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Welcome to the Cabbage Looper Database

Cababge looper genome and annotation

About the Cabbage Looper Database

This database provides access to the cabbage looper (Trichoplusia ni) genome assembly and annotation. Github All Releases

Genome assemblies

The latest cabbage looper genome assembly (tn1) contains 1,031 scaffolds spanning 368.2 Mb. The scaffold N50 is 14.2 Mb, with >90% of the bases in 28 chromosome-length scaffolds. Contig N50 is 621.9 kb.

Scaffolds and Contigs

Annotation resource

The latest official gene set (OGS v1.0) is based on the tn1 genome assemnbly and contains 14,034 protein-coding genes.

OGS v1.0 GFF

OGS v1.0 gene annotation

OGS v1.0 transcripts

OGS v1.0 peptides

RepeatMasker output

Repeat Consensus sequences

Genomic variants called using sequencing data from Hi5 cells

piRNA clusters

piRNA clusters

Visualization

UCSC genome browser

If you prefer loading the track hub yourself, it is available here

BLAST

Search T. ni nucleotides using a nucleotide query: blastn

Search translated T. ni nucleotides using a protein query: tblastn

Search translated T. ni nucleotides using a translated nucleotide query: tblastx

Raw data

This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession NKQN00000000. Sequencing data are available through the NCBI Sequence Read Archive under the accession number PRJNA336361.

Figure source data

NCBI

Ensembl

SilkDB

KAIKObase

DBM-DB

FlyBase

VectorBase

Citation

Fu, Y., Yang, Y., Zhang, H., Farley, G., Wang, J., Quarles, K.A., Weng, Z., and Zamore, P.D. (2018). The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology. ELife Sciences 7, e31628. 10.7554/eLife.31628

Contact us

Trichoplusia ni (Trichoplusia.ni {at} gmail.com)

Yu Fu (Yu.Fu {at} umassmed.edu)