Genome Browser

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

Search

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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Browse

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.