RnoINT0071661 @ rn6
Intron Retention
Gene
ENSRNOG00000028619 | Hoxc8
Description
homeobox C8 [Source:RGD Symbol;Acc:2821]
Coordinates
chr7:144605058-144608538:+
Coord C1 exon
chr7:144605058-144605507
Coord A exon
chr7:144605508-144606847
Coord C2 exon
chr7:144606848-144608538
Length
1340 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGA
5' ss Score
8.94
3' ss Seq
TGGGGTTCTGTTCTGTTCAGCTC
3' ss Score
6.84
Exon sequences
Seq C1 exon
TTCATGTACCCAGCATGAGCTCCTACTTCGTCAACCCCCTGTTCTCCAAATACAAAGGCGGCGAGTCCCTGGAACCGGCCTATTACGACTGCCGGTTCCCTCAGAGCGTGGGCAGAAGCCATGCGCTGGTGTACGGGCCCGGCGGCTCAGCGCCCGGCTTCCAGCACGCCTCGCACCACGTCCAAGACTTCTTCCACCACGGCACCTCCGGCATCTCCAACTCGGGCTACCAGCAGAACCCGTGCTCGCTGAGCTGCCACGGAGACGCCTCCAAATTCTATGGCTACGAGGCGCTCCCCAGACAGTCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTGGTGCAATATCCCGACTGTAAATCCTCCGCCAACACTAACAGTAGCGAAGGACAAGGCCACTTAAATCAGAACTCGTCTCCCAGCCTCATGTTTCCATGGATGAGACCCCACG
Seq A exon
GTGAGAAGCCTTTTCTCTTTCCCCCTTGGTCTCCCGCGCTCCAGGGTCTTCCCCCCTCCCTCGCCTCCTTTTTGTCTGCTCTCGCTCGCTTTCCTTCCTGGCTTTGGGGGTCTCTCCCACTCCACTCTTGTGCCTGGGTGGGTTCCTGGGAGATTGAAAAGCTTGGCTGGGGGTGGGGCGTGGGGCGCCCGAGACATTGTGCTTGTTGGGGTGAAGGTGGGGGAAAGGTGATTTGTGGGTGCAAAGGGTTAAAAATCGTTTTCTCCATTCCTTCTGTCTCTTCTCTCCATCTACAAAGCCAAAGTTGGGGAGATGACTGACAAGGACACCCTGAGTAAACTGAGCTTATCAGTCTTTGGGGTTGCTAGCCAGTTTTCCCAAAGACATTTCCCAACGCCAGCCATCCCAAGACAGTGACCAGACTGTTGGGTGAAAAGGAGACCCTTTGCTATCTCCCCTAGCCAGGCAGAGGGGCAAGACCCCACCAAGGACAAGCATTCTGGCTCTCTGGGATCTTCACTTCTTCCTCTCAGAGAAGCAGCCTGAAGGCCACTGCCCCAACTTTTCTGTACTTCCTCCAGTTGGAGAGAAGACTGAAAGCCCGAGAAGAGGAAAATCATTGCTCAAAAAGAGAGCAGGGTCGTACCACGTAGGGGCCTCTGAAATCCAGGGGACTCAGTCAGGCTGCCCGCCAATCAAGAGCTATGGGATCTCTTGGAAAGCTGTTCAGGTCATGAGCCCCTCCAAGGGTGGCCCTTCATGGCCCAATTTCGAAGTACAGGGGGAAGCGATAACGACAAGTTCCGGCAGGGATGGCCCTTGATTTATTTGTTGGTCTCTAGTTAGCAATCAGGCAGAGCAGTGATACATACCAGAAGATCAATTATTTTTTCTTATTGGAAAAGCATTAGGCAGAGATGGGCAAGGAGGGGGCAGTGGGCACAGCCTCCTCTCCTTTAACCCCAGCCCTTTTCCTTTCTTTTGGAAGCAGATTATATCCCTAGGCCCGCCTCACTAAATGCCATTCTGCACTTGTAAACAAAGCTGCAAGGGCCAGGCTGTAGGCCTGAGGGACCCTGCAGGCTTCCTTGTCCACCTCAAGCCCTTACTTTTCAGACAGCCACATCCCAGCCCCCACCTTCACCCACCTCCCAAGGTGAAGGAAGTCAAACCAAAACGTCTAAGGAAACTTTTCCTGCCCTTGCTTGCCTTCTGCTGTCGGCCTGATCGGCAGGAGGGAGGGAGAACTGGGAATAGCAGAGAGGGAACTTTGTGGGGCAGTGTTTGTGGGGGGGAGCCCCCACCCAGACATAACCAGACTGGGGTTCTGTTCTGTTCAG
Seq C2 exon
CTCCTGGGCGGCGCAGCGGACGACAAACTTACAGCCGGTATCAGACCTTGGAACTAGAGAAGGAGTTTCTCTTTAATCCTTATTTGACCAGAAAGCGCCGGATTGAAGTCTCTCACGCCCTGGGACTGACGGAAAGACAAGTGAAGATTTGGTTCCAGAATCGAAGGATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTTCCTGGGGCCCGAGATGAGGAGAAGGTGGAAGAAGAAGGGAATGAGGAAGAGGAGAAGGAGGAGGAGGAAAAGGAAGAAAATAAGGACTAAGAAAAAAGAGAAAATCAGCCCCCCCCACAACTCCCTTGAAGTTTCGTTTTATGGTAGCAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAATAGAATGACACTCACAACTGTAACTACCTGTCAGATAGTTGCAGCTCTGCTTTTATTACCTTTGGCCTTCCCCCACTCTTTATTTGTCTGGGGGTTGGGAGGGGGAACCTGAGACACAGGGAAAAGTTCTGTTCCACTCCATGCCCAGCACACACTCACTTGTCCCTACTTCCACTTCTGAGCCCTTCCCGATAAAGCCTAACCCTACACACACACACACACACACACACACACACACACACACACACACCACACACACTTCTCTCCACACTCTTTACACGATTCTCTGGTATTTATTTTAAAAGGGATTCCCCTGAAGATGTAGAAGATGATTCCTGGCTTTGCTTGTATGCTGGGAATTAGAATACTGGATTGACTTTTTTTTTTAAATGAAAAGAAAGAAGGGGAAAAAAACAGGAAAGGGGGAAATGAAAGGGAAAATTTAAAAAGAAAAAAAAAGATAGCAAAGAAGATTCCCCTCCCCCATCTGAGGCTGTTTCCTTAGAAAACCCCCCTTGACTTTCTCCAGGAATCTACTGGAAATCAAGGAAATGTGGGTTTCTCTACCCACCTCCTTCCTGAGGGTTCTATAAGGACTGGCAATGGTCTCTGAAATCCTACCTATCCATCCCATAGTCACTTGGGTCCATGCCTTCCTTGCCTTGCCTTTGCTGTTTGATCTTTTGGGCCCTGGCTTCCTCTGAGCTGTGTTAGTGTTTGTGCTCAGAAATCACCATAATCATGAAGATAATATACTGATAATAAATCTTTAACATACTACCTAAAGGGAACCTGCAATAATCTTGGGGGAAAAAAAGAAAGAAAAAAAATCCTAATACAGGAGGGAGAAAAAAAGAAGAAAAAAAAAGAAAAAAAGAAACAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTGTTGTTGTTTGTTGCTGCTTATTTCTCCATGAAAAAAAAAAAAAACCCAACAACTGAGACTGCCTAGCCCGCCGGTCTTGTGCGCTTTTATTGTGCTTCTAACCCCAGTAGAGTAGAACTAAACTGCACTGAATGTATAGTTACTCTGTCTTGAATTTCTCTGTTTATGCAATGTGCTCGAAAGGTTAAAGAAAAACGTTAAAATATATCTATAACAATGATTTTGGTCATTTGTCTTTATGTCCAGCTATGAATGTAGATTTTGTGTCCTGAAAGCTCTGTTCCTGGTCCAAGTACTTTGTATTGTATATGTGAGTCATAATAATAAAAAAAAAAACAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000028619:ENSRNOT00000031404:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.253 A=NA C2=0.526
Domain overlap (PFAM):
C1:
PF095335=DUF2380=PU(74.1=56.8)
A:
NA
C2:
PF095335=DUF2380=PD(25.0=28.6),PF0004624=Homeobox=WD(100=58.2)
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:
ATCTCCAACTCGGGCTACCAG
R:
GTGAGAGACTTCAATCCGGCG
Band lengths:
354-1694
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]