GgaINT0050432 @ galGal4
Intron Retention
Gene
ENSGALG00000009274 | HOXD12
Description
Homeobox protein Hox-D12 [Source:UniProtKB/Swiss-Prot;Acc:P24343]
Coordinates
chr7:15820669-15822513:-
Coord C1 exon
chr7:15821952-15822513
Coord A exon
chr7:15821681-15821951
Coord C2 exon
chr7:15820669-15821680
Length
271 bp
Sequences
Splice sites
5' ss Seq
ATGGTATGC
5' ss Score
7.14
3' ss Seq
TATCGACGTGTTTGTTGTAGGTT
3' ss Score
9.42
Exon sequences
Seq C1 exon
ATGTGTGATCGCAGTCTCTACAGATCTGGCTACGTTGGTTCTCTCTTGAACTTGCAATCTCCAGATTCCTTCTATTTTCCCAATTTGCGGGCTAATGGCAGTCAGTTGGCGGCTCTGCCCACCATTTCCTACCCCCGGAGCTCGATCCCGTGGACGTGCCCCAGTCCGTGCGCAGCCCAGCCGCAGGGCCACGCGTTCGGCGGCGCGGCGCAGCCGTACCTCCCCGGCTCCGTTCCAATCAGCATCAGCTCCAACAGCAACAAAGAGTGCCTGGAAGAAAACAGTAAATATTACGCCCACGACGCGAGCTCCAAACAAGAGGAAAGATGCAGGCAGAGGCAATCTTTCGCAAATGACCCAACTATTACTCACGCAGCCAACTTAAAGCCCGCAAAGTATGACCACTCGAGCCTGCCGAGGAGCTTGCACGGCTCGGCCGCTCTTTTTGAAGTGAATTCCTGCACTTCCAGCCTAAAGGAGGACATCAAGAATTCGGTCAACTTGAACCTGACAGTTCAGCCCGCGGCAGTCCAGTCATGCCTCAGACCTTCAGTGCAGGATG
Seq A exon
GTATGCCTTAAATCTCTCGCTTTAGTCCGAGGCGACCTAGCGCTTCGTGCTTTCTAAGAGCTGCCTGTAATTGTTTGTACCCCTCCCTCCCCCCGTAACCCGTTCTGTTGGCGATAGCTTAACCCGACCGGGGGGGTGGATAAAATCGTGCTGTCAGACGTGCCGTGCCAGATTGTGCCGACCTAACGTTGCCCCTCTGCCTCGCGGCTTTGCGTGTGTCCTCCGTAACCCACAGCCGTGCCCCGCTAAATTATCGACGTGTTTGTTGTAG
Seq C2 exon
GTTTGCCTTGGTGCCCCACCCAGGGGAGATCGAGAAAGAAACGGAAACCGTACACAAAACAGCAAATCGCCGAATTGGAAAACGAGTTTCTCCTCAATGAGTTTATTAACCGACAGAAGAGGAAAGAACTATCAAACAGACTGAATTTAAGCGACCAGCAAGTGAAAATTTGGTTTCAGAACCGACGAATGAAAAAGAAAAGAGTGGTAATGCGCGAGCAGGCGCTCTCTATGTACTAGCGCGGCGCCCGCCCGTTCCCGCATGAACTTGCGTTCGCCCCGTAGAGTAGCGTGTGGTCGCGGCTGCGAGGCGGGAGCTGGGTGGGTTTTCCCCTTTAAGCCGAGCTCTCGGAACGCGTAGGATCCCCGCGTGCGTCGGCAACCGCTGAGCTCTTAGGCAGAGCGAAGAAGACGAGCCAGCCCAGCACTGAAACCCGTATTATCAGCTTTTCCCCCTTTCTTTCTCCTTTTATATAGATCTTCTCCCGCTTCTAACCCCCTCTTTCCCCGGAGAACGTGCGGCGCTAAACTAAAATCGATGCCTTTTAACTGTATGTAAACACCACTTTGCAGGAAAAAAAAAAAAAAAGAAAAAAAAAAGAATAAAAGAATAATGCCTAGTAAAGACGTCTGTAAATGCCGGCTGGTCCCTTCATGTGTTCCCCGCTTCTGAAGGCGAGCATGCGGCGCTCGCGTGTTTTGTGGTTTGGAATAACCTGTTGGAGCACAGATCGCACAAAGCGGTTACCAAATAAACCTTTTTAGTTTTCATTTGGTAGTTTTTTTCCCGGCCCCGCTCGCATCCACAGCCGCGGCCCGGCGGAGAGGGCACGTGACGCTCGCTCGAGGCCCGCGCGTAACCCGCGCACCGACTCCGCGCCCGCCGGCACCGCCGCTCCGCGCCCCGCGCTGCCGCCGCCCACCCCGACGGCTCTGCCCCGACGGCTGCGGCGGGACGGGAGGAGCGGAGCTCCGGGGGGTCGCCGCTCCCCGCGGGGCCGGGCCGACGTCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009274:ENSGALT00000015086:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.170 A=NA C2=0.241
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=71.2)
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:
GCGAGCTCCAAACAAGAGGAA
R:
CTTTCTCGATCTCCCCTGGGT
Band lengths:
297-568
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]