HsaINT1015868 @ hg38
Intron Retention
Gene
ENSG00000170178 | HOXD12
Description
homeobox D12 [Source:HGNC Symbol;Acc:HGNC:5135]
Coordinates
chr2:176099730-176101193:+
Coord C1 exon
chr2:176099730-176100375
Coord A exon
chr2:176100376-176100521
Coord C2 exon
chr2:176100522-176101193
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
TCTGAGCCTGTCCTCTTATTCCCGGTTGTAACTAAATACTGTTGCGAGCGCAGCCGAAGCCCTTTGTTGGAGATGTGTGAGCGCAGTCTCTACAGAGCGGGCTATGTGGGCTCGCTTCTGAATCTGCAGTCGCCAGACTCTTTCTACTTCTCCAACCTGAGGCCGAATGGCGGCCAGTTGGCCGCGCTTCCCCCTATCTCCTACCCGCGCGGCGCGCTGCCCTGGGCCGCCACGCCCGCCTCCTGCGCCCCCGCGCAGCCTGCGGGCGCCACTGCCTTCGGCGGCTTCTCGCAGCCCTACCTGGCTGGCTCCGGGCCTCTCGGCCTGCAGCCCCCAACAGCCAAAGACGGACCCGAAGAGCAGGCTAAGTTCTATGCGCCCGAAGCGGCCGCTGGGCCAGAGGAGCGCGGTCGTACCCGGCCGTCCTTCGCCCCCGAGTCTAGCCTGGCTCCTGCAGTGGCTGCTCTCAAAGCGGCCAAGTATGACTACGCTGGTGTGGGTCGTGCCACGCCGGGCTCCACGACCCTGCTCCAGGGGGCTCCCTGCGCCCCTGGCTTCAAGGACGACACCAAGGGCCCGCTCAACTTGAACATGACAGTGCAGGCGGCGGGCGTTGCCTCTTGCCTGCGACCTTCACTGCCCGACG
Seq A exon
GTAAACGGTGCCCATGCTCCCCGGGCCGGTTTGGGCCGGGATGGGAGGTGGGGTTCAAGGGAGAGTGTAAGGGGAGGTGAACCGCCTGGGGGCGGGCAATAGACAGAGTACGGGCTGGGTTGACGTGGGTTGGGGCTGTGTTGCAG
Seq C2 exon
GCCTGCCGTGGGGGGCGGCCCCGGGGAGGGCCCGCAAGAAGCGGAAACCCTACACGAAGCAGCAGATTGCGGAGTTGGAGAACGAATTCCTCGTCAACGAATTCATCAACAGGCAGAAACGCAAGGAATTGTCCAATAGGCTGAACCTCAGCGACCAGCAAGTCAAAATCTGGTTCCAGAACAGGCGTATGAAGAAGAAGCGCGTGGTGCTTCGGGAGCAGGCGCTGGCGCTCTACTAGCCGCGCGCGTGGCCAGGGCCGGGTTGGATCTGCCCTTTTGGACAGAGGCCTTGTTTGGGGAGGGGGATCTGGGGCTAAGGCTAAGGCTTTTCCTTCGGTTCCTTCTCTGCTGGCCCCAGAAGCCACCAAGAGATTTACAGACCAGGCCAGTTGGGCCTCCTTGCTTTCCTCAGTCCCTGAGAAGCCCGTGAGAAACGTGCGGAAGTACCAGTGCAACTCTGGCTGGCCTTAAGGCTTCCACGTTGGGGGACTGAGGCCAACTCTCCTTGCTCCTGGCTGGGGCATTTGCACCCACCGCTCATTCTTGCTCCCCGGTACCTGGATTTTTCTGTTTCCACCCAATTCGTTCTCCCTTTCCCCCTCTCTCCAGCCCCTTCAGCGTATAGCAGTCGCCTAGTTAGGGCTCAGAGTGGAAGGCCTCCTGAGGGAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000170178:ENST00000406506:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.364
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]
SPECIAL DATASETS
- Autistic and control brains