GgaINT0050294 @ galGal4
Intron Retention
Gene
ENSGALG00000023419 | HOXD4
Description
homeobox protein Hox-D4 [Source:RefSeq peptide;Acc:NP_001012293]
Coordinates
chr7:15777579-15779976:-
Coord C1 exon
chr7:15778828-15779976
Coord A exon
chr7:15778530-15778827
Coord C2 exon
chr7:15777579-15778529
Length
298 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
TCTCCGTGTTTCTTTCCCAGTGA
3' ss Score
10.25
Exon sequences
Seq C1 exon
CTTTAGCGGCCAAAAGTGGACGGTTTCTCGTTATCTGGACGCTTTCATGCACACACACGCGCAGATTTTGTATGTGAGTGTGCGAGCGAGCGTGCGTGCCCACGTGTGCACACGTACGTGTTGAGGTCGCGAAGTGAATGAGAAGTTACTGATTGCCTAATTTTATTCAGCAGAACGAAATTCTGGTAACTTTTGGATGACCTCTGCGAGACAAAGACAGGACAGATCTATTGTACATCATATTGCCCTCTTCTTTGATGTCTTTTCTTTTCCTCGCCTCCTTATCGGTTCCCTCCCTCCACGTCCCGCTCCGACTCCTCGCCCCGCATCTCTCTCGAGATTTTATTCGTATCGGAGCCCGGCGGCCATCCCGCCCGGCGGATGGGGCGGAGGGGTGGGGGGGTGAGGGGGAGGTGAGGGCTCTGCTCAGACAAAGGCTGCCCGCACCTGGGGGCAGGGAGGCGGCCGCACGCGGGGAATGGCCCCAAAACTCCGGGATCGGCCCCGGAGGGCGAAGCCCGCCGCGGAGGGGTCGCTCAGCTCCGCGTATATTATTTAGTTAAATTCGTGGAAATTCTGAGGCGCACACAAATCCGGTGATCGGCTCCCCGCCTCCCCATTGGCCGGGCCGGTCACATGCACGCCTAACTTTATTCAGTTGACAGCAAGTAGGAGGGCTCTATGGAAGGAGAAAAAAAGACAACACGAGAAAAATTAGTATTTTCTACCTTCCGAAATTAATGGCCATGAGTTCGTATATGGTGAACTCTAAGTATGTGGATCCCAAATTTCCTCCTTGCGAGGAATATTTGCAGAGCAGCTACCTAGGCGAGCAGGGGGCCGAGTATTACGGGGCCTCGCAGGGCTCCGATTTCCAGCACCAGGGGCTCTACCCACGGTCAAACTACAGCGAGCAGCCCTTTGGCTGCGCCGGTGCCCAGGGCTCCGCCGTGCAGCCGCGGGGTCACGGACAGGAGCAGTCCGCCCCTCCGAGCCACTTCCCCGGCCAAGCCGAGCATTGTCCTCCGCCTCCAATGTCCAACTCCCGAGCCTGCGGCCAGCAGCCAGCCCTCAAAGCCCCCCACGGGTCAGCAGTTAAGCAGCCAGCAGTAGTTTATCCCTGGATGAAGAAAGTCCATGTTAACTCGG
Seq A exon
GTAAGGATCCTCTTCTTACTTTGCTCTTCTACCCCGCTCCCGCGTGTGTCCTCAGGGATGCTCGCTCGAGCCCTGGCGAGGCTTTAAGGCGAGGCGGCCAATTACACTCGTCGTAAATTTTTATTGCCGAGGAAATAGGCCGTCGGCGTGCGGGGCTCTTCCGCGCAGGAACCGCGGTAGGAGCCGGCCCCGCGGAACGGCCGCGCCGGGCACCGCCGGAGCGCTCCTGGGGCCGCGTGGGAAGGCGAGGCGGAAAGTCCCCCTTCGGTCTGTAAAGTTCTCCGTGTTTCTTTCCCAG
Seq C2 exon
TGAACCCCAATTACAGCGGAGGGGAACCTAAGCGCTCCCGAACAGCTTACACCAGGCAGCAAGTCCTAGAACTGGAAAAAGAATTTCATTTTAACAGGTACCTGACCCGGCGCCGCCGTATCGAGATAGCGCACACTTTGTGTCTCTCTGAGCGCCAGATCAAGATCTGGTTTCAGAACAGAAGAATGAAGTGGAAAAAAGACCACAAACTGCCCAACACTAAGGGCAGGTCTTCCTCCTCCGCTTCTAACCCCCACTTACAGACTGTTCCCAAGGACCATCAGACTGACTTGACAACTTTATAGAAGAGGTGAAATTTTCCATTTCATCCTTCGATTCTGACCAGTACTGTACATAAGTGACACTATCCAAGCAGAACCTGCGTGTAGCAGCCAAGGACTCGAGAAACTGCCATCTCTCCGTAAGGTACTGTGGTACAAAGGAGACTGAATGACGCTACTCCGGACTTTATTTTATTTGCCTCTCGCTAGCACAGAAAGAAAGGGGGGAAAAAAAGCATCATACAGGCAGTAGGAATTGGGAAAGTCTTAAACGAGACCTTCTGTCCATAAAAAGTAATAAATCATTGAAAATGAAACTGTCCTGTGTTTCAGTTTGGGATTTGAAAGTGAAGGTTTGATGCTTTATTCTGGGATTTTATTATTATTATTTTGCTTTTAATTGTCTTTTTATCCCGCACAGCGAGTGTGATGCTTTTGGGGCAAGTCGAGGACAGGAAATTTATGGCACGGTCCTTTATTTGAACACAAAGCCTCGCGTTTGTGAACTTTTTTGTGCTGCTTTACCTTTACTTGGTGTAATGAAAATACTCACTCATTTCCATAACGTCTCAGAAGATGTGCATAGGAATTAAGTGAAAACGGGTTATTTTGTGTCCTGATGGTGTTAGCGTATTTATTTATTTGTTATGTAGAAGAGTGAAGATTAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000023419:ENSGALT00000038691:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.489 A=NA C2=0.545
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGTCAAACTACAGCGAGCAG
R:
CTGGTGTAAGCTGTTCGGGAG
Band lengths:
308-606
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]