HsaINT0077314 @ hg19
Intron Retention
Gene
ENSG00000170178 | HOXD12
Description
homeobox D12 [Source:HGNC Symbol;Acc:5135]
Coordinates
chr2:176964530-176965488:+
Coord C1 exon
chr2:176964530-176965103
Coord A exon
chr2:176965104-176965249
Coord C2 exon
chr2:176965250-176965488
Length
146 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAC
5' ss Score
5.88
3' ss Seq
GGGTTGGGGCTGTGTTGCAGGCC
3' ss Score
5.25
Exon sequences
Seq C1 exon
ATGTGTGAGCGCAGTCTCTACAGAGCGGGCTATGTGGGCTCGCTTCTGAATCTGCAGTCGCCAGACTCTTTCTACTTCTCCAACCTGAGGCCGAATGGCGGCCAGTTGGCCGCGCTTCCCCCTATCTCCTACCCGCGCGGCGCGCTGCCCTGGGCCGCCACGCCCGCCTCCTGCGCCCCCGCGCAGCCTGCGGGCGCCACTGCCTTCGGCGGCTTCTCGCAGCCCTACCTGGCTGGCTCCGGGCCTCTCGGCCTGCAGCCCCCAACAGCCAAAGACGGACCCGAAGAGCAGGCTAAGTTCTATGCGCCCGAAGCGGCCGCTGGGCCAGAGGAGCGCGGTCGTACCCGGCCGTCCTTCGCCCCCGAGTCTAGCCTGGCTCCTGCAGTGGCTGCTCTCAAAGCGGCCAAGTATGACTACGCTGGTGTGGGTCGTGCCACGCCGGGCTCCACGACCCTGCTCCAGGGGGCTCCCTGCGCCCCTGGCTTCAAGGACGACACCAAGGGCCCGCTCAACTTGAACATGACAGTGCAGGCGGCGGGCGTTGCCTCTTGCCTGCGACCTTCACTGCCCGACG
Seq A exon
GTAAACGGTGCCCATGCTCCCCGGGCCGGTTTGGGCCGGGATGGGAGGTGGGGTTCAAGGGAGAGTGTAAGGGGAGGTGAACCGCCTGGGGGCGGGCAATAGACAGAGTACGGGCTGGGTTGACGTGGGTTGGGGCTGTGTTGCAG
Seq C2 exon
GCCTGCCGTGGGGGGCGGCCCCGGGGAGGGCCCGCAAGAAGCGGAAACCCTACACGAAGCAGCAGATTGCGGAGTTGGAGAACGAATTCCTCGTCAACGAATTCATCAACAGGCAGAAACGCAAGGAATTGTCCAATAGGCTGAACCTCAGCGACCAGCAAGTCAAAATCTGGTTCCAGAACAGGCGTATGAAGAAGAAGCGCGTGGTGCTTCGGGAGCAGGCGCTGGCGCTCTACTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170178-HOXD12:NM_021193:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.374 A=NA C2=0.724
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=71.2)
Main Inclusion Isoform:
NA
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:
GCTCTCAAAGCGGCCAAGTAT
R:
CTGCTGCTTCGTGTAGGGTTT
Band lengths:
249-395
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)