RnoINT0071659 @ rn6
Intron Retention
Gene
ENSRNOG00000016598 | Hoxc5
Description
homeo box C5 [Source:RGD Symbol;Acc:1307584]
Coordinates
chr7:144628120-144631542:+
Coord C1 exon
chr7:144628120-144628647
Coord A exon
chr7:144628648-144629336
Coord C2 exon
chr7:144629337-144631542
Length
689 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAC
5' ss Score
5.88
3' ss Seq
TTGGGGGATTTATGTTCCAGAGA
3' ss Score
4.68
Exon sequences
Seq C1 exon
CCCCTCAACTTCAAAGAGTCACAAATCACCCTTAATCAAAAAGGGTGCAGAAATTTTTTTGGGCCCTCCCCGCCATGAGCTCCTACGTAGCCAATTCATTCTATAAGCAGAGCCCCAATATCCCTGCCTATAACATGCAAACTTGTGGGAACTATGGATCGGCCTCAGAGGTGCAGGCATCCAGGTACTGCTACGGCGGATTGGACTTAAGCATCACTTTCCCACCGCCTGCGCCTTCCAACTCTCTCCACGGGGTAGACATGGCTGCCAACCCCCGGGCTCACCCCGACCGCCCCGCCTGCAGCGCTGCGGCCGCTCCGGGACACGCTCTGGGCAGAGACGAAGCGGCTCCTCTGAACCCTGGGATGTACAGTCAGAAGGCGGCCCGCCCGGCGCTGGAGGAGCGAGCTAAGAGCAGTGGGGAGATCAAAGAGGAGCAGGCGCAGACAGGGCAGCCTGCCGGACTGAGCCAGCCACCGGCCCCGCCACAGATTTACCCGTGGATGACCAAACTGCACATGAGCCACG
Seq A exon
GTAAACTTTAGGACTTCATTTTGCGCGCTCGGGTCCGCCTGGGTTTTATAGGCCATGCGGGGCAAATAAAGAAAAAAAAACCTGCGGCCATAAATTTTACGATCCAGGCATCAATGGCTCGTAAAACTGTCCACTAAAAGGCTTAGAGGCTGTGTGCGCCCAAATTTACGACGACATAATTGGATCATAGGAACAAAACGTGTATAAAAGGCAATATTCAATTTTGGGGGGAGAGGGAGGGAGTTAAAAAAATAGAGGGATCTGAAGGGTGAGGAGCATGGGGCTCCAGAGTGGGGATCCCCCCGCGGCTCCCTCCCTCCCCTGCGGAGCCGGCTCGGCCAGTGTTCGCGGCTCCGGAGGATTCCAGCGACTCGGGAGGGGCGGGAGGGGGGTCCCCGGTGCTCGGATCTCGAGGGTGCTTATTGTTCGGTCCGAGCCTGGGTCTCCCTCTTCCCCCCATCCCCCCTCAGCCCCTCCGGCCGCAGAGTGAAGGCGGCGGTGGAAAGTTTCCTGCCCAGGCAGAGGCTCTTCTCCCGGGACTGGGCCTGTCCGCCTGCGGCCCTTCTGGCCTGTCCCACCGCGCTCACCTCCACTCCCTCCGACCACGGGTGGGGCCTGGGACTGGGGTGGGACGTTGGGGTGCTGCACGCTATTCACCCCTCCCTGGTTTTGGGGGATTTATGTTCCAG
Seq C2 exon
AGACGGATGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCAGACCCTGGAACTCGAGAAAGAATTCCATTTTAACCGCTACCTCACTCGCCGCAGGCGCATAGAGATCGCCAACAACTTGTGTCTCAACGAGAGACAGATCAAGATCTGGTTCCAGAACCGCAGGATGAAGTGGAAGAAAGATTCCAAAATGAAGAGCAAAGAGGCTCTTTAGAGCAAGCAGGGAGCCCTCCTCAGAGAGCACCCTGGTCCGCTGTGGTCCCTGCGCCCTTCCTTTTCGGTTTTCCTCCTTCTAGATTTTGAGGCAAAGGCTAGAGCACTGGCTCCCGGCCTCCCAGACAAAAGCGCATTTCTTTGGCATTCCGAATCCCCATCGACCCAGGGTTCTGCAGGACCGCCTGCACTGCCTGTCTTGCCTCAGCTCAGCTGAGCACCCCAGGCCCGGGGCACATTCTTGTAGGGCGGGTACTGAATAAGCCTCAGTCTGGGTTGCCTCTCCCAGCTCTGAGCCCTAGCTCGGCTAACCTGAGTTAAGGTGAGACAGACTGTAACCCCTTCTCCCCGACCTCCACCTCACCCCCTTCTTTGTTCCTGCCTAGGCTGGCCAGGCTGCTGAAGGCTGGTTGTGCCAGGCAGAGCCTATGGCCAGAATCCGGGGTGCTTTCAACTAACCTTTATAACTTCTAAACTCGTCTTTGCTTATTAATGATTTGCATATGAAAGAGGGAGATAAGTGAAAGTGGGCCTGTAGCCCTGGAGGTTGTCCTATGCTCTCTAAACCTTCCAACCCCCTCCCTAAAGCCCGGGATCTTCCCTAGCCTGGCTTGCTGCATGCACTCTCAGGTTCACAGTCCCAGCCTGCTAGCTAGCTCAACTATTGGGGTCTCTTGCCTTTGGACCCTAGCAAGTGGTTCTTTGAAGCTTTTTGCTATCCTATGTATCTTGCCATGACTTTCTCACCTTCCTGCCCCCATTGCAGTTGCCCAACTATTTATTGACTCCAAGTCCTTCCTGAAACTATATTTTGTCATATCAAATAAAGCCAGAAAAAGAACAGGACTAAAGATTCAATGACTTCTGTCTGTTTAGGGCATGCATTGAGTAGATGTGTGTAAATAGGCTCTGAGATGTATGGGGAGGCCCTGTCTCTAAGCCACCCCTTTAAAAATATTTTTAAGCACGTTTAGGATCAGCAAGGATAGGGAAAAACTGAGTGCCTTTTTGATTCATGGTTCCAAGAAGGGCCTCTGGGGTGAAGGGGAGTACACTGGAGAGCTCCTGTACTGTTGTACTGTCGTTTCCACATGATGTGGGGTGTACAAGGCACCCAGACTTTTCTATATCTTATTCTCATGTTGGCTAAAAAGACTCGAGGCTTCTAGACTTTCTGTAGTCTGTGCTTTATGTCAGAGCAAAGGAACTTGTGGCTCCACTGACTTAGATTCAGGCCCTTCTGGGTCTAGGTTATCCCTGGGGTTCTTTTCTGGACATGGAAGAACGGCTGGGTCCTCAGTCTTGGGCTATGTTTGATCTCAGAGGATTCTCAGCAATCGTAGGCAGTACTTGGTAAAGGGGTTTTGGAGAAGAGGAGTTGACCTTGGTTTGAGATGTTCTTCAGCTTTCTAAGACATGGGATGGGGCAAGGGGGACTAGGGGGACACTGAATGCAACCTGCAGTGTGTGCTTGCCTTAGAGAAAACATACAAACTGCTCCCTGTCTTCTAAGGTCTAAGCCAATGCAGGGCAGTTAACTGGAGTAAGAGCGGTGTAGACCAGGGCAGGATCCATGCCTATTTGTCATCTATCACAGTCTCTGAGATTTTGTATAAATGGGGAGGGTGGCTGATAGGAGAGGGGACACAGCTAATTCACAGGGGGCGGGGCTGGCCTAGGCTCATGCTCTTGCCAGCTCCACTCCAGGGTCCACGAGATGGAGGAGGGAGTACTTTACAGGAGAAACAAATGCGGTGTAGGTCCATAAAACTTTACTGCACTTCCTCTCCAGCTTCCCACAATGGGGTGATTTCCTGGAGCCAAGCCTAGGCCCCCCACCCTGGAGGAGTGGGGATCTGAAGCCGGGCTAAAGGCTGCTCTACACTAGGACAGAAAGAGAACAGAGTAACTCTGAGGAGGGGCAGGGAGATTTCTTTTTATGATTATTAATGTTTATGCTCTTTGGATTTATTGAAGGTCTGACTTCACTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016598:ENSRNOT00000022247:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.684 A=NA C2=0.282
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=79.2)
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:
CTCCTCTGAACCCTGGGATGT
R:
CACTTCATCCTGCGGTTCTGG
Band lengths:
355-1044
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]