HsaINT1015867 @ hg38
Intron Retention
Gene
ENSG00000128645 | HOXD1
Description
homeobox D1 [Source:HGNC Symbol;Acc:HGNC:5132]
Coordinates
chr2:176188579-176190907:+
Coord C1 exon
chr2:176188579-176189453
Coord A exon
chr2:176189454-176189807
Coord C2 exon
chr2:176189808-176190907
Length
354 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
GCCCTGTCTTTACGTTGCAGGCA
3' ss Score
9.88
Exon sequences
Seq C1 exon
GCCGAGCGGAGAGGCCGCCCATTGGCCGGCCAGCGCCACGTGGCCGCCCCCGCCGGTATATTAGGCCACTATTTACCTCCGGCTCACTCGCCATGGGTTGGAGAGGGCAGCTCGGGTAGAGAGGGCTGGCGGAGCGGCGCAGACGGCGGCAGTCCTGCTCAGCCTCTGCCCGGCTCCGTACTCCGGCCCCGGCCTGCGCCCTCAGAAAGGTGGGGCCCGAACCATGAGCTCCTACCTGGAGTACGTGTCATGCAGCAGCAGCGGCGGGGTCGGCGGCGACGTGCTCAGCTTGGCACCCAAGTTCTGCCGCTCCGACGCCCGGCCCGTGGCTCTGCAGCCCGCCTTCCCTCTGGGCAACGGCGACGGCGCCTTCGTCAGCTGTCTGCCCCTGGCCGCCGCCCGACCCTCGCCTTCGCCCCCGGCCGCCCCCGCGCGGCCGTCCGTACCGCCTCCGGCCGCGCCCCAGTACGCGCAGTGCACCCTGGAGGGGGCCTACGAACCTGGTGCCGCACCTGCCGCGGCAGCTGGGGGCGCGGACTACGGCTTCCTGGGGTCCGGGCCGGCGTACGACTTCCCGGGCGTGCTGGGGCGGGCGGCCGACGACGGCGGGTCTCACGTCCACTACGCCACCTCGGCCGTCTTCTCGGGCGGCGGCTCTTTCCTCCTCAGCGGCCAGGTGGATTACGCGGCCTTCGGCGAACCCGGCCCTTTTCCGGCTTGTCTCAAAGCGTCAGCCGACGGCCACCCTGGTGCTTTCCAGACCGCATCCCCGGCCCCAGGCACCTACCCCAAGTCCGTCTCTCCCGCCTCCGGCCTCCCTGCCGCCTTCAGCACGTTCGAGTGGATGAAAGTGAAGAGGAATGCCTCTAAGAAAG
Seq A exon
GTAAGTCCGCGGGCCTTGGATGGGGCCACCTGGGGTTGGGGACGGAGCCTCCCCCGCGGAAATGCGCTGGGAGCGTGGTGTCGCTGCCTTTCCAGACAGCGGTTTGGGTTTTGTGGAGGAGACGCGTTCCCGGGCGAATTCCATGGAGTCTGCCTCGAGTACAGATTCGGAAAATGTGCCAGGCATTGAGAAAATTTCAGGAAGGAGCTCTCCGTGGAACTTCTCCTGGTACAAATTCTGTTCCTAGGGACCCAGGAGGGCTGCGCTGGGACTTTGATTCTAACTAGCTCCACTGCTCACCCACATTCTGTCCCCGGCCTCAGGCCTGGCTGACGCCCTGTCTTTACGTTGCAG
Seq C2 exon
GCAAACTCGCCGAGTATGGGGCCGCTAGCCCCTCCAGCGCGATCCGCACGAATTTCAGCACCAAGCAACTGACAGAACTGGAAAAAGAGTTTCATTTCAATAAGTACTTAACTCGAGCCCGGCGCATCGAGATAGCCAACTGCTTGCACCTGAATGACACGCAAGTCAAAATCTGGTTCCAGAACCGCAGGATGAAACAGAAGAAAAGGGAACGAGAAGGGCTTCTGGCCACGGCCATTCCTGTGGCTCCCCTCCAACTTCCCCTCTCTGGAACAACCCCCACTAAGTTTATCAAGAACCCCGGCAGCCCTTCTCAGTCCCAAGAGCCTTCGTGAGGCCGGTACTTGGGGCCGAAAAACTGTGGCCTGCAGAAGTCCCAGGCGACCCCCATCCCTATCTAGACTTAGGAGCTCAGTTTGGGATGGAGGTGGGAGAACAAAAATGAATAGGGATTTCACTTGGGAAATGAAGTACTTTAGTTGGCTTCCGAGTTCCAGACTATATGTCCAGATATTAATTGACTGTCTTGTAAGCCACTTGTTTGGTTATGATTTGTGTCTTATCAGGGAAAAGGTGCCCAGCTGCCAGCCCAGCTCCGCTGCTATCTTTGCCTCACTTAGTCATGTGCAATTCGCGTTGCAGAGTGGCAGACCATTAGTTGCTGAGTTCTGTCAGCACTCTGATGTGCTCAGAAGAGCACCTGCCCAAAGTTTTTCTGGTTTTAATTTAAAGGACAAGGCTACATATATTCAGCTTTTTGAGATGACCAAAGCTAGTTAGGGTCTCCTTGATGTAGCTAAGCTGCTTCAGTGATCTTCACATTTGCACTCCAGTTTTTTTTTCTTTAAAAAAGCGGTTTCTACCTCTCTATGTGCCTGAGTGATGATACAATCGCTGTTTAGTTACTAGATGAACAAATCCACAGAATGGGTAAAGAGTAGAATCTGAACTATATCTTGACAAATATTATTCAAACTTGAATGTAAATATATACAGTATGTATATTTTTTAAAAAGATTTGCTTGCAATGACCTTATAAGTGACATTTAATGTCATAGCATGTAAAGGGTTTTTTTTGTAATAAAAATTATAGAATCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128645:ENST00000331462:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.147 A=NA C2=0.306
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
CAGCACGTTCGAGTGGATGAA
R:
GCTGCCGGGGTTCTTGATAAA
Band lengths:
355-709
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains