NCBI Citrus sinensis Annotation Release 100

The RefSeq genome records for Citrus sinensis were annotated by the NCBI Eukaryotic Genome Annotation Pipeline, an automated pipeline that annotates genes, transcripts and proteins on draft and finished genome assemblies. This report presents statistics on the annotation products, the input data used in the pipeline and intermediate alignment results.

The annotation products are available in the sequence databases and on the FTP site.

This report provides:

For more information on the annotation process, please visit the NCBI Eukaryotic Genome Annotation Pipeline page.

Annotation Release information

This annotation should be referred to as NCBI Citrus sinensis Annotation Release 100

Annotation release ID: 100
Date of Entrez queries for transcripts and proteins: Dec 20 2013
Date of submission of annotation to the public databases: Dec 27 2013
Software version: 5.2


The following assemblies were included in this annotation run:
Assembly nameAssembly accessionSubmitterAssembly dateReference/AlternateAssembly content
Csi_valencia_1.0GCF_000317415.1China sweet orange genome project12-12-2012Reference10 assembled chromosomes; unplaced scaffolds

Gene and feature statistics

Counts and length of annotated features are provided below for each assembly.

Feature counts

Genes and pseudogenes help25,066
  with > 5% ab initio help2,265
  known RefSeq (NM_) help0
  model RefSeq (XM_)31,305
  model RefSeq (XM_) with correction help63
Other RNAs help4,261
  with > 5% ab initio help0
  known RefSeq (NR_) help0
  model RefSeq (XR_) help3,873
  with > 5% ab initio help2,419
  known RefSeq (NP_) help0
  model RefSeq (XP_) help31,305
  model RefSeq (XP_) with correction help63

Detailed reports

Masking of genomic sequence

Transcript and protein alignments are performed on the repeat-masked genome. Below are the percentages of genomic sequence masked by WindowMasker and RepeatMasker for each assembly. RepeatMasker results are only used for organisms for which a comprehensive repeat library is available.

For this annotation run, transcripts and proteins were aligned to the genome masked with WindowMasker only.
Assembly nameAssembly accession% Masked with RepeatMasker% Masked with WindowMasker

Transcript and protein alignments

The annotation pipeline relies heavily on alignments of experimental evidence for gene prediction. Below are the sets of transcripts and proteins that were retrieved from Entrez, aligned to the genome by Splign or ProSplign and passed to Gnomon, NCBI's gene prediction software.

Depending on the other evidence available, long 454 reads (with average length above 250 nt) may be aligned as traditional evidence and reported in the Transcript alignments section or aligned with short reads and reported in the Short read transcript alignments section.

Transcript alignments

Short read transcript alignments

The following short reads (RNA-Seq) from the Short Read Archive were also used for gene prediction:

  Hide alignments statistics

Protein alignments


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