HsaINT0077307 @ hg19
Intron Retention
Gene
ENSG00000172789 | HOXC5
Description
homeobox C5 [Source:HGNC Symbol;Acc:5127]
Coordinates
chr12:54426832-54429144:+
Coord C1 exon
chr12:54426832-54427360
Coord A exon
chr12:54427361-54428061
Coord C2 exon
chr12:54428062-54429144
Length
701 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAC
5' ss Score
5.88
3' ss Seq
GGGTGGGGTTTATGTTCCAGAGA
3' ss Score
5.27
Exon sequences
Seq C1 exon
ACCCCTCAACTTCAAAGAGTCACAAATCACCCTTAATCAAAAAGGGTGCAGAAATTTTTTTGGGCCCTCCCCGCCATGAGCTCCTACGTAGCCAATTCATTCTATAAGCAGAGCCCCAATATCCCTGCCTATAACATGCAAACTTGTGGGAACTATGGATCGGCCTCAGAGGTGCAGGCATCCAGGTACTGCTACGGCGGATTGGACTTAAGCATCACTTTCCCACCGCCTGCGCCTTCCAACTCTCTCCACGGGGTAGACATGGCTGCCAACCCCCGGGCTCACCCCGACCGCCCCGCCTGCAGCGCCGCGGCCGCTCCGGGACACGCTCCGGGCAGAGACGAAGCGGCTCCTCTGAACCCCGGGATGTACAGTCAGAAGGCGGCTCGCCCGGCGCTGGAGGAGCGAGCTAAGAGCAGTGGGGAGATCAAAGAGGAGCAGGCGCAGACAGGGCAGCCCGCCGGACTGAGCCAGCCACCGGCCCCGCCACAGATTTACCCGTGGATGACCAAACTGCACATGAGCCACG
Seq A exon
GTAAACTTTAGGACTTCATTTTGCGCTCTCGGGTCCGCCTGGGTTTTATAGGCCATGCGGGGCAAATAAAGAAAAAAAACCTGCGGCCATAAATTTTACGATCCAGGCATCAATGGCTCGTAAAACTGTCCACTAAAAGGCTTAGAGGCTGTGTGCGCCCAAATTTACGACGACATAATTGGATCATAGGAACAAAACGTGTATAAAAGGCAATATTCAATTTTTGGGGGAGAGGGAGGGAGTTAAAAAAATAGAGGGATCTGAAGGGTGAGGAGCGCGGGGCTCCAGAGCGGGGATCCCCCCGCGGCTCCCTCCCTCCCTCCCCTGCGGAGCCGGCTCCGCCGGCGCTTGCGGCTCCGGAGGATTCCAGCGACTCGGGAGGGGCGGGAGGGGGGTCCCCGGTGCTCGGATCTCGAGGGTGCTTATTGTTCGGTCCGAGCCTGGGTCTCCCTCTTCCCCCCAACCCCCCCTCAGCCCCTCCGGCTGCAGAGTGAAGGCTGCGGTGGAAAGTTTCCTGCCTGGGCGGAGGCGCCTCTCCCGGGGCTGGGCTGGGCTGGCCCGCCTGCGGCCCGCGTGGCCTGTCTTGCGGCTCTCGCCTCCTCTCCCTCCGGCCGCGGGTGGGGGCCTGGGCTGGGGTGGGGACGGGGGAACGCTGCAAGCTATTCACCCCTTCCTGGCTTGGGGTGGGGTTTATGTTCCAG
Seq C2 exon
AGACGGACGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCAGACTCTGGAACTCGAGAAAGAATTCCACTTTAACCGCTACCTCACTCGCCGCAGGCGCATAGAGATCGCCAACAACTTGTGTCTCAATGAGAGACAGATCAAGATCTGGTTCCAGAACCGCAGGATGAAGTGGAAGAAAGATTCCAAAATGAAAAGCAAAGAGGCTCTTTAGAGGCAGCGGGGGAGGCCCGCAGAGCGCGCCCCTAGCCGGTTCCTGTCCCTGCGCCTTTCCTTTTCGCCTTTCCTCTCTATATTTCGGGTCGGGGGCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCACAGACAAAAGCGCTTTTCCTTGGCATTCCGCATCCCTACCGACCCAGGGTTCCCGCGGGGCTGTCGGCGCTGCCCCATCTCCCCTCAGCTCGGCTCAGCTCGGTACCCGGGGCCCAGGGCAAGCTCCGCAGGACTTCCCCGGAGGGCTGCGGCGTACAGGCTGGCGCAGAACGAACCTTGGCCTGGGCCGTATCTCCGGCTCCCAGCCTCAGCGCGGCCCTCCCGAGTTAAGGTGGGCCCGGCCCGCGCCACAGGACCCTCGCCGGACCCTCTAACCTCGCCCTCTCCTTTGTTCCCGGCTGGACGGGTTAGACAGCCAAAGGCTGGCGAGAGTCTGGCCCTAGACTCGGGGTGCTTCCTTGTAGCGACTAAACTAGATTTTCACTTATGAATGATTTGCATATGAAAGGAGAGCATCGGCCTAGGGCCCCCACAGTTGCTCTATGCTTTCCAAACCTTATCTCCACAACCTCTTCCCCCCAAAACCCGGGAACCTCCCCAGCCTGCGCCTGCTGCATGCCCTCTCAGGCCGGCAGCCCCAGCCTGCTAGCTAGCTCAACTAGTGGGGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTAGAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCCTCCTGACCCATTGCTGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAATAAAGAGAGAACAGGACTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000172789-HOXC5:NM_018953:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.684 A=NA C2=0.282
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=79.2)
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:
GATGTACAGTCAGAAGGCGGC
R:
CTTCCACTTCATCCTGCGGTT
Band lengths:
343-1044
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
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)