RnoINT0071664 @ rn6
Intron Retention
Gene
ENSRNOG00000001581 | Hoxd10
Description
homeo box D10 [Source:RGD Symbol;Acc:1306511]
Coordinates
chr3:61613774-61617367:+
Coord C1 exon
chr3:61613774-61614977
Coord A exon
chr3:61614978-61616339
Coord C2 exon
chr3:61616340-61617367
Length
1362 bp
Sequences
Splice sites
5' ss Seq
AAGGTCGGT
5' ss Score
7.13
3' ss Seq
TTTCCCTTTAATTTTGTTAGAGG
3' ss Score
4.9
Exon sequences
Seq C1 exon
TGCCTGGGTATGTGCAGGGAAAGCACTTCTGTGAGCAGGCGCCACAGCGCTCTCACTTCCCTCAGTGCGCGTGTCCTCCCGGAGGCCCCTCGAATGAAGCCTTTCCTTCCGCTGGCGGGGCCCGGTGGCCGGGTGGGGGACTCGAGTGGGGCAGGCAGGCCGGCCAAACAAGCCCCGGGAGACAGGCTGGCCGGCAGCAGAGCTCTGGGCCGGTTGTCTCCAGCGCGCACTATCACAGGCGCTTAGTAGATGTCGCTGTTGTCCGTGCTTCCGCGGCCGGCCGGCCGGGCTGTGGAACACGTGACCTGCAAGGAGGCTGCGGCTCAAGGCCATTTTCAAATCTCATTGGCTTGGTTGTCATGTGGTCGGCAGAGGCATCCACAATTACACCGGGAATGTTTTCCTAGCGATGTCAGCCTACAAAGGACACAATCTCTCTTCTTCAAATTCCTCCCCAAAATGTCCTTTCCCAACAGCTCTCCTGCTGCTAATACTTTTTTAGTAGATTCCTTGATCAGTGCCTGCAGGAGTGACAGTTTTTATTCGAGCAGCGCCAGCATGTACATGCCACCACCTAGCGCAGACATGGGGACCTATGGAATGCAAACCTGTGGACTGCTCCCGTCTCTGGCCAAAAGAGAAGTGAACCACCAAAATATGGGTATGAATGTACATCCTTATATACCTCAAGTAGACAGTTGGACAGACCCGAACAGATCTTGTCGAATAGAGCAACCTGTTACACAGCAAGTCCCCACTTGCTCATTCACCGCCAACATTAAAGAAGAATCCAATTGCTGCATGTATTCTGATAAGCGCAACAAACTCATTTCTGCCGAGGTCCCTTCGTACCAGAGGCTGGTCCCCGAGTCTTGTCCTGTTGAGAACCCCGAGGTTCCTGTCCCTGGATATTTTAGACTGAGTCAGACCTACGCCACCGGGAAAACCCAAGAGTACAATAACAACCCCGAAGGCAGCTCCACTGTCATGCTCCAGCTCAACCCTCGTGGCGCGGCCAAGCCGCAGCTCTCGGCTGCCCAGCTGCAGATGGAAAAGAAGATGAACGAAACCGCGAGCGGCCAGGAGCCCACTAAAGTCTCCCAAGTGGAGAGCCCCGAGGCCAAAGGCGGCCTTCCAGAAGAGAGGAGCTGCCTGGCTGAGGTCTCCGTGTCCAGCCCCGAAGTGCAGGAGAAGGAAAGCAAAG
Seq A exon
GTCGGTATGAACAGAGTTGCCACCCCAGCGGGGCGTGCAGTCCGGTAAAACCTCGAAATGGGAGCGCTCGGGTGCCCAGAGCGGAGCCCCGGCAGCGGAGCCCAGAGCCCAACTCCGCAGGTGCTGCTCCACCCAGCTTTTAGAAGGGAGACCCCAGCCTTGAAGGGGTCGCGGCTTCTCTCCCGCTGCTCCGGCCAGACCTGGCCCCAAGCTGATGGCGCCTGGGCAGAGGAGAGGCTTGCCGGGTTTATCTGTCTTGGGCCAGATCTGAAATACAACAAAAGAGCTAAAAGGAGACCAGCCGCTTGTAAACAGGGCTCCAGTGCCCGCTTTTCTTTGGCTCAGATTTGCAGCCCTCGTTTTGCCTTTAACACAGGGATCATTTTAAGGTAGCCCAAGACACGGTGTTTGTGTTCAAGGGTTTGCACCCCGCATCCTGCGATCTGAGAGGGGAAGGAAATGGTTTGGCCTGTTGGTGCTTGGGTGGGGAAGCAAAGGACTTGCCTTTACTGAGCTAGGTAACCTTGGCTTTGTCTGGGGAAAGTGCCGCAGGCTTTGCGATCTTCTACAAAGAGGGCAAAAGCAGAGGAGGGGGTGAGAAGGGATCTGCATAGCCCTCCTAGGGTTGGGATAAAGCAAAGAACCAGAGATAGGGGTTTCTAAGAAGGAATCTTGAGCCCCCACCCCTATTTCTGCAGTCTGTCCCTCAGTGTCTACCGGTGAGCCACAGAGTTATATTTCTGGAGGAAGGCTTTTGTGTGAGAGCAAAGAAAAATTGAGGAAATTCGGGGAGGGGGGAGGGGGAATTAATTGCAACAATGCCCAGTCAGGGTGGAGAAGGTATCCTTGCTTCCTCGGCTATCTCTTGAAACAGACTTGGTCCCTATAAAGCTGGTTGTAGAGCTCCTTGTGTGCCTAGGAGGGGTGGGTAAGAAGCGACCGACCTGGGGCCCTGGAGCAGCAGTGAGATTGGTAGATGAAGCAAGCTCCTGTTCCTCCTGGTGATCGCTTAGAATGTTATTTTGAGGAAATCCTGTAAAGTTTGCTATTATAGTCTCATTTTGTGCAAGCCAGAAAGTTGTGTAGGAGAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATATCCTTTCATTCATCGAGTTAAGCATTGAGTTCTAAATTGGTACCAATTTGCAATCCCCTTCATGCCCACCTTTGTAAGTAAGTAATGCTTAATACCAGCATTGTCAAAAGCAGCCTGTCTGGCAGCAGGGTCATGGCCAAGGGTATATTTGAATGGACTGAGAGAAAAAAAAATTCTTGATTTTTTTCTTTTCCCTTTAATTTTGTTAG
Seq C2 exon
AGGAAATCAAGTCTGATACTCCAACCAGCAATTGGCTCACTGCAAAGAGTGGCAGAAAGAAGAGGTGCCCTTACACTAAACACCAAACGCTGGAATTAGAAAAAGAGTTCTTGTTCAATATGTACCTCACCCGCGAGCGCCGCCTAGAGATCAGTAAGAGCGTTAACCTCACCGACAGGCAGGTCAAGATTTGGTTTCAAAACCGCCGAATGAAACTCAAGAAGATGAGCCGAGAGAATCGAATCCGAGAACTGACCGCCAACCTCACCTTTTCTTAGGTCTGAGGCCCATGTGAGGCCAGGATCCGAGAGGGGGCACCGAGTTCCAGGCCCGAGTACTGAAGGACTAGGGAGGCGGAAACAAAACCTTCATTGCTCTTTGGTTGTTTTGTTTTGTTTTGTTTTGTTCTGTTCTGTTTTCCTGCTAGAATGTGACTTTGGGGTCATTCTGTTCGTGCTGCAAGTGATCTGTAATCCCTACGAGTATACATATATATATATTAAAAAAACTTAGCACGTGTAATTTATTTTTTCATCGTAATGCAGGGTAACTATTACTGCGCATTTTCATTTGGGTCTTAACTTATTGGAACTGTAGAGCATCCATCTAACCTTATCCACCCAGCCAGCCAGCCAGCAATGTGACTTTTCCATGTTTTTCCTAACATAAAAGTTCTCTCTGTGTGTGGTTAGCCCATGAACTCATGACATTTTGAAAACATCCAGTACTTAAAAAAAACAACAAAAAAATCCTATATCTATATATATTTCAAAAGATTAAGAAAACCCACAAGCTTTGGGGGGGAGGGGGACTTTAAAAGCACATTACAATGTATCTTTTCACAAACGAACTTAGCAATTGTCCTTGGTGAAATGGATTATTGACTTATGCCTTGTAGCCTTTCCTTGTGGTGCATCTGTGGTTTGGTAGAAATACAAGAGCAACCTGTGCTTTTTTGTGCATGTTCTGGTCGCATGTGTAATGCAATAAACTCTGGAAATGAGTTTGTTCCCTCTGCTTTCTGAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001581:ENSRNOT00000002148:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.386 A=NA C2=0.293
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=61.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTTCCAGAAGAGAGGAGCT
R:
AAGAAAAGGTGAGGTTGGCGG
Band lengths:
351-1713
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]