGCCCATCGCTGGTTTTGGGGTAGGCTCTTTGTCTGCCTGAGGCCCCGCACTCGCAGGGCAAGAAGCTTAAAGGAATCCAACTCCAAACTCCTCCGAAGTTAAATATTGACCAGAACCTCTTTCAACAG
Seq C2 exon
GCCGCGGTTGCCAGGAACCGTGGAGGGCCAACTCCTCCCAACCGCCCTGGTGCAAAGTCCCACGCGGCGAAGAGTTTTGGAGCAGCGCTTACCTAGAAAGATGTTTAAATTCTGAACCAGGAATTGTCTCCAACTCCAGGCGCTCAGGGAATCGCCTTTTCCGGTGTCCAGGCGCTCTGCAGACAAATAAACAGCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000253552:ENST00000517550:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
NonCoding
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGAAAAGGAAACGCCAAGACA
R:
CTTCTGCTGTTTATTTGTCTGCA
Band lengths:
310-750
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains