Intro

As part of transcriptome annotation (GitHub issue) for DuMOAR (GitHub repo), I’ve already run TransDecoder ( run on 20231107), as well as DIAMOND BLASTx (run earlier today). The final part of getting the transcriptome annotated was to run Trinotate. Trinotate uses a combination of tools to generate a pretty thorough annotation of transcriptomes. This was run on Mox.

SLURM script

20231109-mmag-trinotate-transcriptome.sh (GitHub)

#!/bin/bash
## Job Name
#SBATCH --job-name=20231109-mmag-trinotate-transcriptome
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=4-00:00:00
## Memory per node
#SBATCH --mem=120G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20231109-mmag-trinotate-transcriptome


# Script to run Trinotate on M.magister transcriptome.


###################################################################################
# These variables need to be set by user

# Input files
## BLASTx
blastx_out="/gscratch/scrubbed/samwhite/outputs/20231109-mmag-transcriptome-diamond-blastx/trinity_denovo.Trinity.blastx.outfmt6"

## TransDecoder
transdecoder_dir="/gscratch/scrubbed/samwhite/outputs/20231107-mmag-transdecoder-transcriptome"
blastp_out="${transdecoder_dir}/blastp_out/blastp.outfmt6"
pfam_out="${transdecoder_dir}/pfam_out/pfam.domtblout"
lORFs_pep="${transdecoder_dir}/trinity_denovo.Trinity.fasta.transdecoder_dir/longest_orfs.pep"

## Transcriptomics
transcriptomes_dir="/gscratch/srlab/sam/data/M_magister/transcriptomes"
trinity_fasta="${transcriptomes_dir}/trinity_denovo.Trinity.fasta"
trinity_gene_map="${transcriptomes_dir}/trinity_denovo.Trinity.fasta.gene_trans_map"

###################################################################################

# Exit script if any command fails
set -e

# Load Python Mox module for Python module availability

module load intel-python3_2017

# SegFault fix?
export THREADS_DAEMON_MODEL=1


wd="$(pwd)"
timestamp=$(date +%Y%m%d)


## Paths to input/output files

## New folders for working directory
rnammer_out_dir="${wd}/RNAmmer_out"
signalp_out_dir="${wd}/signalp_out"
tmhmm_out_dir="${wd}/tmhmm_out"


rnammer_prefix=${trinity_fasta##*/}
prefix="${timestamp}.${rnammer_prefix}.trinotate"

# Output files
rnammer_out="${rnammer_out_dir}/${rnammer_prefix}.rnammer.gff"
signalp_out="${signalp_out_dir}/${prefix}.signalp.out"
tmhmm_out="${tmhmm_out_dir}/${prefix}.tmhmm.out"
trinotate_report="${wd}/${prefix}_annotation_report.txt"

# Paths to programs
rnammer_dir="/gscratch/srlab/programs/RNAMMER-1.2"
rnammer="${rnammer_dir}/rnammer"
signalp_dir="/gscratch/srlab/programs/signalp-4.1"
signalp="${signalp_dir}/signalp"
tmhmm_dir="/gscratch/srlab/programs/tmhmm-2.0c/bin"
tmhmm="${tmhmm_dir}/tmhmm"
trinotate_dir="/gscratch/srlab/programs/Trinotate-v3.1.1"
trinotate="${trinotate_dir}/Trinotate"
trinotate_rnammer="${trinotate_dir}/util/rnammer_support/RnammerTranscriptome.pl"
trinotate_GO="${trinotate_dir}/util/extract_GO_assignments_from_Trinotate_xls.pl"
trinotate_features="${trinotate_dir}/util/Trinotate_get_feature_name_encoding_attributes.pl"
trinotate_sqlite_db="Trinotate.sqlite"

# Generate FastA checksum, for reference if needed.
md5sum ${trinity_fasta} > fasta.checksum.md5

# Make output directories
mkdir "${rnammer_out_dir}" "${signalp_out_dir}" "${tmhmm_out_dir}"

# Copy sqlite database template

cp ${trinotate_dir}/admin/Trinotate.sqlite .

