RnoINT0071660 @ rn6
Intron Retention
Gene
ENSRNOG00000016442 | Hoxc6
Description
homeo box C6 [Source:RGD Symbol;Acc:620626]
Coordinates
chr7:144623555-144625516:+
Coord C1 exon
chr7:144623555-144624153
Coord A exon
chr7:144624154-144624878
Coord C2 exon
chr7:144624879-144625516
Length
725 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTTTGTGCCCGGATCTCTAGGGG
3' ss Score
6.81
Exon sequences
Seq C1 exon
GGAATCAACAGAAGCAGAAGCGATTTTTTTCCCCTTTCTTGACATCTGGCTTGCGATTGGCTGGAAGGGGGTCAGCTGACTTTGTCATTTTGTCTGTCCTGGATTGGAGCCGTCCCTATAACCATCTAGTTCCGAGTACAAACTGGAGACAGAAATAAATATTAAAGAAATCATAGCCCGACCAGGTAAAGGCAAAGGGATGAATTCCTACTTCACTAACCCTTCCTTATCCTGCCACCTCGCCGGGGGCCAGGACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGGCATTTCTCGACCTATGGAGCAGCCGTAGCTCAGAACCGGATCTACTCGACTCCCTTTTATTCGCCACAGGAGAATGTCGTGTTCAGTTCCAGCCGGGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTG
Seq A exon
GTGAGTTTTACAGCTCCGAGATATAAATTAAATAAACTGAACTGGCTTTATGACCGGCTTCCCTAGAAGAACGGGCGGAGAGAGTTTTTTATGGCCCCATAAAAACAATCACGCTCGTCTCCTCGCCGACACCGAGACAGGGCCCCCTCTTCAGCCCCCTCTGCTCGCCTCCCGCGCTGGCTCGCAGGGGCTTGGCCCCCTCGATCCCTGACAGATTGGAGGGCTCCAAGGGGAGCTGAGGGGGTAGGAACAGGGCAGGGAATGAGGGGATAGGACAGAAGGTGGAGGAGCCCCACTAAAGTCTAGTTAGGCCGGAGAGAAGGGAGGGAGTTAAGAGTGGGCAAAGAAGTGGGGGAGAACTTTCCAGGGAACTAGAGTGTTGGGGAAGATGGGGGGAGCCCAATCCTTGAGAGATGGGGTCCTTATCCCCAGTAGTTTTTTTTTTTTAATCAGTTTTTAGACAGCCAGCTTTCTGCCTGGTTTTTGCCCCGCCCCCCAGCTTTCTTTGGGACACACATCTCCCACCTCGTGGGAGAACTGAATGAACTTGGGGTTCTGGCTGAACCCCCAGTGGGGGTGGGGCAGAGCAAAAGGGAGAAGGCTGAAGCCCGAGAAGGCTGCGAGCTGTGGGCCAAGTTGAGAGGGTCTGGACTTTGCTAGACAAAAATGTCTGCAGAGGACGCCTTGCTGATTGTTTTTAGTGTGTTTTGTGCCCGGATCTCTAG
Seq C2 exon
GGGTCGGTTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCTCGGTACCAGACCCTGGAACTGGAGAAAGAATTTCACTTCAACCGCTACCTAACTCGGCGCCGGCGCATCGAGATCGCCAATGCTCTGTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCCGGATGAAGTGGAAAAAAGAATCTAATCTCACGTCCACGCTCTCAGGGGGTGGCGGAGGGGCAACTGCCGACAGCCTGGGAGGAAAAGAGGAAAAGCGAGAAGAGACAGAAGAAGAGAAACAGAAAGAGTGACCAGGACTGCCCTTGCACCCCTATCTCCTCCCTTGCTCATCCCAGCTCCCCGAATCACACACTCTGTATTTATCTCTGGCACAATTGATGTGTTGTGACTTCCTAAAACAAAACAGGGAGTCAAACGTGGACCTGAAAGTCAGCTCTGGACCCCATCCCTCACTGCACAACTCTTCACTCGCCTCTTCCTCTAGCTCCCTCGCTAGTTCCTTCCTGGCTTGTCTGCAGGCCCCTTTCCCTTGCCTAGGCCTAGGGGACCTGAACCTCGCTTCAGATTCCACAGATGTCCCTCCAAGTGAGCCCTAGCCTCCCTCCCCACCTCCCGACGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016442:ENSRNOT00000022217:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.172 A=NA C2=0.422
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGTGAGGCATTTCTCGACC
R:
TACCGAGAGTAGATCTGGCGG
Band lengths:
356-1081
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]