RefSeq GFF3 Files

The following files are gff3 for RefSeq genes. These are the files that have been loaded into HymenopteraMine and the JBrowse/Apollo browsers. The original gff3 were downloaded from the NCBI ftp site (species subdirectories within ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/invertebrate/). We parsed and reformatted the files to meet our requirements. Each original gff3 was divided into three files: protein coding, lncRNA, and other RNA. Pseudogenes are not included in these files. For species with full-length chromosome assemblies, the chromosome identifiers were changed to reflect the chromosome numbering system used by the communities (e.g. chromosome ids like "LG1" for Apis mellifera), as provided in the NCBI assembly report. The unassigned scaffold ids remain as RefSeq ids. All of the chromosome or scaffold ids in these files match the ids used in the genome assembly files.

 

Acromyrmex_echinatior_Aech_3.9_RefSeq_lncRNA.gff3

Acromyrmex_echinatior_Aech_3.9_RefSeq_other_rna.gff3

Acromyrmex_echinatior_Aech_3.9_RefSeq_proteincoding.gff3

Apis_cerana_ACSNU-2.0_RefSeq_other_rna.gff3

Apis_cerana_ACSNU-2.0_RefSeq_other_rna.gff3

Apis_cerana_ACSNU-2.0_RefSeq_proteincoding.gff3

Apis_dorsata_Apis_dorsata_1.3_RefSeq_lncRNA.gff3

Apis_dorsata_Apis_dorsata_1.3_RefSeq_other_rna.gff3

Apis_dorsata_Apis_dorsata_1.3_RefSeq_proteincoding.gff3

Apis_florea_Aflo_1.0_RefSeq_lncRNA.gff3

Apis_florea_Aflo_1.0_RefSeq_other_rna.gff3

Apis_florea_Aflo_1.0_RefSeq_proteincoding.gff3

Apis_mellifera_Amel_HAv3.1_RefSeq_lncRNA.gff3

Apis_mellifera_Amel_HAv3.1_RefSeq_other_rna.gff3

Apis_mellifera_Amel_HAv3.1_RefSeq_proteincoding.gff3

Athalia_rosae_Aros_2.0_RefSeq_lncRNA.gff3

Athalia_rosae_Aros_2.0_RefSeq_other_rna.gff3

Athalia_rosae_Aros_2.0_RefSeq_proteincoding.gff3

Atta_cephalotes_Attacep1.0_RefSeq_lncRNA.gff3

Atta_cephalotes_Attacep1.0_RefSeq_other_rna.gff3

Atta_cephalotes_Attacep1.0_RefSeq_proteincoding.gff3

Atta_colombica_Acol1.0_RefSeq_lncRNA.gff3

Atta_colombica_Acol1.0_RefSeq_other_rna.gff3

Atta_colombica_Acol1.0_RefSeq_proteincoding.gff3

Bombus_impatiens_BIMP_2.2_RefSeq_lncRNA.gff3

Bombus_impatiens_BIMP_2.2_RefSeq_other_rna.gff3

Bombus_impatiens_BIMP_2.2_RefSeq_proteincoding.gff3

Bombus_terrestris_Bter_1.0_RefSeq_lncRNA.gff3

Bombus_terrestris_Bter_1.0_RefSeq_other_rna.gff3

Bombus_terrestris_Bter_1.0_RefSeq_proteincoding.gff3

Camponotus_floridanus_Cflo_v7.5_RefSeq_lncRNA.gff3

Camponotus_floridanus_Cflo_v7.5_RefSeq_other_rna.gff3

Camponotus_floridanus_Cflo_v7.5_RefSeq_proteincoding.gff3

