Replaces accession AI629892
Strong BLASTx hits with sequences annotated as polyprotein.
BLASTn of repeat database at MAGI produced the following highetst hits:
ZRSiTERTOOT0306 tekay_af448416-1 tekay_af448416-1 af448416 bases... 835 0.0
ZRSiTERT0020050 gi|3420038|gb|AF050455.1|AF050455 Zea mays gypsy... 624 e-179
ZRSiTERTOOT0305 tekay_438D03-1part tekay_Z438D03-1part Z438D03 b... 367 e-101
Running sequence through repeatmasker at MAGI web site produced the following:
Repeats>DV942864 1000136-E04.T7-1 UGI-Reseq Zea mays cDNA, mRNA sequence. (725 bp masked -- 94.40% masked)
CCCGAAATTCATTTTTAAGAACTCTAAAAATTATAAGAAAATTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
Interpro scan supported blastx:
noIPR
unintegrated
|
unintegrated
|
|
PANTHER
|
PTHR10178
|
GAG/POL/ENV POLYPROTEIN
|
6.1e-56 [6-144]T
|
|
PANTHER
|
PTHR10178:SF14
|
RETROVIRUS POLYPROTEIN
|
6.1e-56 [6-144]T
|
|
SUPERFAMILY
|
SSF54160
|
Chromo domain-like
|
2.3e-05 [88-146]T
|
Parent no parent Children no children Found in no entries Contains no entries GO terms none
| Family: |
GAG/POL/ENV POLYPROTEIN (PTHR10178) |
| Subfamilies: |
24 |
| PANTHER Links: |
|
| Abstract: |
The retroviral genome is characterized by the presence of three canonical genes, gag, pol, and env. The products of these genes are synthesized as a single precursor gag-pol-env that is proteolytically processed into individual protein components. The gag gene encodes the major structural proteins that make up the viral capsid; pol encodes enzymatic proteins including protease (PR), reverse transcriptase (RT), and integrase (IN); and env encodes surface proteins that make up the viral envelope [PMID:12873766][PMID:12908769]. Members of this subfamily are homologous to the gag-pol polyprotein and are found in the genomes of plants and fungi.
|
| PANTHER Molecular Function: |
 Molecular function unclassified
|
| PANTHER Biological Process: |
Biological process unclassified
|
| Pathway Categories: |
No pathway information available |
| Training Sequences: |
1066
|
| HMM Length |
1112 |
| Downloads: |
HMM (HMMER format) |
Related Literature:
Vol. 110, No. 1-4, 2005
Free Abstract Article (Fulltext) Article (PDF 168 KB)
Retrotransposable Elements and Genome Evolution
Editor: Jean-Nicolas Volff, Würzburg
Retrotransposable Elements, Chromosomes and Chromatin
A comparative study of retrotransposons in the centromeric regions of A and B chromosomes of maize
J. Theuria, T. Phelps-Durra,b, S. Mathewsa,c, J. Birchlera
Division of Biological Sciences, University of Missouri, Columbia, MO (USA)
Address of Corresponding Author
Cytogenetic and Genome Research 2005;110:203-208 (DOI: 10.1159/000084953)
Abstract.
Bacterial Artificial Chromosomes (BACs) derived from the B chromosome, based
on homology with the B specific sequence, were subcloned and sequenced.
Analysis of DNA sequence data indicated the presence of 23 common retroelements,
as well as novel sequences of B chromosome origin. Generally, where the same
retrotransposon type was observed in both A and B chromosomes, there were
more copies per unit of sequence in the B centromeric region (the major
site of B repeat) than in the A centromere, except for Huck-1. Based on
previous estimates of the age of the major burst of transposition into
the maize genome, the oldest retrotransposons (Ji-6 and Tekay, ~5.0 and
5.2 million years ago, respectively) were found in the B centromere region
only, while the next two oldest (Huck-1 and Opie-1) were found in both the
A and B sequences. Phylogenetic analysis of Opie retroelements from both A
and B centromeres indicated that some of the B Opie centromeric sequences
share a more recent common ancestor with A Opie retroelements than they do
with other B Opie centromeric sequences. These results imply that the supernumerary
maize B chromosome has coexisted with the A chromosomes during that period of
transposition. They also support the hypothesis that the B chromosome had its origins
from A chromosome elements, or that alternative origins, such as being donated to the
maize genome in a wide species cross, preceded six million years ago, because the
spectrum of retrotransposons in the two chromosomes is quite similar.
Copyright © 2005 S. Karger AG, Basel
