RnoINT0071682 @ rn6
Intron Retention
Gene
ENSRNOG00000042480 | Hoxd8
Description
homeobox D8 [Source:RGD Symbol;Acc:6489440]
Coordinates
chr3:61627864-61628628:+
Coord C1 exon
chr3:61627864-61627942
Coord A exon
chr3:61627943-61628332
Coord C2 exon
chr3:61628333-61628628
Length
390 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGG
5' ss Score
5.87
3' ss Seq
TGTTGTTGTTTTTTAATCAGCAG
3' ss Score
5.13
Exon sequences
Seq C1 exon
AATATTGGCGGGACCCCAGACCCCTTAAATCAGAGCTCGTCTCGCTTCTCAAATCGTTTCCCTGAGATGAGACCACAAG
Seq A exon
GTGGGGATCACTTTTTTTTTTTTTTTTTAAGGGAGGGGAGATAAGGGTACGAAAATCTTGCTTTCATATCACGTCCTAGCTTTAAAACTCCCCTGTCCTTTCCCTCTCCCCCTCCTTTTCCTTCTAGTGTAGCCACTGTGGCTCTTGTACATAAACTAATACAGACTTTTAAAAAGTATGTAAAGATGGGGACAGAATAATTGTGAAGACTTTGTCTCTGCCTCTCTTGCCTGCACACCCTGTATCTGTATCAGAATTAAAGACCAGTGTGTGTTTCACCTCTTAAGCCTGTTCCAGAAACTCCAGCAGCGTTCAAAGAATCAACCATTTTTTTAAAAAAAACGTTGATTTTCCTCCCCCCCCCTTTTTTTGTTGTTGTTTTTTAATCAG
Seq C2 exon
CAGCTCCTGGTAGACGGAGAGGAAGACAAACCTACAGTCGCTTCCAAACCTTAGAGTTGGAAAAGGAATTCCTTTTTAACCCTTATCTGACCAGGAAGAGAAGAATCGAGGTCTCCCATACTCTGGCCCTCACGGAGAGACAGGTAAAAATCTGGTTCCAGAACAGGAGAATGAAGTGGAAAAAAGAGAACAACAGAGACAAGTTTCCAGCGTCCCGGCCGGAGGCAAAGGATGGAGACCCCAAAAAGGAAGTCTCAGGGCTGGAGGAAGACGGAGCCGAAGGCCCCACAAACTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000042480:ENSRNOT00000067861:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.510
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=57.6)
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:
GGGACCCCAGACCCCTTAAAT
R:
GTCTTCCTCCAGCCCTGAGAC
Band lengths:
342-732
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]