Cephus_cinctus_Ccin1_RefSeq_lncRNA.gff3

Cephus_cinctus_Ccin1_RefSeq_other_rna.gff3

Cephus_cinctus_Ccin1_RefSeq_proteincoding.gff3

Ceratina_calcarata_ASM165200v1_RefSeq_lncRNA.gff3

Ceratina_calcarata_ASM165200v1_RefSeq_other_rna.gff3

Ceratina_calcarata_ASM165200v1_RefSeq_proteincoding.gff3

Ceratosolen_solmsi_CerSol_1.0_RefSeq_lncRNA.gff3

Ceratosolen_solmsi_CerSol_1.0_RefSeq_other_rna.gff3

Ceratosolen_solmsi_CerSol_1.0_RefSeq_proteincoding.gff3

Copidosoma_floridanum_Cflo_2.0_RefSeq_lncRNA.gff3

Copidosoma_floridanum_Cflo_2.0_RefSeq_other_rna.gff3

Copidosoma_floridanum_Cflo_2.0_RefSeq_proteincoding.gff3

Cyphomyrmex_costatus_Ccosl1.0_RefSeq_lncRNA.gff3

Cyphomyrmex_costatus_Ccosl1.0_RefSeq_other_rna.gff3

Cyphomyrmex_costatus_Ccosl1.0_RefSeq_proteincoding.gff3

Diachasma_alloeum_Dall1.0_RefSeq_lncRNA.gff3

Diachasma_alloeum_Dall1.0_RefSeq_other_rna.gff3

Diachasma_alloeum_Dall1.0_RefSeq_proteincoding.gff3

Dinoponera_quadriceps_ASM131382v1_RefSeq_lncRNA.gff3

Dinoponera_quadriceps_ASM131382v1_RefSeq_other_rna.gff3

Dinoponera_quadriceps_ASM131382v1_RefSeq_proteincoding.gff3

Dufourea_novaeangliae_ASM127255v1_RefSeq_lncRNA.gff3

Dufourea_novaeangliae_ASM127255v1_RefSeq_other_rna.gff3

Dufourea_novaeangliae_ASM127255v1_RefSeq_proteincoding.gff3

Eufriesea_mexicana_ASM148370v1_RefSeq_lncRNA.gff3

Eufriesea_mexicana_ASM148370v1_RefSeq_other_rna.gff3

Eufriesea_mexicana_ASM148370v1_RefSeq_proteincoding.gff3

Fopius_arisanus_ASM80636v1_RefSeq_lncRNA.gff3

Fopius_arisanus_ASM80636v1_RefSeq_other_rna.gff3

Fopius_arisanus_ASM80636v1_RefSeq_proteincoding.gff3

Habropoda_laboriosa_ASM126327v1_RefSeq_lncRNA.gff3

Habropoda_laboriosa_ASM126327v1_RefSeq_other_rna.gff3

Habropoda_laboriosa_ASM126327v1_RefSeq_proteincoding.gff3

Harpegnathos_saltator_Hsal_v8.5_RefSeq_lncRNA.gff3

Harpegnathos_saltator_Hsal_v8.5_RefSeq_other_rna.gff3

Harpegnathos_saltator_Hsal_v8.5_RefSeq_proteincoding.gff3

Linepithema_humile_Lhum_UMD_V04_RefSeq_lncRNA.gff3

Linepithema_humile_Lhum_UMD_V04_RefSeq_other_rna.gff3

Linepithema_humile_Lhum_UMD_V04_RefSeq_proteincoding.gff3

Megachile_rotundata_MROT_1.0_RefSeq_lncRNA.gff3

Megachile_rotundata_MROT_1.0_RefSeq_other_rna.gff3

Megachile_rotundata_MROT_1.0_RefSeq_proteincoding.gff3

Microplitis_demolitor_Mdem2_RefSeq_lncRNA.gff3

Microplitis_demolitor_Mdem2_RefSeq_other_rna.gff3

Microplitis_demolitor_Mdem2_RefSeq_proteincoding.gff3

Monomorium_pharaonis_ASM326058v2_RefSeq_lncRNA.gff3

Monomorium_pharaonis_ASM326058v2_RefSeq_other_rna.gff3

Monomorium_pharaonis_ASM326058v2_RefSeq_proteincoding.gff3

Nasonia_vitripennis_Nvit_2.1_RefSeq_lncRNA.gff3

