HsaINT0077309 @ hg19
Intron Retention
Gene
ENSG00000037965 | HOXC8
Description
homeobox C8 [Source:HGNC Symbol;Acc:5129]
Coordinates
chr12:54402890-54406545:+
Coord C1 exon
chr12:54402890-54403504
Coord A exon
chr12:54403505-54404872
Coord C2 exon
chr12:54404873-54406545
Length
1368 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGA
5' ss Score
8.94
3' ss Seq
TGGGGTTTTCTTCTGTCCAGCTC
3' ss Score
6.44
Exon sequences
Seq C1 exon
GCCGAGCTCAGCACCGAGGCGCCCCCCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCCAGCTGGCCTGGGGTTCGGTCCCGGGGGGAGGGGAGTTTCGGGGGTACTGGGCGGGGTACTCGTGAGCCAGAGGGGAGGGGGCCGCGGGTTTTCATGTACCCAGCATGAGCTCCTACTTCGTCAACCCCCTGTTCTCCAAATACAAAGCCGGCGAGTCCCTGGAACCGGCCTATTACGACTGCCGGTTCCCTCAGAGCGTGGGCAGGAGCCATGCGCTGGTGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACTTCTTCCACCACGGCACCTCCGGCATCTCCAACTCAGGCTACCAGCAGAACCCGTGCTCGCTTAGCTGCCACGGAGACGCCTCCAAATTCTATGGCTACGAGGCGCTCCCCAGACAGTCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTGGTGCAATATCCCGACTGTAAATCCTCCGCCAACACTAACAGTAGCGAAGGACAAGGCCACTTAAATCAAAACTCGTCTCCCAGCCTCATGTTTCCATGGATGAGACCCCACG
Seq A exon
GTGAGAAGCCTTTTCTCTTTCCCCCTTGGTCTCCCGCGCTCCAGGGTTTCCCCCCCTCCCTCGCCTCCTTTTTGTCTGCCCTCGCTTTTTCTCCTGGCTTTGGGGTCTCTCCCGCCCCACCCCCGTGCCTGTGCCTGGGTGGTTTTCTCGAAGTTGGGAAGGCTCCGCTGGGGCGGGGCAGGGAGGGGGTGCCTAGAACATTTAGGGGATTGGGGTGAAGGTGAGAGAAAGCTGGTGTGTGGCCGCAAAGGGTTAAAAATCGTTTTCTCCATCTCTGTCTGTCTGTCTCTCTCTGACTCTCCCACTCCCCATCTCTAAAGTCAAAGTTGGGGAGGTGGCTGGGAATGGTACCCTGAGTACCCTGAGACTGTCAGCCTTTGGAACAAACCAGTTTCTCCAGAGGCAGGGAGCCTGGAGTCCAGGACACTGGCCAGGCTGTCTTGGGGCAAAGGGAGACAGACCCCTGTTGCTCTGCCCTAGCCAGAGTGTGGTGAGACTCTAAGGACAGGCTCTCTGGCTCTCTAGGGCACCCATAACCTCCTCTCAGAGAACCAGCCTGAGGGCCACTACCCCAACTTTTTTATACTTCCCCCAGTTGGGAGAAGACGGGGGAGCCTGAGAGGAGGGGGAAAAAAGAGTGCTCAAAAGGAGAGAGGCCATAGAGATTAGGGGTTCCTGAGGTCCAGAAGACCCTAGCCGCCCCCCCAATCAAGGACTTGTGGGGTCTCCCTGAGACCTGCAGAGTAGCTTAGGTCATGAGCCCCTCCAAGGGTGGCCCCTCATGGCCCAATTTCGAAGTACAGGGGGAAGCGATAAAGCGACAAGTTCCGGCGGGGATGGCCCATGATTTATTTGCTGGTCTCCAGTTAGCAATCAGGCGGAGCGGTGACACATTCCAGCAGATCAATTATTTTTCTTATTGGAAAAGCATTAGGCAGAGAGAGACAAGGAGAGGGCAGTGGGCAGAGCCCCTCTTCTTTACCCCCAGCTTTTTTTCCTTTCTTTTGGAAACAGTCTGTCCCCAGCCTCGCTCACTAAATGCCCTGCTGCACTTGTAAACAAAGCTGCAAAGGCCAGTTCCTAGGATTACAGGCCTGGTGGGGGGGATTCTACAGGGCTCCCCAGCCCCTGAAAGGCCCCAGTTTCCAAACAGACCCTAGCCCCCACCCCCACCCCACCTCCCAAGGTGAAGCCAAACAAAAACAATCCCCCAACTTTTCTGCCCTTGTCTGCCTTCTGCTCTAGCCTTTTCCATAGAGGGGAGGCGAACTGAGGAGATCAGAGAGGGGAGTTTAGAGTAGGAAGAGTGGCAAAGGAAAACCAAGCCCCCATCCAAACGTAACCAGACTGGGGTTTTCTTCTGTCCAG
