Genome Browser


Browse the Mnemiopsis genome assembly, protein models, RNA-seq data, and public EST and mRNA sequences using the JBrowse genome viewer.


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The genome browser is searchable using a Mnemiopsis scaffold or gene identifier, a GenBank mRNA or EST identifier, or a Pfam-A domain name (e.g., ML0001, ML00011a, MLRB00011, AF293700.1, AF293700, FC475136.1, FC475136, Glyco hydro 20).

          


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The following tracks are currently available for viewing:
Embryonic 00-20 h
Aligned RNA-seq data from time-course (0-20 hours) developmental gene expression studies (GSE60478; GSE111748).
HISAT2
RNA-seq data (SRR1971491) derived from Mnemiopsis embryos aligned using HISAT2.
CL2
RNA-seq reads derived from Mnemiopsis embryos (between 15 and 30 hours post-fertilization) assembled into transcripts using Cufflinks.
StringTie
Aligned RNA-seq reads (from HISAT2 above) assembled into transcripts using StringTie.
TRN15-30hpf
RNA-seq reads derived from Mnemiopsis embryos (between 15 and 30 hours post-fertilization) assembled into transcripts using Trinity.
RACE
Experimentally-verified Mnemiopsis RACE (Rapid Amplification of cDNA Ends) transcripts.
EST
Publicly available Mnemiopsis ESTs from Genbank.
GBNT
Publicly available Mnemiopsis mRNAs and other non-EST sequences (e.g., rRNA, ncRNA) from Genbank.
2.2
Consensus Mnemiopsis gene models.
2.2UF
Unincorporated Mnemiopsis gene models.
PFAM2.2
Non-redundant Mnemiopsis protein domains derived from PFAM HMMscans using the 2.2 and 2.2UF datasets and the six-frame translations of the Mnemiopsis genome.
MASK
Genomic regions that have been repeat-masked using VMatch are highlighted in light blue.
SCF
Assembled genomic scaffolds (SCF) appear as solid black tracks, with intermittent gaps shaded bright pink.