RnoINT0071673 @ rn6
Intron Retention
Gene
ENSRNOG00000001577 | Hoxd3
Description
homeo box D3 [Source:RGD Symbol;Acc:1588601]
Coordinates
chr3:61666286-61670282:+
Coord C1 exon
chr3:61666286-61666909
Coord A exon
chr3:61666910-61668677
Coord C2 exon
chr3:61668678-61670282
Length
1768 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCT
5' ss Score
6.52
3' ss Seq
CTATCTCCCTCCTTGCCCAGGAG
3' ss Score
8.69
Exon sequences
Seq C1 exon
GTTACCTGGAGCTTGGAAACTGGCCCAGCTCTCTCAAGATTAGCAGACACTGGCCTTGGTGGAGAAGGAGACAGTGGTAGTCAATGTTATTTGAGCAGGGTCAGCAGGCCCTGGAGCTTCCTGAGTGCACCATGCAGAAGGCTGCATACTATGAGAACCCAGGACTCTTTGGAGGCTATGGATACAGCAAAGCCACTGATGCATATGGCTATAGCACTCCTCATCAACCCTACCCACCCCCTGCTGCTGCCAACTCCCTGGACAGTGATTACCCAAGTTCTGCCTGCTCCATCCAGAGTTCTGCACCTCTTCGAGCCCCAGCCCACAAAGGAGCGGAACTCAACGGTAGCTGCATGCGGCCTGGCACTGGGAACAGCCAGGGTGGGGGTGGAGGCAACCAACCTCCTGGCCTGAACTCAGAGCAGCAGCCACCGCAACCTCCCCCTCCACCACCCACCCTGCCCCCATCCTCACCCACCAATCCCGGAAGCGGAGTGCCTGCCAAGAAGACCAAGGGTGGGCCCAATGCTTCTAGCTCTTCCTCTACCATCAGCAAGCAGATCTTCCCCTGGATGAAGGAATCCCGACAGAACTCAAAGCAGAAGAACAGCTGTGCCACTTCAG
Seq A exon
GTAGCTCTCTAAGCAGGTCATCCCTTCAAATGGGCCCCAAGAACCTATTACTCAAAAACCAAGAGACTATAAGGGCTCTAAGGGCAGCATTAGCAACAATGTATCCAAACTCCCATTCCTGTAGAAATGTCCATCCTTTTTAGTGACTTTGATTGGGTACATACCCTGCAGAGAAAGTTTACTCTCTCATTGCTGGTGCCAATGCTGAACTAGACCCATACTTATTAATAGAAAGTCCTTCCTTCCACTGACATATTATCTGCCTTCCAAGGCTGCTGGTCATAACTCAGCCTCCTCTCCTACCCAATAGCCCTTCAAACGTGAAGACAGGTTGGGTATAGTTTTGTATACCCATAATCCCACCACTTGAGGCTGAGACAGGAGTGTGTTGAGTTTAAGGAGAGTCTGGGCTGCATAGTGAGTTCCCAGAAACCTTGAAGAGACCTTGTTTTAAAACAGAAACCCAAGTAGAAACAAACAACACGCAAAACAGAAGAAAAAGACTCATGCCCAAATAAGTTACAAACGTTATCCATTTCTTTTATTTAACTTTCCAAAGAACTCTTTAAAACAGATACAAGGTAACATCCTCACTTATCCCAGATCCACAGAACTGCAAAGTGGTGGGCTTGGATCTAACTGGTATGTCTTCAAGGCCTTTAAGGCAGAACTGTGAGACTCACTCTAGTGAAGCTGTAACAGGAAGAGTGTGTTCCAAGGGGAGAAAATAATTTGCAGCAAGAGCAGCTGTCCCTTTCTTGCCCTTGAAAGAGAAACTCTAGGGCTGAGAAAGACTTCTAGCCGGCCATTCTGAGTTTGAAAGAAAGTGGGCATGGTGAGGGGCTGATGGCTTCTGGTTGCTCTGACTGCTACTCCTTGGAAATGTCTAGCTTTGTGTTCGTAATGGGGATTATTTTCCAGGTTCAGGGCTAGTCTGAAGCCTGGGATATGATTTGTTATCAGGTCTCTGTTCTGTCTGATGCTCCCTGGGCTGTTGCTCCTAAGGGAAAGTGTCTCCCTGCCTGAAAGCTCGCTCCTCTGCCCCTCCCTCCTTAGCTCAGACACAGGCCCTCCCTCCCAGGAGAAATCCATTTGTCTTCCCACTGAAGGAGTGGACAAGCAGCTGAGGGGTGGCAGGGGAGGTGACGCCAGTGCTGAGGCTGCTGCTCCTAGCATTGCCATATGCACCATGCTTCCAGCCTGGCCTTGGGATCCCCTAAAACTCCAGGGCAGTATCTTTGGGGAGGGTATTTTCACCTCCCTGCCTTTGGGTGCCCCTGGCTTGAGTCGGGTGCCAAGACCCCCCCACCCCCATTTCCTTCTTCGCTCTTTGGAGTGTTTGACCTGTAAACAAACAAGGCTGGCTGAAGCTGCCTCAGATCCCCATCTTAGCTCCCAGCCCCAAGCAGCAGAGGTTGGGAGGGGTGTTCATAGAAGCTCTTTTGGTGGAAGAGTGTCTCATGAACTGCTTTTAGTCTCACAATAATGTCTTTTATGGCCTTTGGGTTAGGATGAAACGATGGGCTAGAATGGAGGAGGGAGAGAGGGCAGAGTAAGGCAGAGAGGTTACAGGTGCGACAAACAGGTAGGCCTAGCGGTGTGTGGAGTGTGTTCCCTCAGACTTTTACCTCTCAAAAGACCCCACCCTGCTCTAAACAGGGATGGAGGTGAGAGCTGGGGAGGAACATGGAGTCAGAGAAGCATCTCTTTCCGTTTGGGGGTTCCTTACTCCTCGCTCAGCACCCTCTCTATCTCCCTCCTTGCCCAG
Seq C2 exon
GAGAGAACTGCGAGGACAAGAGCCCACCGGGCCCGGCATCCAAGAGGGTGCGCACGGCGTACACGAGTGCTCAGCTGGTAGAGCTGGAGAAGGAGTTCCACTTCAACCGCTACCTGTGCCGGCCGCGCCGCGTGGAGATGGCTAACCTGCTGAACCTCACCGAACGCCAGATCAAGATCTGGTTCCAGAACCGTCGCATGAAGTACAAGAAGGACCAGAAGGCCAAGGGCATCCTGCATTCTCCCGCAGGCCAGTCCCCGGAGCGCAGCCCACCTCTTGGAGGAGCGGCGGGCCACGTGGCCTACTCCGGCCAGCTGCCGCCCGTGCCCGGCCTGGCCTACGACGCACCCTCGCCGCCGGCTTTCGCTAAATCGCAGCCCAATATGTACGGCCTGGCCGCCTACACGGCGCCTCTCAGTAGCTGCCTGCCGCAGCAGAAGCGTTACGCGGCGCCCGAGTTCGAGCCCCACCCCATGGCGAGCAACGGCGGCGGCTTCGCCAGCGCCAACCTGCAGGGCAGCCCGGTGTACGTAGGTGGCAACTTCGTCGACTCCATGGCGCCCGCGTCCGGGCCGGTCTTCAATCTGGGTCACCTCTCGCACCCGTCTTCGGCCAGCGTGGACTACAGCTGCGCCGCGCAAATCCCTGGCAACCATCACCACGGACCGTGCGACCCTCATCCCACCTACACAGATCTCTCGGCTCACCACACGTCTCAGGGACGCCTGCCCGAGGCCCCCAAACTGACACATCTGTAGCGGTTGCCGCCGGCCTGGCGCAATTACCTCTCTGGTTTTGGTGGCAGGGGTGGTGGCGGGGCGGGGCCCGAAAGGCAGTTTAGGGGAACCCCCCTCCCTGATCTGGCCTGGCAGATGCCACACGAGTTTCGGGCTTCCAGCGGCCGAGGCTGACGCGACTGGGCCTCCCCTCCAGGCGTGTCCTCCTTTGGGTGACTCGCTATAAATCAGCCGCAAGGATCCTCCCCTGTAAACCTGACAGTGCCATAAACTGCGGACCGAGGGACTCTAATCTGGTAATGGTGTCCCTAAGGTAAGTCCTAGACCTATCCGTGGCGTGTCCTGAAGAGAGGGACTAGAGCCTGGAGAACCCCGGGCCTGGCCCTTCTGTCTAGCTTAGTTTCAGAGACCTTAATTTATAATGCTCCTTCCCTTCCTGTAAAGATTGCATCGGACTAAACAATCTGTATTTATTATTTGAAGCGAGTAATTTCGTTTCCCTGATTATTTATCCTAGTCTTAATGTATTTATGTGTATATTTGTAGAATTCTGCAGCCGGGCCTAGGTACTCGCTCCCAGGCCTTTTGGGGGGGGGGCATATTTCATCTCTTTAGTCCCCTTGGTCTGAACTAGTTGAGAGAATAGTCTTGAACAGTTGTAACCGTGGCTGGTGTCTGTAGTTGTTGTAAAGGACTGAGATCACAAATGGTCCTTCATGGGTAGAGTCAGGCAGCCCGGTGGCATAGCGCGACTCAAGCGAGTCGTTTCTCAACAGCCGAAGCCCTCACCACTCGACACAGCTTACTGATTTCAAATTGTCTGGTACTATTTGAACAAACATTTAGAATAAAACATTTTTTTCAGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001577:ENSRNOT00000033511:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.829 A=NA C2=0.484
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=22.5),PF132931=DUF4074=WD(100=24.9)
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:
GAGTTCTGCACCTCTTCGAGC
R:
GCTCTTGTCCTCGCAGTTCTC
Band lengths:
352-2120
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]