Seq C2 exon
CTCCGGGGAGGCGCAGTGGACGGCAAACTTACAGCCGGTATCAGACCTTGGAACTAGAAAAGGAGTTTCTCTTTAATCCTTATTTGACACGAAAACGTCGGATTGAAGTCTCTCATGCCCTGGGACTGACCGAGAGACAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTGCCGGGAGCCCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAGAAGAGGAGGAAAAGGAAGAAAACAAGGACTAAGCAAAAAAGAAAGACCCCCCCCCCCTTAGCAACTCCCTTGAAGTTTCGTTTTATGGTAGCAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAATAGAATGACACTCACAACTCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGTTCGGACTCTCTGTCTCACTCCTTGCCCCACACACACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGTCTCTCACCACACTCCCACCTCCCTGCTTCTCTGGTATTTATTTTAGAGGGGAGCCCCCTCGAAATGCAGAAAAGGACTTGTGGTTTTGTTTTTATGCTAAGGCTAGTGTACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAGGAAAGGAAGACAAATGTAAAGAAATAAGGAAAAAAGCAAGGAATATCCCCTCCCCCTCCCCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCTCTAGGAACCTGATGGAAACCTGAAGGAGATGTGGGTCTTTCCCCTCCCCCCATTTCCAGAAGGGTAGATAGGAGCCTGCAGTCGCCTCTAAAATCCTACCTAACCATCCCATGGTCACTCGGGCCCATGCCTTCCTCTCCTTCGCTGTTTGATTTCTATTCTGTTGGGCCCGCCTTCCTCTGAGCTGCATTAGTGTTAGTGCTCAGAAATCACCATAATCACGAAAATAATAATAATAAATCTTTAACATACTACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTTTAAAATCCTGCTATAGGAGAAAAAAAGAGAAAAAAATAAAAATCAAAAAAAAAAAAAAGAAAGAAAGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTGTTGTCGTTTGTTGCTGCTTATTTCACTAAGAAAACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGTGCTTCTAACCCCAGTAGAGTAGAACTAAATTGCACTGAATGTATAGTTAACTCTGTCTTGAATTCTCTGTTTATGCAATGTGCTCGAAAGAAAAAAATGTTAAAAATATATCTATAATAATAATTTTTTGTCATTTGTCTTTATGTCCAGCTATGAATGTAGATTTTGTGTCCCGACAGCCCTGTTCCTGGTCCAAGTACTTTGTATTGTATACGTGAGTCATAATAATAAAAAGAAGAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000037965-HOXC8:NM_022658:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.247 A=NA C2=0.526
Domain overlap (PFAM):
C1:
PF095335=DUF2380=PU(74.1=56.8)
A:
NA
C2:
PF095335=DUF2380=PD(25.0=28.6),PF0004624=Homeobox=WD(100=58.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGGTGCAATATCCCGACTG
R:
TCCACCTTCTCCTCATCTCGG
Band lengths:
348-1716
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- 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)