RnoINT0071658 @ rn6
Intron Retention
Gene
ENSRNOG00000016613 | Hoxc4
Description
homeo box C4 [Source:RGD Symbol;Acc:1586210]
Coordinates
chr7:144647587-144650129:+
Coord C1 exon
chr7:144647587-144648452
Coord A exon
chr7:144648453-144648927
Coord C2 exon
chr7:144648928-144650129
Length
475 bp
Sequences
Splice sites
5' ss Seq
CGGGTAGGC
5' ss Score
7.5
3' ss Seq
TTCCCCTCCCCCTCCCCCAGTGA
3' ss Score
10.08
Exon sequences
Seq C1 exon
TGGAAAGGCACTGGAGCCGAGGCCCACCGGGTCCACTGAAGGCCGGAGAGGAGACTCTGGGTGGGGGCTGAATCACAGCCTACCAACAGCCCCCAATGCCCAGACATTGGAGTCGAGCTGGGAGCCACCCATCTTCTGCAAGGGAGGATTGTCAGTCTGGTGGGGTGTGCAATGGTGAGCACCCCAGCTTCTGCCAGCCATCCCCCCACCCCACCCCCTCAGCAGCAGCAGCACCACACACACAAAAAATTGGATACATTTTGAATAAAGCGATTCGGTTCCTTATCCGGGGACTGAGTTGCTCGGTGTGATTGGCCGGCGGAGTCACATGGTGAAAGTAACTTTACAGGGTCGCTAGCTAGTAGGAGGGCTTTATGGAGCAGAAAAACGACAAAGCGAGAAAAATTATTTTCCACTCCAGAAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGTCAGTATAGCTGCACCAGTCTCCAGGGGCCCGGCAATTCGCGAGCCCACGGGCCGGCCCAGGCGGGCCACCACCACCCTGAGAAATCGCAGCCGCTCTGCGAGCCGGCGCCTCTCTCAGGCGCCTCTGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCTGACCATCCCTCCAGCGCCGCCAGCAAGCAGCCCATAGTCTACCCTTGGATGAAAAAAATTCACGTTAGCACGG
Seq A exon
GTAGGCAACTTTGCTTTTTGCCCCCCTCCCTTCCCGGGCGCTCCCCACCCTCCCTGGCCCCCTCTGGCCCCGTCCTCCTTTCTCTCCTTCCCCCTCTCTCTCCAGGAGCGACTCTGGGTTAGCACAATTGAACTGGATTTACGAGCGAGAATGGGTAATTACATCCCCCATAAATTTTATGGCTTAGCTACTCTGGGCAGTCCGAGCCATGTGCTACGATCTGTTATGTATGTGTGAAAACTATGCTCGCTTTCTAAGGGCGCATAAATAATTCAGTGTCGTTACAATGAGGATTCCCCTCTTATTACACTACAAAGTCTCTAGCTTCCTTCAACTTCTTTATAACCCATTTAGCTTGATGACTTTATTTCCACCACTCCCTCCTGTTCCTCAAAGCTGAGGATGGGGTGAGGGTGGGGGCAGGGAGCCTGCTGCCTCTGAACCCCACTATTTGCTTCCCCTCCCCCTCCCCCAG
Seq C2 exon
TGAACCCCAATTATAACGGAGGGGAGCCCAAGCGCTCGAGGACAGCCTACACCCGGCAGCAGGTCCTGGAATTAGAGAAAGAGTTTCATTACAACCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTGAGGTCAGCGCCCCCGGCCGGCGCTGCACCCAGCACCCTCTCGGCAGCCACCCCCGGCACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATCACCAGGTTATAAGACATAACTTACACCCCTGCCCCCACCCTGTGCTCCGTGCCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATTTTTGGTTCTTTTTTTCTCTCTCTTCCTCCTGTCTCCTCCCTTGTCAGTTCCAAACAGACAAAACAGATAAACAAACAAGCCCCTTGCCCTTTTCCCTTTGCTGTTAAGGACCCCTTTAAGCATGTGGTGTTGTCTTAGCATGGTACCTGCTGGGTTTTATTTTTTGTTGTTTTGTTTTGTTTTGCTTTGCTTTGCTTTTAAGGCCATTGGGGGGTATTTATTTTTTAAGGAAAAAAAGCTGCAAAAATTATATATTGCAAGGTGTGATGGTCTGGTTTGGGTGAATTTCAGGGGAAATGAGGAACAGAAAAAGGAAAGGGAGATTTGTAAGTGGATTCTCATCCTCTCTCCTCCTCACCCCCCCTCCCTTTCCTTAGGCCTTTTGCATTGAAAATGCACCAGGGGAGGTTAGTGAGGGGGGGGAGTCATTTTAAGGAGAACAAAGCTATGAAGTTCTTTTGTATTCTTGTGGGGGGGTGGTAGGAGGGGGGAGGACAGCAAACAAAGCTAAATGCATCTGGAGAGCCTCTGGGAGCTGTTCAGTTTGAGGAGCCAAAAAATAAATAAATAAATAAAAATGAACTTTCAGTTCAGAGAGGCAGTCTATAGGTAGATGCTCCCCTACCCCCATCGTGGTTATTGTGTTTTTGGACTGAATTTACTTGATTATTGTAAAACTTGCAATAAAGAATTTTAGTGTTGATGTGAAATGCCCCCGTGATCAATAATAAACCAGTGGCTGTGAATTAGTTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016613:ENSRNOT00000022398:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.793 A=NA C2=0.669
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=47.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATTCCAGCATCACCACCAG
R:
CTTGGGCTCCCCTCCGTTATA
Band lengths:
342-817
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]