HsaINT0077303 @ hg19
Intron Retention
Gene
ENSG00000123388 | HOXC11
Description
homeobox C11 [Source:HGNC Symbol;Acc:5123]
Coordinates
chr12:54366910-54370203:+
Coord C1 exon
chr12:54366910-54367707
Coord A exon
chr12:54367708-54368964
Coord C2 exon
chr12:54368965-54370203
Length
1257 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
GCCCCCTCCCCTCCCTCCAGACG
3' ss Score
11.1
Exon sequences
Seq C1 exon
GTGCTCAGAGAGAGAGAGACTAAGACGGATAACGCGTCATCTCGCCTTCCCAAATTTTCCCCCCTCGCTAGACCGGGTCCAAAACCTCCATCCGGAGCCGGCAGGAGAGGAGAACGATGTTTAACTCGGTCAACCTGGGCAACTTCTGCTCTCCGTCGCGCAAGGAGAGGGGCGCAGATTTCGGCGAGCGAGGGAGCTGCGCCTCCAACCTCTATCTGCCCAGTTGCACTTACTACATGCCCGAGTTCTCCACGGTCTCCTCCTTCCTGCCCCAGGCCCCCTCTCGTCAGATCTCCTATCCCTACTCGGCCCAAGTGCCCCCGGTCCGGGAGGTCTCCTACGGCCTGGAGCCATCCGGCAAGTGGCACCATCGGAACAGCTACTCCTCCTGCTATGCGGCGGCCGACGAGCTTATGCACCGGGAGTGCCTGCCTCCTTCCACCGTCACCGAGATCCTCATGAAAAACGAAGGCTCCTACGGCGGCCACCACCACCCCAGCGCCCCGCACGCAACCCCCGCCGGCTTCTACTCCTCAGTCAACAAGAACAGCGTCCTGCCTCAAGCCTTCGACCGTTTCTTCGACAACGCCTACTGCGGTGGCGGCGACCCGCCCGCCGAGCCCCCCTGCTCCGGCAAGGGCGAGGCCAAGGGGGAGCCCGAGGCACCCCCGGCCTCGGGACTGGCGTCCCGGGCTGAGGCGGGTGCCGAGGCGGAGGCTGAGGAGGAGAACACAAATCCCAGCTCGTCCGGTTCAGCCCACTCCGTGGCCAAGGAGCCGGCCAAAGGAGCCGCCCCCA
Seq A exon
GTAGGTAGCAGCGGCCGGGGAACGGGCGGGCAGCGAGGGAGGGAGCGAGAGAGGGAGGGCGAGAGAAGGGGGGAGGCAAGGGGAGCGGGGACGGCCTCGTGTTTTGGGTCAGTCCGATTTTATGTGGAGTTTTATAAGCATTCAAAGGATTTTATTATAACCTACAAAGCCCTCTCTCCCAACGACTCGACTTTTTACGATGGAGAAGGGGTGGGGAGGGAGGGAAAAGGGCTCTTTGGAAAAGCCGGGTGAACCCCCCTCCCCCGTTATCTCCCTCGGTCTGTGAAATTTTTAAAAGCGCAACCATTGCGGGCGATATTAACTTTGATCGTGAACTTAGAGGAGCATTTAAGGAAGTATGGGGAGCCGGGCTGCCGAGGAGTGGGGAGGAGGGGAGGGGTGGAGGGGGAGAAAGGGGAGGGCGAGGGAAAGACAGGGAGAGATCCAGAGAGGGGGAGAGGTGGGGGAGAGGAGCAATGGAGCAGAACCTGAGACCGGAGAGGCAAGCCAGGACCGCTATGATCCTTCTTAAAACTAGTTTTGAAAATGTTCAAACTATGTGTTCGCGGGTCCTCGAGCAGAAACCCAAGCAACTCTGGGGTCAGCGGCGACAGGGGAATGGGGCGAGGCGGCGCAGGACTCCACTGCGTTCCAGGCGGGGGTCTGGGCGTTTCTCCCGGGTCCGCGGCCTTAGTGCTTGCCTAGAACTGCGGTGTGGAAGGCGCTGCCCCGCGGGCTTCCCGGGGCGCCAGGGCCCCGGAAGCGGCTCTCTGGTGTCTCGGTGCCTGCTGGCCGGCTTCCTCCCCGCCTCCCGACTGCTCTCGCCAGATTTCACTGCTTCGCGCCTGTTCTCAGCTTTCCCCCCAGATTTCTGGGGGAGGGGTTGGGCTTTCCGAACCACTAGGAGGGCGGCCCAGGAAGGGCCCGAGGGCGGAGGGGGAGCAGACAGGGGGCCCGAGGGGACGCACGTGTACCTGGAGGGCTTTCCTTCTGTCCCAGACCCTGTCAGCCGCGGCTCTCGCCTGAGAACTGGGGACGGGGTGGCGCAGTGGCGGGGGGGTGGGGACCCGCTAGACCTGGCAGGGGGTCGAGGCTTGCCCGGGTGCTGCGGCTGCAGGAGAGCCAGCCGCCTGGCGGGAGGGCTGCCCGCGGTGGGCTAGGAGAAGGGCCGCTGAGCGCTCAGCGGGCTGGGGTCGCCCGGGTCTCACGTGTCTCTCTCCCCCCTCTCCTCGCACTTGCCCCCTCCCCTCCCTCCAG
Seq C2 exon
ACGCCCCCCGCACCCGCAAGAAGCGCTGCCCTTATTCGAAATTCCAGATCCGGGAACTGGAGCGAGAGTTTTTCTTCAACGTGTATATCAACAAAGAGAAGCGGCTGCAGCTGTCCCGGATGCTGAACCTGACGGACCGACAAGTGAAAATTTGGTTTCAGAACAGAAGGATGAAAGAAAAGAAACTGAGCAGAGACCGGCTGCAGTATTTCTCGGGAAATCCTCTGCTGTAACCTGCAGACCGGGCCCTTTTGGGGGCGGGGGGAGGGGAAAATTATTTTATTTTATTTTTATTTTTTATTTTCTAACTCGTCTTCTTTCCGCCGGTGGAAAACTGGACTGTGGCCAGGGCTGGCCCCCACCGCTGTGGCCGGCACTCCATTCCGGAACCTCCTGGACCCTCTATCTGACTCTCGCTGTGGGACAGGGACCGGGCCTGGAAAGGGGGTGAAGGGAAGTGTCTGATGCACGGCGAGTGAACACCGTTGGCGCCGAGGCCAAGACTTTGATTTAAAAGAAAACACACCTCGGCGACAATGTCTTGCTGCTCGGATTAGGTGGGGGAGGGGCGACAGTAGTGAGCGCCTGAGCCGAACAATCCTCGAACTAAAAGCCTTCCCTTGCCCATGTGAAAAGATCCGCTAAGACAGCATGTCTGCCAGCGGAAACTTCTCGAGCTCCCCCCTCTACCCCGCCCCACCTTGCAGCTAAATGTGATCCTGCCTTGCTGTGAAATTTCTGTACCTTCAACCTGGTGTTAGGTGTGCAAAGTCCGTGTCCTACCTCCGTCTTCGCCAAGGCCCCGCCCGAGCCTAGTTGTTCTCCCCCTGAATGTGTAGAACCTTCCTTTGAAATTTCTTAATCGGTGCATTGAGGTTTCCACATCTTTTTCCAAGCAGTGCCCCACTTCATGGATTTATAGCTATAGTCTATGCAGTCGTTACCTCTTTTTTTTTTTTTTTTAAGAAAATTGAAGATTGGGGTGGTGGAGGCAGTAGGGAGATGGGATTGGGCACCTCCCCCGTGCTGGGGCCTGGATTTTTGTAAATAAATTTCCCAAGCGTTTCTTTCCACCTGGAGGGAAAGGGGGGGACGCCCCCAGTGAGATTCAAATCACGCATCTCTACTCCTCTGCGTGAGTGCGTGTGTACATGTGCACTCCCCACCCTGCTCCCTTCCCAGAGGGATTGCTGTGAAATTTTTTTGGTGGCAAATAAAGATAAATTTCATTCTGTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000123388-HOXC11:NM_014212:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.408 A=NA C2=0.195
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=62.7)
A:
NA
C2:
PF0004624=Homeobox=WD(100=73.1)
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:
CCGGCTTCTACTCCTCAGTCA
R:
AAAACTCTCGCTCCAGTTCCC
Band lengths:
351-1608
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)