RnoINT0071655 @ rn6
Intron Retention
Gene
ENSRNOG00000016141 | Hoxc11
Description
homeobox C11 [Source:RGD Symbol;Acc:6489991]
Coordinates
chr7:144565392-144567580:+
Coord C1 exon
chr7:144565392-144566073
Coord A exon
chr7:144566074-144567347
Coord C2 exon
chr7:144567348-144567580
Length
1274 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
GCCCCTTCCCCTCCCTCCAGACG
3' ss Score
11.81
Exon sequences
Seq C1 exon
ATGTTTAACTCGGTCAACCTGGGCAACTTCTGCTCGCCTTCGCGCAAGGAGAGGGGCGCTGACTTCGGCGAGCGAGGGAGCTGCACCTCCAACCTCTATCTGCCCAGTTGCACTTACTACGTGCCCGAGTTCTCCACCGTCTCCTCCTTCCTGCCCCAGGCCCCCTCTCGTCAGATTTCTTATCCCTACTCAGCCCAAGTGCCCCCGGTCCGGGAGGTCTCCTACGGCCTGGAACCGTCCGGGAAGTGGCACCATCGGAACAGCTACTCGTCTTGTTATGCGGCGGCCGACGAGCTTATGCACCGGGAGTGCCTGCCTCCTTCCACAGTCACTGAGATCCTCATGAAAAATGAAGGCTCCTACGGCGGCCACCACCACCCCAGCGCCCCGCACGCGGCACCCGCCGGTTTCTACTCCTCAGTGAACAAGAACAGCGTCTTGCCCCAAGCCTTCGACCGCTTCTTCGACAACGCCTACTGCGGTGGCGGAGATGCACCCGCCGAGCCCCCCTGCTCCGGCAAGGGCGAGGCCAAGGGGGAGCCTGAGGCGCCCCCCGCCTCGGGACTTGCGTCCCGGGCAGAGGCCGGTGCTGAGGCCGAGGCCGAGGAGGAGAACACGAATCCCAGCTCGTCCGGTTCTTCCCATTCGGCGACCAAGGAGCCGGCCAAGGGAGCCGCCCCCA
Seq A exon
GTAGGTAGCAGCGGCCGGGAACCCGAGGGCAGCGAGGGAGGGAGCGGAGAGGGAGGGCTGGAGTAGAGGGGGGGGCAGGGGAGCGCGGACAGTCTCGTGTTTTGGGTCAGTCCGATTTTATGTGGAGTTTTATAAGCATTCAAAGGATTTTATTATAACCTACAAAGCCCTCTCTCCCAACGACTCGACTTTTTACGATGGAGAAGGGGTGGGGAGGGAGGGAAAGGGGCTCTTTGGAAAAGCCGGGTGAGCCCCCCTCCTCCGTTATCTCCCTCGGTCTGTGAAATTTTTAAAAGTGCCACCATTGCGGGCGATATTAACTTTGATCGTGAACTTAGAGGAGCGTTTAAGAAAGGATGGGGAGTCGGGCTGCTGGGGGGGGGGTGGGAGGGAGGGGAGGGGTGGAGGGGGAGAAAGGGGAGGGCGAGGGACAGACTGGGAGAAATCCAGAGAAGGGGAGAGGTAAGGGACAGACGCGACGCGGCAGAACTGGAGTCCAGAGAAGCTCTTCAAGGCCGCTCCGCTTCTTTTTAAAACAACTTATAAAAAATGTTCATATTACGTATTCGCGGGTCTTTGAGAAGAAACCCGGACGNAAGCCAGGGTTTGGTGGTGACAGGAGAGAAGGGAAAGGATCGGAGCTCTCTTGTGCTTCAGGCGAGGGTGGCGATGGCTCTCCGGGGTCTGAGGCCTCTGGGTAGGCCCAGCCTGGTTGTGTACAAGGCAGGGCTGGCAGGGCAGGCAGACGGCGGGGTGTCCCGGGGCGCCAGGGCACCGCAGGAGGTTCGTGGGTGTCCAGCTACCTCTACTGGCTAGTTTCCTCCAGGATTCCTCACTGCTCTCGCCTGATCTTACTCCTTTGCGCCGATTCTCCGCGGTTCCCTCCGATTTCTGGAGGAAGGGATCCTGGATTTGAGAAGCATTAGGAGGGTGGCTTGGAAAGGGCAAGGGCAGCGACCAGGAGCAGACAGGGCGCCCCAGGGAAAGCACGTGGCGCGGGCAGGTTTTCCTCTACTCGCAGACCCTGTCAGCTAGGGCTCTGGCCTGAGGGGCAGGGGGAACTTGGTTCTCAGTGAACCTGGCAGTGGGATCGGGGCTTGCCCCAGCGCAGTGGAGACGGAAGAAGAGGCGCCGGTCTTAGAGGGAGGGTTGCCCGGCGGCGGGACTGGGAGCTGTGCGGCTGAGCTTTCAGCGGCCCGGGTTGGCTGGGGTCGCCCGGGGTCTCACGTGTCTCTCTCCCCTCTCCTCGCACTTGCCCCTTCCCCTCCCTCCAG
Seq C2 exon
ACGCCCCCCGAACCCGCAAGAAGCGCTGCCCTTATTCGAAATTCCAGATCCGGGAACTGGAGCGAGAGTTTTTCTTCAACGTGTACATCAACAAAGAGAAGCGGCTGCAGCTGTCCCGCATGCTGAACCTGACAGACCGACAAGTGAAAATTTGGTTTCAGAACAGAAGAATGAAAGAAAAAAAACTGAGCAGAGACCGGCTGCAGTATTTTTCAGGAAATCCGCTGCTGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016141:ENSRNOT00000021589:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.399 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
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCGACCGCTTCTTCGACAA
R:
CTGCAGCCGCTTCTCTTTGTT
Band lengths:
343-1617
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]