HsaINT0077309 @ hg38
Intron Retention
Gene
ENSG00000037965 | HOXC8
Description
homeobox C8 [Source:HGNC Symbol;Acc:HGNC:5129]
Coordinates
chr12:54009106-54012362:+
Coord C1 exon
chr12:54009106-54009720
Coord A exon
chr12:54009721-54011088
Coord C2 exon
chr12:54011089-54012362
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
CTCCGGGGAGGCGCAGTGGACGGCAAACTTACAGCCGGTATCAGACCTTGGAACTAGAAAAGGAGTTTCTCTTTAATCCTTATTTGACACGAAAACGTCGGATTGAAGTCTCTCATGCCCTGGGACTGACCGAGAGACAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTGCCGGGAGCCCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAGAAGAGGAGGAAAAGGAAGAAAACAAGGACTAAGCAAAAAAGAAAGACCCCCCCCCCCTTAGCAACTCCCTTGAAGTTTCGTTTTATGGTAGCAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAATAGAATGACACTCACAACTCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGTTCGGACTCTCTGTCTCACTCCTTGCCCCACACACACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGTCTCTCACCACACTCCCACCTCCCTGCTTCTCTGGTATTTATTTTAGAGGGGAGCCCCCTCGAAATGCAGAAAAGGACTTGTGGTTTTGTTTTTATGCTAAGGCTAGTGTACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAGGAAAGGAAGACAAATGTAAAGAAATAAGGAAAAAAGCAAGGAATATCCCCTCCCCCTCCCCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCTCTAGGAACCTGATGGAAACCTGAAGGAGATGTGGGTCTTTCCCCTCCCCCCATTTCCAGAAGGGTAGATAGGAGCCTGCAGTCGCCTCTAAAATCCTACCTAACCATCCCATGGTCACTCGGGCCCATGCCTTCCTCTCCTTCGCTGTTTGATTTCTATTCTGTTGGGCCCGCCTTCCTCTGAGCTGCATTAGTGTTAGTGCTCAGAAATCACCATAATCACGAAAATAATAATAATAAATCTTTAACATACTACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTTTAAAATCCTGCTATAGGAGAAAAAAAGAGAAAAAAATAAAAATCAAAAAAAAAAAAAAGAAAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000037965:ENST00000040584:1
Average complexity
IR
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