# Run signalp
${signalp} \
-f short \
-n "${signalp_out}" \
${lORFs_pep}

# Run tmHMM
${tmhmm} \
--short \
< ${lORFs_pep} \
> "${tmhmm_out}"

# Run RNAmmer
# Has "||" operator due to previous lack of matches
# Need "||" to continue with annotation.
cd "${rnammer_out_dir}" || exit
${trinotate_rnammer} \
--transcriptome ${trinity_fasta} \
--path_to_rnammer ${rnammer}

cd "${wd}" || exit

# Run Trinotate
## Load transcripts and coding regions into database
${trinotate} \
${trinotate_sqlite_db} \
init \
--gene_trans_map "${trinity_gene_map}" \
--transcript_fasta "${trinity_fasta}" \
--transdecoder_pep "${lORFs_pep}"

## Load BLAST homologies
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_swissprot_blastp \
"${blastp_out}"

"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_swissprot_blastx \
"${blastx_out}"

## Load Pfam
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_pfam \
"${pfam_out}"

## Load transmembrane domains
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_tmhmm \
"${tmhmm_out}"

## Load signal peptides
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_signalp \
"${signalp_out}"

## Load RNAmmer
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_rnammer \
"${rnammer_out}"

## Creat annotation report
"${trinotate}" \
"${trinotate_sqlite_db}" \
report \
> "${trinotate_report}"

# Extract GO terms from annotation report
"${trinotate_GO}" \
--Trinotate_xls "${trinotate_report}" \
-G \
--include_ancestral_terms \
> "${prefix}".go_annotations.txt

# Make transcript features annotation map
"${trinotate_features}" \
"${trinotate_report}" \
> "${prefix}".annotation_feature_map.txt

####################################################################

# Capture program options
if [[ "${#programs_array[@]}" -gt 0 ]]; then
  echo "Logging program options..."
  for program in "${!programs_array[@]}"
  do
    {
    echo "Program options for ${program}: "
    echo ""
    # Handle samtools help menus
    if [[ "${program}" == "samtools_index" ]] \
    || [[ "${program}" == "samtools_sort" ]] \
    || [[ "${program}" == "samtools_view" ]]
    then
      ${programs_array[$program]}

    # Handle DIAMOND BLAST menu
    elif [[ "${program}" == "diamond" ]]; then
      ${programs_array[$program]} help

    # Handle NCBI BLASTx menu
    elif [[ "${program}" == "blastx" ]]; then
      ${programs_array[$program]} -help

    # Handle StringTie prepDE script
    elif [[ "${program}" == "prepDE" ]]; then
      python3 ${programs_array[$program]} -h
    fi
    ${programs_array[$program]} -h
    echo ""
    echo ""
    echo "----------------------------------------------"
    echo ""
    echo ""
  } &>> program_options.log || true

    # If MultiQC is in programs_array, copy the config file to this directory.
    if [[ "${program}" == "multiqc" ]]; then
      cp --preserve ~/.multiqc_config.yaml multiqc_config.yaml
    fi
  done
  echo "Finished logging programs options."
  echo ""
fi


# Document programs in PATH (primarily for program version ID)
echo "Logging system $PATH..."
{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log
echo "Finished logging system $PATH."

/———-

RESULTS

Runtime

Runtime was just under 3.5hrs:

Files

Output directory:

20231109-mmag-trinotate-transcriptome/

Annotation Feature Map

Annotation feature map (10MB; TXT):

20231109.trinity_denovo.Trinity.fasta.trinotate.annotation_feature_map.txt
- This can be used to update Trinity-based gene expression matrices like so:
  - ${TRINITY_HOME}/Analysis/DifferentialExpression/rename_matrix_feature_identifiers.pl Trinity_trans.counts.matrix annot_feature_map.txt > Trinity_trans.counts.wAnnot.matrix

