The nucleic acid data:
IRESite Id: 622 Version: 1
Originaly submitted by: Martin Mokrejš Submission date: 2009-08-29 20:37:43
Reviewed by: Martin Mokrejš Last change: 2009-08-29 23:16:26
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  end-to-end_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  HoCV-1
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
84316420
The mRNA/+RNA description: 
Homalodisca coagulata virus-1, complete genome.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  unknown
The organism containing this mRNA with IRES segment in its genome:
Homalodisca coagulata virus-1
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
The total number of notable open-reading frames (ORFs):
  2
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
NS
The description of the protein encoded in this ORF:
non-structural polyprotein
The translational frameshift (ribosome slippage) involved:
  0
The ribosome read-through involved:
  no
The alternative forms of this protein occur by the alternative initiation of translation:
  not tested
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  420-5807
ORF
ORF position:   2
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
CP
The description of the protein encoded in this ORF:
capsid protein
The translational frameshift (ribosome slippage) involved:
  0
The ribosome read-through involved:
  no
The alternative forms of this protein occur by the alternative initiation of translation:
  not tested
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  5990-8740
Citations:
Hunnicutt LE, Hunter WB, Cave RD, Powell CA, Mozoruk JJ (2006) Genome sequence and molecular characterization of Homalodisca coagulata virus-1, a novel virus discovered in the glassy-winged sharpshooter (Hemiptera: Cicadellidae). Virology. 350(1):67-78
Hunter WB, Katsar CS, Chaparro JX (2006) Molecular analysis of capsid protein of Homalodisca coagulata Virus-1, a new leafhopper-infecting virus from the glassy-winged sharpshooter, Homalodisca coagulata. J. Insect Sci. 6:1-10
IRESs:
IRES:
Version: 1 Last change: 2009-08-29 21:28:20
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  HoCV1_IGRpred
Warning: please make ires_name same as the gene_name and optionally append to it coordinates. E.g. when gene/virus name is EMCV-R use EMCV-R_-222_to_-1 or EMCV-R_1-456, etc. but not Emcv-R-... or EMCV-222_to_-1. Please keep case of letters as well. This rewards when searching through the database.
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  5802-5989
Conclusion:
  putative_IRES
How IRES boundaries were determined:
guessed
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
The IRES was NOT characterized experimentally. The presumed IRES region was taken over from Nakashima and
Uchiumi (2009) from Table 1.
Citations:
Nakashima N, Uchiumi T (2009) Functional analysis of structural motifs in dicistroviruses. Virus Res. 2(139):137-147
Last change to the database: 2015-04-16 16:45:23 GMT+1