XENLA Annotation

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Summary

UTA annotation

Gene annotation mainly based on de novo assembled transcripts (from RNA-seq), ESTs and cDNA sequences.

JGI annotation

History of JGIv18 (July, 2016 version)

  1. Originally it was released by Adam Session/Daniel Rokhsar group (Berkeley), together with JGIv9 genome.
  2. With manual curation (mainly from Japanese group led by Atsushi Suzuki/Masanori Taira, Taejoon Kwon revised this twice (JGIv18pV2 and JGIv18pV3).
  3. In a mean time, XenBase revised this annotation twice.

JGI annotation from Taejoon

XENLA_JGIv60p_cds.fa.gz           >XeXenL6RMv10036376m
XENLA_JGIv610p_cds.fa.gz          >JGIv610_0000001
XENLA_JGIv10p_cds.fa.gz           >JGIv10_10020581
XENLA_JGIv14p_cds.fa.gz           >JGIv14_28700620
XENLA_JGIv15p_cdna.fa.gz          >JGIv15_15055292
XENLA_JGIv16pa_cdna.fa.gz         >JGIv16_16066762
XENLA_JGIv16p_cdna_annot.fa.gz    >Xetro.D01015.S|hs=CDHR5|Xelaev16061684m
XENLA_JGIv16pV4_cdna_annot.fa.gz  >Xetro.D01015.S|hs=CDHR5|Xelaev16061684m
XENLA_JGIv17p_cdna_annot.fa.gz    >unnamed|Xelaev17004902m
XENLA_JGIv18p_cdna_final.fa.gz    >unnamed|Xelaev18002747m
XENLA_JGIv18pV2_cdna_final.fa.gz  >unnamed|Xelaev18002747m
XENLA_JGIv18pV3_cdna_final.fa.gz  >42Sp43.L|Xelaev18043180m

JGI annotation available at XenBase

Xla_L6RMV10_cds.fa.gz                     ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla6.0/
LAEVIS_6.1.longestCDS.fa.gz               ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla6.1/
XlaevisJGIv1.3.longest.CDS.fa.gz          ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla7.0/
XlaevisJGIv1.5.primaryTrs.fa.gz           ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla7.1/
Xlaevisv1.6.primaryTrs.fa.gz              ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla7.2/
Xla_8.0.primaryTrs.Named.fa.gz            ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla8.0/
Xlaevisv1.8.Named.primaryTrs.fa.gz        ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.1/
XL9.1_annot_v1.8.1.primaryTrs.fa.gz       ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.1/
XL9.1_v3.transcripts.primary.mRNA.fa.gz   ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.1/1.8.3.1/
  • Sequence header format
Xla_L6RMV10_cds.fa.gz                     >27051543
LAEVIS_6.1.longestCDS.fa.gz               >Xelaev12035491m
XlaevisJGIv1.3.longest.CDS.fa.gz          >28269546
XlaevisJGIv1.5.primaryTrs.fa.gz           >Xelaev15055292m
Xlaevisv1.6.primaryTrs.fa.gz              >Xelaev16061684m locus=Xelaev16061684m.g annot-version=v1.6
Xla_8.0.primaryTrs.Named.fa.gz            >Xelaev17004902m
Xlaevisv1.8.Named.primaryTrs.fa.gz        >Xelaev18000268m
XL9.1_annot_v1.8.1.primaryTrs.fa.gz       >Xelaev18000268m
XL9.1_v3.transcripts.primary.mRNA.fa.gz   >Xelaev18005893m.g