HsaINT1015863 @ hg38
Intron Retention
Gene
ENSG00000197757 | HOXC6
Description
homeobox C6 [Source:HGNC Symbol;Acc:HGNC:5128]
Coordinates
chr12:54028358-54030823:+
Coord C1 exon
chr12:54028358-54028921
Coord A exon
chr12:54028922-54029654
Coord C2 exon
chr12:54029655-54030823
Length
733 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTTTGTGCCCGGATCTTTAGGGG
3' ss Score
6.34
Exon sequences
Seq C1 exon
TTCCTGACATCTGGCTTGCGATTGGCTGGGAGGGGGTCAGCTGACTTTGTCATTTTGTCTGTCCTGGATTGGAGCCGTCCCTATAACCATCTAGTTCCGAGTACAAACTGGAGACAGAAATAAATATTAAAGAAATCATAGACCGACCAGGTAAAGGCAAAGGGATGAATTCCTACTTCACTAACCCTTCCTTATCCTGCCACCTCGCCGGGGGCCAGGACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGGCATTTCTCGACCTATGGAGCGGCCGTTGCCCAGAACCGGATCTACTCGACTCCCTTTTATTCGCCACAGGAGAATGTCGTGTTCAGTTCCAGCCGGGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTG
Seq A exon
GTGAGTTTTACAGCTCCGAGATATAAATTAAATAAACTGAACTGGCTTTATGACCGGCTTCCCTAGAAGAACGGGCGGAGAGAGTTTTTTATGGCCCCATAAAAACAATCACGCTCGTCTCCTCACCGAGACAGGGCCCCCTCTTCTGCCCCCTCAGCTCGCCTCTCGCTCGCTTGCAGGGGCCTGGCCCCCTTGGCCCCTGACGGATTGGAGGGCCCCAAGGCGGGCTGAGGGGGCAGGAACAGGGCAGGGGATGAGGGGAGGGAGCAGAAGATAGGGGAGCCCCCCAAAGTGGAGTCAGTCTGAGGAGAAGGGAGGGGGAGAGGAGAGGCAGATAAGTGGGGAGAAGTTTCCAAGGAACTAGGATGCTTGGGGAGATGGGGGAGCCCAGTCCTTGAGAAAGGGGGCCCTCATCCCCATTATCTGGGATTTTTCAAAAATCTGCTTTTAGACTTGCAGCTTTCTGTTTGCCTTTTGCCCCGCCCCCCCGCCCCCCCCCCCACCACACACCTTTCTTTGGGACACACAGGTCCCACCTTATAGGAGGTCTGAAGTTGGGGTCCTCGCTGTACCCCCAGTGGGGGTGGGGCAAGGCAAAAGGGAGAAGGCTAGAGCCCTAAGGAGGCTGTGAGCTGCTGGCCAGGTTGGGAGGGTCAGGACTTTGCTAGGCGAAACAGTCTGCAGAGGACGCTTTGCTGATTGCTTTTAGTGTGTTTTGTGCCCGGATCTTTAG
Seq C2 exon
GGGTCGGCTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCGCGGTACCAGACCCTGGAACTGGAGAAGGAATTTCACTTCAATCGCTACCTAACGCGGCGCCGGCGCATCGAGATCGCCAACGCGCTTTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCCGGATGAAGTGGAAAAAAGAATCTAATCTCACATCCACTCTCTCGGGGGGCGGCGGAGGGGCCACCGCCGACAGCCTGGGCGGAAAAGAGGAAAAGCGGGAAGAGACAGAAGAGGAGAAGCAGAAAGAGTGACCAGGACTGTCCCTGCCACCCCTCTCTCCCTTTCTCCCTCGCTCCCCACCAACTCTCCCCTAATCACACACTCTGTATTTATCACTGGCACAATTGATGTGTTTTGATTCCCTAAAACAAAATTAGGGAGTCAAACGTGGACCTGAAAGTCAGCTCTGGACCCCCTCCCTCACCGCACAACTCTCTTTCACCACGCGCCTCCTCCTCCTCGCTCCCTTGCTAGCTCGTTCTCGGCTTGTCTACAGGCCCTTTTCCCCGTCCAGGCCTTGGGGGCTCGGACCCTGAACTCAGACTCTACAGATTGCCCTCCAAGTGAGGACTTGGCTCCCCCACTCCTTCGACGCCCCCACCCCCGCCCCCCGTGCAGAGAGCCGGCTCCTGGGCCTGCTGGGGCCTCTGCTCCAGGGCCTCAGGGCCCGGCCTGGCAGCCGGGGAGGGCCGGAGGCCCAAGGAGGGCGCGCCTTGGCCCCACACCAACCCCCAGGGCCTCCCCGCAGTCCCTGCCTAGCCCCTCTGCCCCAGCAAATGCCCAGCCCAGGCAAATTGTATTTAAAGAATCCTGGGGGTCATTATGGCATTTTACAAACTGTGACCGTTTCTGTGTGAAGATTTTTAGCTGTATTTGTGGTCTCTGTATTTATATTTATGTTTAGCACCGTCAGTGTTCCTATCCAATTTCAAAAAAGGAAAAAAAAGAGGGAAAATTACAAAAAGAGAGAAAAAAAGTGAATGACGTTTGTTTAGCCAGTAGGAGAAAATAAATAAATAAATAAATCCCTTCGTGTTACCCTCCTGTATAAATCCAACCTCTGGGTCCGTTCTCGAATATTTAATAAAACTGATATTATTTTTAAAACTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197757:ENST00000243108:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.271 A=NA C2=0.422
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
PF0004624=Homeobox=WD(100=55.3)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCTGGATGCAGCGAATGAAT
R:
GGGACAGTCCTGGTCACTCTT
Band lengths:
352-1085
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains