RnoINT0071678 @ rn6
Intron Retention
Gene
ENSRNOG00000001578 | Hoxd4
Description
homeo box D4 [Source:RGD Symbol;Acc:1309690]
Coordinates
chr3:61648815-61651056:+
Coord C1 exon
chr3:61648815-61649644
Coord A exon
chr3:61649645-61650199
Coord C2 exon
chr3:61650200-61651056
Length
555 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
CTGTCTGTTTTATCTCATAGTGA
3' ss Score
9.35
Exon sequences
Seq C1 exon
TAGGAGAATTCACTCTTCTTTGAACTATGCCCATTCTGGGGGCTGCTTCAGGCGATGGTGAGTGAGGAGGGCATGGGAGGTTAGCAAAGTCAGTGGAAGACAAAAGCGAAGATTATCTGCTGCAAATTGGGGTCTCGGGGATAGAATCAAAACTATATTAACATCTGTCAGGGACTCTCAAATGTGGCATGGCAAGTCACTTGATTACACGTATGTTATTTAGTTAAATTTGTGAAAATTATGAGATGCTCACCAACCCGGTGATAAACATGCTCTCTTCCTATTGGCTGGCCTGGTCACATGGCCGCCCAACTTTATTCAGTTGACAGCAAGTAGGAGGGCCCAATGGAAGGAGAAAAAAGACAACACGAGAAAAATTAGTATTTTCTACCTTCTGAAATTAATGGCCATGAGTTCGTATATGGTGAACTCTAAGTACGTGGACCCCAAGTTTCCTCCGTGCGAGGAATATTTGCAGGGTGGCTACCTAGGCGAGCAGGGAGCCGACTACTACGGCAGCGGTGCACAGGGCTCCGACTTCCAGCCCCCGGGGCTCTACCCACGGCCCGACTTCGGTGAGCAACCCTTCGGAGGCGGCGGGCCCGGGCCTGGCTCAGCGCTGCCCGCGCGGGGTCACGGACAGGAGCCGAGCGGCCCGGGAAGTCACTACAGTGCCCCGGGAGAGCCGTGCCCAGCGCCCCCGCCTGCGCCCCTGCCTGGCGCTCGGGCCTGCAGCCAGCCCACCGGCCCCAAGCAGCCGCCCCCCGGGACAGCACTCAAGCAGCCCGCTGTGGTCTACCCTTGGATGAAGAAGGTGCATGTGAATTCGG
Seq A exon
GTAAGGAGCGGGTGCAGCGACCTCATAGCCCTCCCTCACCCCTACTCGCATCTTTTGGCCTGGGCCCCCCGGAGGGTTGCGAATGGGTGGGGGCTTGGGAAGCTTCCTTGGGCGCCGCAATTACTCTCTCCATAAATTTTTATAGCTGAGGGAGCAGGCCGGGACCATGTGGCTGGCTGCTTGACTGTGGGCGCAAAAGGGGGTGGGGATGGGGGTGGGGTGGGGGAGGACTCCATTTCCAAAGCAGAGGGAACGCAGAGCAAGAGAAGGGCATTTCCAAAATGTTGGAGATCCCGAGCTCTTGGTGGGCCAGGGGCAAGGGAGTACCTTTAAGGACCTGTGAGCGTGGGGAGTGGGTGCTTGGAAGGGGTTGGATGGAGTGAGTGTATGTTTTGGAGGAGGGCGGGAGGTAGGAAGCTGGCCAGCTTGGAGCACGGGGGGGGGGGGGGCACCCGAGGGCTGCGAGACGCGCCAGGAAGTGAGGGCAGAGGCAAGCCTGGGGCCTAACTAGTGGCCGGGCTCTGACCTGGCTGTCCTGTCTGTTTTATCTCATAG
Seq C2 exon
TGAACCCCAACTACACCGGCGGGGAGCCCAAGCGTTCCCGGACGGCCTACACCAGACAGCAAGTCCTAGAACTGGAAAAGGAATTTCATTTTAACAGGTATCTGACCAGGCGCCGTCGGATTGAAATCGCTCACACCCTGTGTCTTTCTGAGCGCCAGATCAAGATCTGGTTCCAGAACCGGAGGATGAAGTGGAAAAAAGATCACAAACTGCCCAACACCAAGGGCAGATCTTCTTCTTCCTCATCTTCCTGCTCCTCTTCAGCTGCCCCCAGCCAGCATTTGCAGCCAATGGCCAAGGACCACCATACGGACCTGACGACCTTATAGAAGTGGGAACCCTGGGCCCATTCCTTCTTGCACTCCAGGTTGAGGCGAAGCTGCGGGTGCAGGCGGGGCCTGCTGTCACCTCACTGGGCTCTAAGGTACTGTGGGGGTGGACCTGGGACCCGCAGGTTACCATCCTGCCTGAGGGCAGCCCCCTCCCTAAAGTGGGGAAGGGTGGGAGGGAGGGCGGGCTTCTTTAAATAGATTATCAAACGGCAGGAGCTACTGAGAACATAAACCCTTGGTGAGTCATTAAACTCCTGAAAATCTCTGCTGTTGGATTTTGAATTTGCAAATGAAGGTCGGAGGCTTCACCCCAGTGTGAACCGGGATGTTCTCCTCCGCACCACCCCTCCAGGGAGCTGCGTGGCATAGTAACTGTGGGGGAGTTGAGGCAGAAGGCCAGCACCCAGTGCTAGGTGCTTCCACTGCAAGCAGGAGAGCTGAGTCAGAAGCTCAGAACTTTCTGAATAATCTATAGAATTTCTTCTGTGATAAAAAGAAATGTTTTGCTCCCAGTGGCCCATGCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000001578:ENSRNOT00000002145:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.734 A=NA C2=0.633
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=51.8),PF105004=SR-25=WD(100=68.2)
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:
ACCCTTGGATGAAGAAGGTGC
R:
AGGTCCGTATGGTGGTCCTTG
Band lengths:
349-904
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]