RnoINT0071663 @ rn6
Intron Retention
Gene
ENSRNOG00000001572 | Hoxd1
Description
homeo box D1 [Source:RGD Symbol;Acc:1309179]
Coordinates
chr3:61685619-61687758:+
Coord C1 exon
chr3:61685619-61686374
Coord A exon
chr3:61686375-61686684
Coord C2 exon
chr3:61686685-61687758
Length
310 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGG
5' ss Score
6.6
3' ss Seq
TGTCTTTCTTTATGTTACAGGCA
3' ss Score
10.87
Exon sequences
Seq C1 exon
ATATGAGGCCACTATTTACCTCGGGCTCGCTCGCCATGGCTCGGCGAGGGCAGCGGGGGTAGCGGACCGGCAGGGTGCGGCGCCTGGGTCTCGCGGATCGAGCCATGAGCTCCTACCTGGAGTACGTATCGTGCGCTGCGGGCGGAGGCAGCGGAGGGGTAGGCGGCGACGTGCTGGGCTTCGCACCCAAGTTCTGCCGCGCCGACGCGCGCCCAGTGGCCCTGCAGCCCGCCTTCCCCCTGGGCAGCGGCGACGGCGCCTTCGTGAGCTGCCTGCCCCTGGCCGCTGCCCGGCCCACGCCTTCACCTCCCGTAGCCCCCGCGCAGCCCCCGGGCCCGCAGCCGGCCGCGTCCCGGTACGCGCCCTGTACCCTGGAAGGCGCCTACGAACGGGGCGCCGCACCTGCCTCTGCCGCCGAGTATGGTTTCTTGGGGTCCGGGCCGGCATTCGACTTTCCGGGCGCGCTTGGGAGAGCAGCGGACGACAGCGGCCCGCACGTCCACTATGCCACCTCGGCGGTCTTTTCCAGCGGAGGATCATTCCTGCTCAGCGGCCAGGTGGACTTCGCTGCCTTTGCCGAGCCTGGCCCCTTTCCCGCTTGTCTCAAGGAACCCGCAGACGGCCACCCCGGGCCCTTTCAGACTGTGTCCCCGGCCCCCGGAGCCTGCCCCAAGCCCGCCTCGCCCACCTCCGGCCTCCCGGCCGCCCACAGCACTTTCGAGTGGATGAAAGTGAAGAGGAACGCCCCCAAGAAAA
Seq A exon
GTAAGGAGGTGGGCGCTGGGGGGAGGCACCTGGGGTCCAGGGAGCCACCTCCTCCATGAAGAGCTGGGAGCCTGTGGCCACCGAGCCCTGGAGAGAGCTTCTGCCCCTAAGCGGTCAGATCCCAGGGTCAGAAAATGCCCCAGGAGCTGAGAAAATTAGGACAGAGGCCTCGGCAGAGCGCTTCTTCTGGTACAGCTGTGTCTATCACTCAGGAGGGCTGCGCTGTGACTTTGATCTTAACTCCTAGTCCCACTGGGTAGTTTCAGCATCTCCTCATCCTGCTCACACCTTGTCTTTCTTTATGTTACAG
Seq C2 exon
GCAAACTGTCCGAATATGGAGCCACAAGCCCCTCCAGTGCCATCCGCACGAATTTCAGCACCAAGCAACTGACAGAACTCGAGAAAGAGTTTCATTTCAATAAGTACCTAACTAGAGCCCGACGCATGGAGATAGCCAACTGTTTACAGCTGAATGACACCCAGGTCAAAATCTGGTTCCAGAACCGGAGGATGAAACAGAAGAAAAGGGAACGAGAGGGGCTTCTGGCCACAGCTGCCTCTGTGGCCTCGCTTCAACTTCCCGGGTCAGAAACAAGTCCCATCAAATCTGGCCGGAATCTAGGAAGCCCTTCTCAGGCTCAAGAGCCTTCCTGAGGCCCACTCTTAAGGCTGAGGACCTTTGGATTATACAGAAGTCACAGACTGCCCCCAGCCACCTTTGTATAGACTTAAAAGCTTAGTCTAGGCTGGAGACGGGCGTGGGTAGAAGTTAATACGGATTTTACTTGGCAAAGGAATTGTCTATACTGGCTTCTGAGGCCCAGAGGCTATGTATAGAGATATATATTTGATACCTTTTATTTGCATATTATTTTTGCCTCATCAGGGGAAAGCTGTCTAGCTACCAGCCTAAACGCTGCTATGTTAGTCATGAACAATTCTTGGGTACGGAATGGCAGGCCTTCTTAGTCTGATGTGGTCAAAACGTACCTCTCTGAAGTCATTTCAGTTTTAAGTTCCTGGACAGACTACATATATTCAGCTTCCTGAAATGACCAAAGCTAGCCAGGGTTCCCTCAATGGAGCTAAGCTGCTTCAATGATGTTCATATTGTACTCCAGTTTTATTTAAAGTCGTTCCTACCTCTTCTTGTGCCTGAGTGAAGATACACAATCGCTCTTTAGTTGGTACCGGAATAAATCCATTGGGTAGATAAGGATTAGAATCTAATTATACCTTGACATCAGTTACTCAAACTTGAAGTATAAATATATACAGTATGTATATTTTTTAAAGATTTGCTTGCAGTGAACCCTATATATGACATTTAATGTCATGCATAGCATGTAAAGATTTTGACCGTTTTTTTGGTAATAAAAGTTACAGAATCTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001572:ENSRNOT00000002140:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.271 A=NA C2=0.477
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAGTGAAGAGGAACGCCCC
R:
GCCTGAGAAGGGCTTCCTAGA
Band lengths:
348-658
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]