Gene Ontology (GO) Annotations

Gene ontology (GO) annotations (26MB; TXT):

20231109.trinity_denovo.Trinity.fasta.trinotate.go_annotations.txt

Code

library(kableExtra)
library(dplyr)

# Read in data frame
go.annotations.df <- read.csv("https://gannet.fish.washington.edu/Atumefaciens/20231109-mmag-trinotate-transcriptome/20231109.trinity_denovo.Trinity.fasta.trinotate.go_annotations.txt",
header = FALSE,
sep = "\t")

# Provide column names
names(go.annotations.df)[1] <- "Gene.ID"
names(go.annotations.df)[2] <- "GO.IDs"

# Create nice HTML table
knitr::kable(head(go.annotations.df))

Table 1: Gene Ontology annotations

Gene.ID	GO.IDs
TRINITY_DN0_c7_g1	GO:0000166,GO:0001678,GO:0001882,GO:0001883,GO:0003674,GO:0003824,GO:0004611,GO:0004613,GO:0005488,GO:0005525,GO:0005575,GO:0005739,GO:0005759,GO:0005829,GO:0005975,GO:0005996,GO:0006006,GO:0006066,GO:0006071,GO:0006082,GO:0006090,GO:0006094,GO:0006114,GO:0006629,GO:0006631,GO:0006950,GO:0008150,GO:0008152,GO:0009056,GO:0009058,GO:0009062,GO:0009605,GO:0009719,GO:0009725,GO:0009743,GO:0009746,GO:0009749,GO:0009987,GO:0009991,GO:0010033,GO:0010243,GO:0014070,GO:0016042,GO:0016051,GO:0016054,GO:0016829,GO:0016830,GO:0016831,GO:0017076,GO:0019001,GO:0019318,GO:0019319,GO:0019400,GO:0019401,GO:0019541,GO:0019543,GO:0019626,GO:0019725,GO:0019751,GO:0019752,GO:0030145,GO:0030154,GO:0030855,GO:0031667,GO:0031960,GO:0031974,GO:0032502,GO:0032549,GO:0032550,GO:0032553,GO:0032555,GO:0032561,GO:0032787,GO:0032868,GO:0032869,GO:0032870,GO:0033500,GO:0033993,GO:0034284,GO:0034637,GO:0035639,GO:0036094,GO:0042221,GO:0042592,GO:0042593,GO:0042594,GO:0043167,GO:0043168,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0043233,GO:0043434,GO:0043436,GO:0044237,GO:0044238,GO:0044242,GO:0044248,GO:0044249,GO:0044255,GO:0044262,GO:0044281,GO:0044282,GO:0044283,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044711,GO:0044712,GO:0044723,GO:0044763,GO:0044767,GO:0046165,GO:0046173,GO:0046327,GO:0046364,GO:0046395,GO:0046459,GO:0046872,GO:0046914,GO:0048545,GO:0048869,GO:0048878,GO:0050896,GO:0051384,GO:0051716,GO:0055082,GO:0065007,GO:0065008,GO:0070013,GO:0070365,GO:0070887,GO:0071310,GO:0071322,GO:0071326,GO:0071331,GO:0071333,GO:0071375,GO:0071383,GO:0071384,GO:0071385,GO:0071396,GO:0071407,GO:0071417,GO:0071495,GO:0071548,GO:0071549,GO:0071704,GO:0072329,GO:0097159,GO:0097367,GO:1901265,GO:1901363,GO:1901575,GO:1901576,GO:1901615,GO:1901617,GO:1901652,GO:1901653,GO:1901654,GO:1901655,GO:1901698,GO:1901699,GO:1901700,GO:1901701
