DreINT0078840 @ danRer10
Intron Retention
Gene
ENSDARG00000057859 | hoxd10a
Description
homeobox D10a [Source:ZFIN;Acc:ZDB-GENE-990415-116]
Coordinates
chr9:1966910-1969274:-
Coord C1 exon
chr9:1968413-1969274
Coord A exon
chr9:1967698-1968412
Coord C2 exon
chr9:1966910-1967697
Length
715 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
TGTGTGCTTTTGTTTTGCAGAAT
3' ss Score
11.65
Exon sequences
Seq C1 exon
ATTTCATTGGTGAGAGTGTCATGTGGTTGCAGAGAGACTCGCTGGGTTATACAGGGATTGTTTTGCTAGATATGTCAGCTTACAGAGGACACTTCTCTGCTTCTTAAAACAAAAAAAGAAAACAAAAAAAAATCCAAAATGTCCTTTCCCAACAGCTCTCCTGCAGCAAACACTTTTTTGGTAGATTCCTTGATTGGGGCGTGCAGAACAGATTTTTATTCCAGCAGTAACATGTACATGCCAGCAGCCACTGCAGAAATGGGAACCTATGGAATGCAAACCTGTGGACTCCTGCCGGCTCTTGGCAAACGGGGGGAAGTAAACCACCAAAACATGGACATGACCGTCCACTCGTACATACCTCAAACTGATACCTGGGCAGATCCGAGCAGGTCCTGCCGATTAGAGCAACCGCTCAACCAGATGTCCACCTGCACATTTTCACAAAGCATAAAAGAAGAGACTAACTGTTGTATGTACTCCGACAAGAGAGCAAAGGTCAGTTCGTCTGAGATACCCGCGTACTCCAGCCTGATTCCCGAATCATGTTCTGTTGATAGTCCTGAGATTCCGGTCCCTGGCTATTTTAGACTGAGCCAAACTTACGCGACGGCGAAAAACCCGGACTATGACAACGAGACGATGAGCCCAAACACCACGTTAATGCAGCTGAACAGGGCGACTCCAAAGGCACAGTCAACGCCCTTTGTCGAGGTGGAAAAAAAGCTTGCGCACGATCGGGACACAAGGAGCTCTTCCCCGGCGCAGAGTCCAGAGCCCAAAGTCAGCACGCTGGAGGAGAAGAATTGCTCAACTGAGGCGTCTGTTTCCAGCCCCGAATTGCCACACAGAGAAGGCAAAG
Seq A exon
GTGGGTACAATAAACGGATTAATCGCGTCTTGGTGTAATGCGAACGCTCTAGCATCATAAAACCCAATATAAAACACAAACAACCCGAAAGTCGTAATGTTTAATGGGAGTCTTACTCAGGTTGCAGTAAAAGCCTTAACAGGAAACGGCGCTGCGAGGGCGCGTTAACATCAAATACCTTTTGTTGCAAGTGACTTGACATTCTTCCTTGGCCAATATAAGCACAGCCTCGGTGGAAAGTATTTGTGACTTCGTCCATTCAGCACGGAAATTAACGTTCTGTTTAATATATAGTAATCATCAGTTGCCATTCATTTGATACCGAGGTAAAGCTCGGGTTGTGGACGAGCAGAATATAAATATGAAAACCTCATACCTATAAAGTGAATTGATTATAACCTGGTTTTACTGGATAGTTTGGGATTTAGCTTATAAAAACAACACAAGCTCATGTGTTACATAATACAATGATGAAACATTAACATTTATTTAGTTAACGCTTTATTACTTAACTTCAGTGGGAATAATTGTGTGATGAAAGAACAAGCGAGGCCACATTGGGCATATGCGTATAACGCAGTGCGTTAACATGTGCATGCTAAAATATGATATCTGTTTGAATCCCCTGTTAATTTTTATCTGGTAAAAAAAAAATGTTTTATTGTCATTTGTGCATGGCTGGCGCTGTTGTTCACTGTGTGCTTTTGTTTTGCAG
Seq C2 exon
AATCTAAAAACGACACACCGACGAGCAACTGGTTAACCGCGAAGAGTGGAAGGAAAAAGAGATGTCCATACACAAAACACCAGACCTTGGAATTAGAAAAGGAGTTTTTATTCAACATGTATCTGACTCGGGAGCGCCGTCTAGAGATAAGCAAAAGCGTCAACCTGACTGACAGACAAGTGAAAATCTGGTTCCAAAACCGCAGGATGAAACTCAAGAAGATGAGCAGAGAAAACCGTATCCGTGAACTGACGTCCAATCTCACTTTTTCGTGAGCACGCAGACAAGTGCAAATCAAAAACCTAGTCCCTCATTTCGGTCCATCTATGTTCTCCTGTGTAATGATGACATGATGGCAGTGTGCATTGTTTTTGGCTACTTTCACGTTGCAGTCTTGTGATCGTCGCTAAATCCTTGTCATTTATTGCTGCATCTTTGAAATGTACATTTGAAATGTGAAGCTTTGTGTAATTATCATGTTACACAGGGTATACAAGTGGTGTTAGGTCTTAACTTATAAAAGAAGATAGAAACCGGCTATTTCTGACGGCTTCATTTCAGCGGGGATAGAAGAAAATGTCGCAAACACATTTGCGTCAGCCTCTAAAAAACAAAAAGTCTTGGACAAGAAAGCACATTTGAAAGTGAAGATTACCCATTCTTTCTCCAGTGAAAACGTACATTTGTCTCAAAATAATAATGTATTTCTGTATAATAGGTGTTTAAATATGTCTGTATAAGTGCATGTTTGTGGCATGTGGTCAATAGACTAATAAATTGATTATGTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000057859:ENSDART00000080608:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.455 A=NA C2=0.363
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=62.0)
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:
GAGATTCCGGTCCCTGGCTAT
R:
TTTTCCTTCCACTCTTCGCGG
Band lengths:
355-1070
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]