GgaINT0102492 @ galGal4
Intron Retention
Gene
ENSGALG00000011053 | HOXA2
Description
Homeobox protein Hox-A2 [Source:UniProtKB/Swiss-Prot;Acc:Q08727]
Coordinates
chr2:32797562-32799404:-
Coord C1 exon
chr2:32798934-32799404
Coord A exon
chr2:32798334-32798933
Coord C2 exon
chr2:32797562-32798333
Length
600 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
CTCTTTTTCTTTTTTAACAGACC
3' ss Score
11.27
Exon sequences
Seq C1 exon
CCTCTCTCTCCTTTTTCCCGGGCCTTCCCCCCCCGAGCCCCCGGCATCCGAGGGAACTTTTTCTCCGCGGGGGCTGCGAGTTGAAGGCCATGAATTTCGAATTCGAGCGAGAGATCGGTTTTATCAATAGTCAGCCATCGCTTGCTGAGTGCCTGACATCTTTTCCCCCTGTCGGTGATACATTTCAAAGTTCATCAATCAAGAACTCGACGCTTTCACACTCGACACTGATTCCTCCTCCTTTCGAGCAGACCATCCCCAGCCTGAACCCCGGCGGCCACCCTCGCCACAGCGGCGGCGGCCGCCCCAAGGCGAGCCCCCGCGCCCGCAGCGGCAGCCCGGGCCCCGCCGGCGCCCCGCCGCCCCCGGAGTACCCCTGGATGAAAGAGAAAAAGGCGTCCAAGCGATCCTCGCTGCCGCCCGCCTCGGCCTCCGCCTCAGCCGCCGGACCCGCCTGCCTCAGCCACAAAG
Seq A exon
GTCAGTCCCGGGGCTCGCCGCCCCCCGGCCGCCCGCAGCCCCCGCTCGGACGGGGCTCCGCGCGGAGCCCAACTTTCCCGAGTCGCCCCAACGCGGGATGATTTATTTGAGTTGGAGCTGACCTCTCTTGTCTCGCTGTCCTAGAGCCGGGCTATTTGACAGTAATGAAGAGTGATAGATTGCTCCCGCTCAGCTCGGCGGCTGATGCATTAATTATCAATCGCGCGATGGCCGATATAAAGTTGGCCGCGGCGTGGGGAGGGCGCGGAGCGGGGGGCGCGGGGCGCGCCGAGGGGCCGGGGGGCTCCGGGCGCCGCACAATGGGGTCCCGCGGCCGAGGGCGGCCATTTTGTTGCAGTCGCTATTTTACGCCGCGAGGACATATAGATAGAGAGGCGCTTCCGCGGGGAAGGAGAGGGAGAAGCGCTGCCCCCCCTTCCAGCCCGGGCCGCGAGGGGCTCGGGGGGCCGCGGCGCCGTCCGCGCTTTCCCCCGACGTGCGCGGGGCTCCGCTTCGCCTCCGCTCTTCGCTGCGCTCCGGGGCGCGCGTGCGTGCGGTGGTGGTGGCGGTGGTTCGCCTTCTCTTTTTCTTTTTTAACAG
Seq C2 exon
ACCCCCTTGAAATCCCCGATAGTGGCAGCGGTGGATCTAGGCGGCTGAGGACGGCCTACACCAACACGCAGCTCTTGGAGCTGGAGAAAGAATTCCACTTCAACAAGTACCTCTGCAGACCGCGCCGGGTCGAGATCGCAGCGCTGCTGGATCTGACCGAGAGGCAAGTGAAGGTCTGGTTCCAGAACCGCAGGATGAAGCACAAGAGGCAGACCCAGTGCAAGGAGAACCAGAACGGCGAGGGGAAATTTAAGGGCTCGGAGGACCCCGAGAAGGCGGCGGAGGACGACGAGGAGGAGAAAGCCCTCTTCGAGCAAGCCCTGGGCACCGTCTCGGGAGCGCTGCTGGAGAGGGAGGGCTACGCGTTTCAGCAGAATGCGCTCTCGCAGCAGCAGGCGCAGAATGCGCACAATGGCGAATCCCAAAGTTTCCCCGTTTCGCCTTTAACGAGCAATGAGAAAAATCTGAAACATTTTCAACACCAGTCACCCACTGTTCAAAACTGCCTCTCAACAATGGCCCAGAACTGCGCAGCTGGCCTCAACAATGACAGTCCTGAGGCCCTCGAGGTCCCCTCTTTACAGGACTTTAACGTTTTCTCCACAGATTCCTGCCTGCAGCTTTCAGACGCGGTTTCCCCCAGTTTGCCGGGCTCTCTGGACAGCCCCGTAGATATCTCCGCTGACAGCTTTGACTTTTTTACAGACACGCTCACCACGATTGACTTACAGCATCTGAATTACTGAGAAATTAAAGACGTCCTCTCCCAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011053:ENSGALT00000043590:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.859 A=NA C2=0.476
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=22.9)
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:
GCCTGACATCTTTTCCCCCTG
R:
GCTGCCACTATCGGGGATTTC
Band lengths:
350-950
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]