TRINITY_DN100001_c0_g1	GO:0003674,GO:0003824,GO:0005575,GO:0005634,GO:0006629,GO:0007165,GO:0008081,GO:0008150,GO:0008152,GO:0009056,GO:0009987,GO:0016042,GO:0016787,GO:0016788,GO:0042578,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044712,GO:0050789,GO:0050794,GO:0065007,GO:0071704,GO:1901575
TRINITY_DN100003_c0_g1	GO:0000166,GO:0000932,GO:0000975,GO:0000976,GO:0000977,GO:0000978,GO:0000987,GO:0001012,GO:0001067,GO:0001159,GO:0001650,GO:0003674,GO:0003676,GO:0003677,GO:0003682,GO:0003690,GO:0003697,GO:0003723,GO:0003824,GO:0003916,GO:0003917,GO:0004672,GO:0004674,GO:0005488,GO:0005515,GO:0005524,GO:0005575,GO:0005634,GO:0005654,GO:0005730,GO:0006139,GO:0006259,GO:0006260,GO:0006265,GO:0006325,GO:0006338,GO:0006464,GO:0006468,GO:0006725,GO:0006793,GO:0006796,GO:0006807,GO:0006996,GO:0007059,GO:0007623,GO:0008150,GO:0008152,GO:0008219,GO:0009058,GO:0009059,GO:0009330,GO:0009987,GO:0010468,GO:0012501,GO:0016032,GO:0016043,GO:0016301,GO:0016310,GO:0016740,GO:0016772,GO:0016773,GO:0016853,GO:0017076,GO:0018105,GO:0018193,GO:0018209,GO:0019222,GO:0019538,GO:0019904,GO:0030529,GO:0030554,GO:0031298,GO:0032501,GO:0032553,GO:0032555,GO:0032559,GO:0032922,GO:0032991,GO:0032993,GO:0034641,GO:0034645,GO:0035639,GO:0035770,GO:0036094,GO:0036211,GO:0036464,GO:0040016,GO:0042221,GO:0042493,GO:0043167,GO:0043168,GO:0043170,GO:0043204,GO:0043226,GO:0043227,GO:0043228,GO:0043229,GO:0043231,GO:0043232,GO:0043234,GO:0043412,GO:0043565,GO:0044212,GO:0044237,GO:0044238,GO:0044249,GO:0044260,GO:0044267,GO:0044403,GO:0044419,GO:0044422,GO:0044424,GO:0044427,GO:0044428,GO:0044444,GO:0044446,GO:0044452,GO:0044454,GO:0044464,GO:0044699,GO:0044707,GO:0044763,GO:0044764,GO:0046483,GO:0048511,GO:0050789,GO:0050896,GO:0051276,GO:0051301,GO:0051704,GO:0060255,GO:0065007,GO:0071103,GO:0071704,GO:0071840,GO:0090304,GO:0097100,GO:0097159,GO:0097367,GO:0097458,GO:1901265,GO:1901360,GO:1901363,GO:1901564,GO:1901576,GO:1990837,GO:1990904
TRINITY_DN100006_c0_g1	GO:0003674,GO:0003824,GO:0008150,GO:0008152,GO:0016491,GO:0044699,GO:0044710,GO:0055114
TRINITY_DN100007_c0_g1	GO:0000166,GO:0003674,GO:0003824,GO:0004854,GO:0004855,GO:0005488,GO:0005506,GO:0005575,GO:0005777,GO:0005829,GO:0006082,GO:0006139,GO:0006144,GO:0006145,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0009055,GO:0009056,GO:0009058,GO:0009112,GO:0009115,GO:0009987,GO:0016491,GO:0016725,GO:0016726,GO:0016727,GO:0018130,GO:0019438,GO:0019439,GO:0030151,GO:0034418,GO:0034641,GO:0036094,GO:0042579,GO:0043167,GO:0043168,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0043546,GO:0044237,GO:0044238,GO:0044248,GO:0044249,GO:0044270,GO:0044271,GO:0044281,GO:0044283,GO:0044424,GO:0044444,GO:0044464,GO:0044699,GO:0044710,GO:0044711,GO:0044712,GO:0044763,GO:0046110,GO:0046113,GO:0046415,GO:0046483,GO:0046700,GO:0046872,GO:0046914,GO:0048037,GO:0050660,GO:0050662,GO:0051536,GO:0051537,GO:0051540,GO:0055086,GO:0055114,GO:0070674,GO:0071704,GO:0071949,GO:0072521,GO:0072522,GO:0072523,GO:0097159,GO:1901265,GO:1901360,GO:1901361,GO:1901362,GO:1901363,GO:1901564,GO:1901565,GO:1901566,GO:1901575,GO:1901576
TRINITY_DN10000_c0_g1	GO:0000149,GO:0000281,GO:0000910,GO:0001505,GO:0001671,GO:0001745,GO:0003674,GO:0005483,GO:0005488,GO:0005515,GO:0005575,GO:0005737,GO:0005774,GO:0005886,GO:0006461,GO:0006810,GO:0006836,GO:0006886,GO:0006891,GO:0006906,GO:0006996,GO:0007154,GO:0007267,GO:0007268,GO:0007269,GO:0007270,GO:0007274,GO:0007420,GO:0008047,GO:0008104,GO:0008105,GO:0008150,GO:0009653,GO:0009887,GO:0009987,GO:0010646,GO:0010807,GO:0015031,GO:0015833,GO:0016020,GO:0016043,GO:0016050,GO:0016082,GO:0016192,GO:0017157,GO:0017158,GO:0019905,GO:0022402,GO:0022411,GO:0022607,GO:0023051,GO:0023052,GO:0023061,GO:0030154,GO:0030182,GO:0030234,GO:0031090,GO:0031201,GO:0031410,GO:0031629,GO:0031982,GO:0032386,GO:0032502,GO:0032781,GO:0032879,GO:0032940,GO:0032984,GO:0032991,GO:0033036,GO:0033267,GO:0034214,GO:0034622,GO:0035249,GO:0035494,GO:0040007,GO:0042886,GO:0043085,GO:0043195,GO:0043226,GO:0043227,GO:0043229,GO:0043234,GO:0043241,GO:0043254,GO:0043462,GO:0043623,GO:0043624,GO:0043679,GO:0043933,GO:0044087,GO:0044093,GO:0044306,GO:0044422,GO:0044424,GO:0044425,GO:0044437,GO:0044444,GO:0044446,GO:0044456,GO:0044463,GO:0044464,GO:0044699,GO:0044700,GO:0044763,GO:0044765,GO:0044767,GO:0044801,GO:0044802,GO:0044877,GO:0045026,GO:0045176,GO:0045184,GO:0045202,GO:0046903,GO:0046907,GO:0046928,GO:0048193,GO:0048284,GO:0048513,GO:0048526,GO:0048589,GO:0048592,GO:0048856,GO:0048869,GO:0050789,GO:0050790,GO:0050794,GO:0050804,GO:0051046,GO:0051049,GO:0051128,GO:0051179,GO:0051234,GO:0051259,GO:0051260,GO:0051336,GO:0051345,GO:0051588,GO:0051641,GO:0051649,GO:0060341,GO:0060560,GO:0060589,GO:0060590,GO:0060627,GO:0061024,GO:0061025,GO:0061640,GO:0065003,GO:0065007,GO:0065008,GO:0065009,GO:0070044,GO:0071702,GO:0071705,GO:0071822,GO:0071840,GO:0090174,GO:0090596,GO:0097458,GO:0097708,GO:0098588,GO:0098693,GO:0098772,GO:0098793,GO:0098794,GO:0098796,GO:0098805,GO:0098916,GO:0098978,GO:0099500,GO:0099531,GO:0099536,GO:0099537,GO:0099643,GO:1902578,GO:1902589,GO:1902803,GO:1903047,GO:1903305,GO:1903530,GO:2000300

