RnoINT0071669 @ rn6
Intron Retention
Gene
ENSRNOG00000051472 | Hoxd11
Description
homeobox D11 [Source:NCBI gene;Acc:102553842]
Coordinates
chr3:61605396-61606400:+
Coord C1 exon
chr3:61605396-61605436
Coord A exon
chr3:61605437-61606165
Coord C2 exon
chr3:61606166-61606400
Length
729 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
GTGGTTTCTTTTTCTTGCAGTGG
3' ss Score
8.94
Exon sequences
Seq C1 exon
CCCCCGGGGGAGGCGGGGGCCGAAAAGAGCGGCGGCCACAG
Seq A exon
GTAGGCGCGGGGAGCCGCCCGAGGGGTGCCGGGGCGGTGGAGGCGGGGGGGCGGGGACCTCCTCTGCTTGCCGTTTATGTGCTACTTTATAAGCATTCGAGGGGGTTTCTACTCCTATAAGATTCCCGGGTCGTTGTAAAGCGTGTTTATGATAGGACCAATTTAGGTGGGCTTAAGGTAGACTTCGAAGAGGCATTAACGCGCTAGAGAGCCTTTCCCTCTAATTGGGTAGGGCGTGGGTGGAGTTGAGGACCTCGAGGGAGGAAGAACATTTTGGAGCCAGTTGGTGAGTGGGAACACGAGAGCCTCTTGCCTTTCAGGGAGGGGGTAGGTGATCTTCCACAACTGGACTTAACCCAAGCCTCTGGCTGGCGCTCAGCTCGGAGTTGAGCAGATGCCCCTGTGGGCGTGCTCCTGTCTCTCTCCCCTCACGTTCCAGGTTCAGAGCCTGCCATGCCATCTTTTTTCCTATCTCAGAGCCAGCCTGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGGTGTGTGTTGTCCGGGCGTGAACACATGTCCACGCCCCCCTCTAATCTGTGCCGCCCATATATCATCCCCCAGACGCAGGCAGGGCCTTTCCAACAGCGGCAAGGGAACGTCCCTAACTGAGCCAAGGCCTGGCCCTAGCTCAGTGGCCACAGCGGGTGGGGGCAAGTAGTAGTTCTCTCACCCCTGTGGTTTCTTTTTCTTGCAG
Seq C2 exon
TGGCCCCCAGAGGTCCCGGAAAAAGCGCTGTCCCTACACCAAGTACCAGATCCGCGAACTGGAACGCGAGTTTTTCTTTAATGTATACATAAACAAAGAGAAAAGACTCCAACTCTCCCGGATGCTCAACCTCACTGACCGGCAAGTCAAAATCTGGTTCCAGAATCGCAGAATGAAAGAAAAGAAACTGAACAGGGACCGTCTGCAGTATTTCACTGGAAACCCCTTATTTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000051472:ENSRNOT00000080456:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.295
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=72.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAAGAGCGGCGGCCAC
R:
TCAAAATAAGGGGTTTCCAGTGA
Band lengths:
255-984
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]