Nasonia_vitripennis_Nvit_2.1_RefSeq_other_rna.gff3

Nasonia_vitripennis_Nvit_2.1_RefSeq_proteincoding.gff3

Neodiprion_lecontei_Nlec1.0_RefSeq_lncRNA.gff3

Neodiprion_lecontei_Nlec1.0_RefSeq_other_rna.gff3

Neodiprion_lecontei_Nlec1.0_RefSeq_proteincoding.gff3

Ooceraea_biroi_Obir_v5.4_RefSeq_lncRNA.gff3

Ooceraea_biroi_Obir_v5.4_RefSeq_other_rna.gff3

Ooceraea_biroi_Obir_v5.4_RefSeq_proteincoding.gff3

Orussus_abietinus_Oabi_2.0_RefSeq_lncRNA.gff3

Orussus_abietinus_Oabi_2.0_RefSeq_other_rna.gff3

Orussus_abietinus_Oabi_2.0_RefSeq_proteincoding.gff3

Pogonomyrmex_barbatus_Pbar_UMD_V03_RefSeq_lncRNA.gff3

Pogonomyrmex_barbatus_Pbar_UMD_V03_RefSeq_other_rna.gff3

Pogonomyrmex_barbatus_Pbar_UMD_V03_RefSeq_proteincoding.gff3

Polistes_canadensis_ASM131383v1_RefSeq_lncRNA.gff3

Polistes_canadensis_ASM131383v1_RefSeq_other_rna.gff3

Polistes_canadensis_ASM131383v1_RefSeq_proteincoding.gff3

Polistes_dominula_Pdom_r1.2_RefSeq_lncRNA.gff3

Polistes_dominula_Pdom_r1.2_RefSeq_other_rna.gff3

Polistes_dominula_Pdom_r1.2_RefSeq_proteincoding.gff3

Pseudomyrmex_gracilis_ASM200609v1_RefSeq_lncRNA.gff3

Pseudomyrmex_gracilis_ASM200609v1_RefSeq_other_rna.gff3

Pseudomyrmex_gracilis_ASM200609v1_RefSeq_proteincoding.gff3

Solenopsis_invicta_Si_gnH_RefSeq_lncRNA.gff3

Solenopsis_invicta_Si_gnH_RefSeq_other_rna.gff3

Solenopsis_invicta_Si_gnH_RefSeq_proteincoding.gff3

Temnothorax_curvispinosus_ASM307098v1_RefSeq_lncRNA.gff3

Temnothorax_curvispinosus_ASM307098v1_RefSeq_other_rna.gff3

Temnothorax_curvispinosus_ASM307098v1_RefSeq_proteincoding.gff3

Trachymyrmex_cornetzi_Tcor1.0_RefSeq_lncRNA.gff3

Trachymyrmex_cornetzi_Tcor1.0_RefSeq_other_rna.gff3

Trachymyrmex_cornetzi_Tcor1.0_RefSeq_proteincoding.gff3

Trachymyrmex_septentrionalis_Tsep1.0_RefSeq_lncRNA.gff3

Trachymyrmex_septentrionalis_Tsep1.0_RefSeq_other_rna.gff3

Trachymyrmex_septentrionalis_Tsep1.0_RefSeq_proteincoding.gff3

Trachymyrmex_zeteki_Tzet1.0_RefSeq_lncRNA.gff3

Trachymyrmex_zeteki_Tzet1.0_RefSeq_other_rna.gff3

Trachymyrmex_zeteki_Tzet1.0_RefSeq_proteincoding.gff3

Trichogramma_pretiosum_Tpre_2.0_RefSeq_lncRNA.gff3

Trichogramma_pretiosum_Tpre_2.0_RefSeq_other_rna.gff3

Trichogramma_pretiosum_Tpre_2.0_RefSeq_proteincoding.gff3

Vollenhovia_emeryi_V.emery_V1.0_RefSeq_lncRNA.gff3

Vollenhovia_emeryi_V.emery_V1.0_RefSeq_other_rna.gff3

Vollenhovia_emeryi_V.emery_V1.0_RefSeq_proteincoding.gff3

Wasmannia_auropunctata_wasmannia.A_1.0_RefSeq_lncRNA.gff3

Wasmannia_auropunctata_wasmannia.A_1.0_RefSeq_other_rna.gff3

Wasmannia_auropunctata_wasmannia.A_1.0_RefSeq_proteincoding.gff3