Full Annotations

Annotation report (107MB; CSV):

20231109.trinity_denovo.Trinity.fasta.trinotate_annotation_report.txt

This table is tab-delimited, but uses ^ for intra-field delimitation:

Code

library(kableExtra)

annotations.df <- read.csv("https://gannet.fish.washington.edu/Atumefaciens/20231109-mmag-trinotate-transcriptome/20231109.trinity_denovo.Trinity.fasta.trinotate_annotation_report.txt",
header = TRUE,
sep = "\t")

knitr::kable(head(annotations.df))

Table 2: Full annotations

X.gene_id	transcript_id	sprot_Top_BLASTX_hit	RNAMMER	prot_id	prot_coords	sprot_Top_BLASTP_hit	Pfam	SignalP	TmHMM	eggnog	Kegg	gene_ontology_blast	gene_ontology_pfam	transcript	peptide
TRINITY_DN8_c0_g1	TRINITY_DN8_c0_g1_i1	sp\|Q63089\|S22A1_RAT^sp\|Q63089\|S22A1_RAT^Q:905-18,H:87-381^36.2%ID^E:1.09e-38^.^.	.	TRINITY_DN8_c0_g1_i1.p1	908-3[-]	S22A1_RAT^S22A1_RAT^Q:2-297,H:87-381^36.156%ID^E:5.87e-43^RecName: Full=Solute carrier family 22 member 1;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus	PF00083.24^Sugar_tr^Sugar (and other) transporter^57-276^E:4.5e-21`PF07690.16^MFS_1^Major Facilitator Superfamily^61-278^E:7e-18	.	ExpAA=119.03^PredHel=5^Topology=i59-81o91-109i116-138o148-170i177-196o	ENOG410XR5P^Major facilitator superfamily MFS_1	KEGG:rno:24904`KO:K08198	GO:0016323^cellular_component^basolateral plasma membrane`GO:0005887^cellular_component^integral component of plasma membrane`GO:0005277^molecular_function^acetylcholine transmembrane transporter activity`GO:0005330^molecular_function^dopamine:sodium symporter activity`GO:0042802^molecular_function^identical protein binding`GO:0008504^molecular_function^monoamine transmembrane transporter activity`GO:0005334^molecular_function^norepinephrine:sodium symporter activity`GO:0015101^molecular_function^organic cation transmembrane transporter activity`GO:0042803^molecular_function^protein homodimerization activity`GO:0015651^molecular_function^quaternary ammonium group transmembrane transporter activity`GO:0008513^molecular_function^secondary active organic cation transmembrane transporter activity`GO:0015872^biological_process^dopamine transport`GO:0006855^biological_process^drug transmembrane transport`GO:0048241^biological_process^epinephrine transport`GO:0010248^biological_process^establishment or maintenance of transmembrane electrochemical gradient`GO:0015844^biological_process^monoamine transport`GO:0015874^biological_process^norepinephrine transport`GO:0015695^biological_process^organic cation transport`GO:0051260^biological_process^protein homooligomerization`GO:0015697^biological_process^quaternary ammonium group transport	GO:0022857^molecular_function^transmembrane transporter activity`GO:0055085^biological_process^transmembrane transport`GO:0016021^cellular_component^integral component of membrane	.	.
TRINITY_DN8_c0_g1	TRINITY_DN8_c0_g1_i1	sp\|Q63089\|S22A1_RAT^sp\|Q63089\|S22A1_RAT^Q:905-18,H:87-381^36.2%ID^E:1.09e-38^.^.	.	TRINITY_DN8_c0_g1_i1.p2	810-1[-]	.	.	.	.	.	.	.	.	.	.
