HsaINT0077311 @ hg19
Intron Retention
Gene
ENSG00000128645 | HOXD1
Description
homeobox D1 [Source:HGNC Symbol;Acc:5132]
Coordinates
chr2:177053307-177055635:+
Coord C1 exon
chr2:177053307-177054185
Coord A exon
chr2:177054186-177054539
Coord C2 exon
chr2:177054540-177055635
Length
354 bp
Sequences
Splice sites
5' ss Seq
TAAGTCCGC
5' ss Score
-8.64
3' ss Seq
TGTCTTTACGTTGCAGGCAAACT
3' ss Score
-7.85
Exon sequences
Seq C1 exon
GCCGAGCGGAGAGGCCGCCCATTGGCCGGCCAGCGCCACGTGGCCGCCCCCGCCGGTATATTAGGCCACTATTTACCTCCGGCTCACTCGCCATGGGTTGGAGAGGGCAGCTCGGGTAGAGAGGGCTGGCGGAGCGGCGCAGACGGCGGCAGTCCTGCTCAGCCTCTGCCCGGCTCCGTACTCCGGCCCCGGCCTGCGCCCTCAGAAAGGTGGGGCCCGAACCATGAGCTCCTACCTGGAGTACGTGTCATGCAGCAGCAGCGGCGGGGTCGGCGGCGACGTGCTCAGCTTGGCACCCAAGTTCTGCCGCTCCGACGCCCGGCCCGTGGCTCTGCAGCCCGCCTTCCCTCTGGGCAACGGCGACGGCGCCTTCGTCAGCTGTCTGCCCCTGGCCGCCGCCCGACCCTCGCCTTCGCCCCCGGCCGCCCCCGCGCGGCCGTCCGTACCGCCTCCGGCCGCGCCCCAGTACGCGCAGTGCACCCTGGAGGGGGCCTACGAACCTGGTGCCGCACCTGCCGCGGCAGCTGGGGGCGCGGACTACGGCTTCCTGGGGTCCGGGCCGGCGTACGACTTCCCGGGCGTGCTGGGGCGGGCGGCCGACGACGGCGGGTCTCACGTCCACTACGCCACCTCGGCCGTCTTCTCGGGCGGCGGCTCTTTCCTCCTCAGCGGCCAGGTGGATTACGCGGCCTTCGGCGAACCCGGCCCTTTTCCGGCTTGTCTCAAAGCGTCAGCCGACGGCCACCCTGGTGCTTTCCAGACCGCATCCCCGGCCCCAGGCACCTACCCCAAGTCCGTCTCTCCCGCCTCCGGCCTCCCTGCCGCCTTCAGCACGTTCGAGTGGATGAAAGTGAAGAGGAATGCCTCTAAGAAAGGTAA
Seq A exon
GTCCGCGGGCCTTGGATGGGGCCACCTGGGGTTGGGGACGGAGCCTCCCCCGCGGAAATGCGCTGGGAGCGTGGTGTCGCTGCCTTTCCAGACAGCGGTTTGGGTTTTGTGGAGGAGACGCGTTCCCGGGCGAATTCCATGGAGTCTGCCTCGAGTACAGATTCGGAAAATGTGCCAGGCATTGAGAAAATTTCAGGAAGGAGCTCTCCGTGGAACTTCTCCTGGTACAAATTCTGTTCCTAGGGACCCAGGAGGGCTGCGCTGGGACTTTGATTCTAACTAGCTCCACTGCTCACCCACATTCTGTCCCCGGCCTCAGGCCTGGCTGACGCCCTGTCTTTACGTTGCAGGCAA
Seq C2 exon
ACTCGCCGAGTATGGGGCCGCTAGCCCCTCCAGCGCGATCCGCACGAATTTCAGCACCAAGCAACTGACAGAACTGGAAAAAGAGTTTCATTTCAATAAGTACTTAACTCGAGCCCGGCGCATCGAGATAGCCAACTGCTTGCACCTGAATGACACGCAAGTCAAAATCTGGTTCCAGAACCGCAGGATGAAACAGAAGAAAAGGGAACGAGAAGGGCTTCTGGCCACGGCCATTCCTGTGGCTCCCCTCCAACTTCCCCTCTCTGGAACAACCCCCACTAAGTTTATCAAGAACCCCGGCAGCCCTTCTCAGTCCCAAGAGCCTTCGTGAGGCCGGTACTTGGGGCCGAAAAACTGTGGCCTGCAGAAGTCCCAGGCGACCCCCATCCCTATCTAGACTTAGGAGCTCAGTTTGGGATGGAGGTGGGAGAACAAAAATGAATAGGGATTTCACTTGGGAAATGAAGTACTTTAGTTGGCTTCCGAGTTCCAGACTATATGTCCAGATATTAATTGACTGTCTTGTAAGCCACTTGTTTGGTTATGATTTGTGTCTTATCAGGGAAAAGGTGCCCAGCTGCCAGCCCAGCTCCGCTGCTATCTTTGCCTCACTTAGTCATGTGCAATTCGCGTTGCAGAGTGGCAGACCATTAGTTGCTGAGTTCTGTCAGCACTCTGATGTGCTCAGAAGAGCACCTGCCCAAAGTTTTTCTGGTTTTAATTTAAAGGACAAGGCTACATATATTCAGCTTTTTGAGATGACCAAAGCTAGTTAGGGTCTCCTTGATGTAGCTAAGCTGCTTCAGTGATCTTCACATTTGCACTCCAGTTTTTTTTTCTTTAAAAAAGCGGTTTCTACCTCTCTATGTGCCTGAGTGATGATACAATCGCTGTTTAGTTACTAGATGAACAAATCCACAGAATGGGTAAAGAGTAGAATCTGAACTATATCTTGACAAATATTATTCAAACTTGAATGTAAATATATACAGTATGTATATTTTTTAAAAAGATTTGCTTGCAATGACCTTATAAGTGACATTTAATGTCATAGCATGTAAAGGGTTTTTTTTGTAATAAAAATTATAGAATCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000128645-HOXD1:NM_024501:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.147 A=NA C2=0.283
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
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]
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)