TRINITY_DN8_c0_g1	TRINITY_DN8_c0_g1_i4	sp\|Q9VIK2\|CART_DROME^sp\|Q9VIK2\|CART_DROME^Q:1209-529,H:114-344^33.8%ID^E:2.21e-27^.^.	.	TRINITY_DN8_c0_g1_i4.p1	1212-475[-]	CART_DROME^CART_DROME^Q:2-242,H:114-358^32.661%ID^E:6.98e-33^RecName: Full=Carcinine transporter {ECO:0000303\|PubMed:26653853, ECO:0000303\|PubMed:26713872};^Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Holometabola; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora	PF00083.24^Sugar_tr^Sugar (and other) transporter^56-219^E:7.4e-19`PF07690.16^MFS_1^Major Facilitator Superfamily^61-209^E:1e-15	.	ExpAA=106.03^PredHel=5^Topology=i59-81o91-109i116-138o148-170i177-196o	ENOG410XSRI^solute carrier family 22	KEGG:dme:Dmel_CG9317	GO:0043679^cellular_component^axon terminus`GO:0016021^cellular_component^integral component of membrane`GO:0005886^cellular_component^plasma membrane`GO:1905131^molecular_function^carcinine transmembrane transporter activity`GO:0005326^molecular_function^neurotransmitter transporter activity`GO:1905130^biological_process^carcinine import across plasma membrane`GO:0050908^biological_process^detection of light stimulus involved in visual perception`GO:0001504^biological_process^neurotransmitter uptake`GO:0046956^biological_process^positive phototaxis`GO:0007601^biological_process^visual perception	GO:0022857^molecular_function^transmembrane transporter activity`GO:0055085^biological_process^transmembrane transport`GO:0016021^cellular_component^integral component of membrane	.	.
TRINITY_DN8_c0_g1	TRINITY_DN8_c0_g1_i4	sp\|Q9VIK2\|CART_DROME^sp\|Q9VIK2\|CART_DROME^Q:1209-529,H:114-344^33.8%ID^E:2.21e-27^.^.	.	TRINITY_DN8_c0_g1_i4.p2	1114-494[-]	.	.	.	.	.	.	.	.	.	.
TRINITY_DN8_c0_g1	TRINITY_DN8_c0_g1_i4	sp\|Q9VIK2\|CART_DROME^sp\|Q9VIK2\|CART_DROME^Q:1209-529,H:114-344^33.8%ID^E:2.21e-27^.^.	.	TRINITY_DN8_c0_g1_i4.p3	497-126[-]	.	.	.	ExpAA=41.12^PredHel=2^Topology=i13-35o104-122i	.	.	.	.	.	.
TRINITY_DN8_c0_g2	TRINITY_DN8_c0_g2_i1	sp\|Q6NY98\|MCE1_DANRE^sp\|Q6NY98\|MCE1_DANRE^Q:665-84,H:7-198^57.7%ID^E:2.12e-77^.^.	.	TRINITY_DN8_c0_g2_i1.p1	707-3[-]	MCE1_MOUSE^MCE1_MOUSE^Q:14-203,H:6-193^56.842%ID^E:4.77e-75^RecName: Full=mRNA-capping enzyme;^Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus	PF00782.20^DSPc^Dual specificity phosphatase, catalytic domain^65-182^E:5.3e-10	.	.	COG5226^Second step of mRNA capping. Transfer of the GMP moiety of GTP to the 5'-end of RNA via an enzyme-GMP covalent reaction intermediate (By similarity)	KEGG:mmu:24018`KO:K13917	GO:0005634^cellular_component^nucleus`GO:0005525^molecular_function^GTP binding`GO:0004484^molecular_function^mRNA guanylyltransferase activity`GO:0004651^molecular_function^polynucleotide 5'-phosphatase activity`GO:0004725^molecular_function^protein tyrosine phosphatase activity`GO:0008138^molecular_function^protein tyrosine/serine/threonine phosphatase activity`GO:0008192^molecular_function^RNA guanylyltransferase activity`GO:0050355^molecular_function^triphosphatase activity`GO:0006370^biological_process^7-methylguanosine mRNA capping`GO:0006396^biological_process^RNA processing	GO:0008138^molecular_function^protein tyrosine/serine/threonine phosphatase activity`GO:0016311^biological_process^dephosphorylation	.	.

Code

number_of_annotations <- n_distinct(annotations.df$X.gene_id)

Number of Trinity genes with annotations: 142402

SQlite Database

SQlite database (797MB; SQLITE):

Trinotate.sqlite