diff --git a/dataAnalysis/GenomeAnnotation/Secreted_Protein_Prediction_with_SignalP_and_TMHMM.md b/dataAnalysis/GenomeAnnotation/Secreted_Protein_Prediction_with_SignalP_and_TMHMM.md new file mode 100644 index 0000000..1dbbad1 --- /dev/null +++ b/dataAnalysis/GenomeAnnotation/Secreted_Protein_Prediction_with_SignalP_and_TMHMM.md @@ -0,0 +1,329 @@ +--- +title: Identify secreted proteins and predict subcellular localization +layout: single +author: Rick Masonbrink +author_profile: true +header: + overlay_color: "444444" + overlay_image: /assets/images/dna.jpg +--- + +# How to identify the secreted protein from an annotation and predict subcellular localization + +Here we will be using a set of predicted proteins from a plant parasitic nematode genome to predict secretion, transmembrane domains, and subcellular localization. + +**Software used in this tutorial** +1. Signalp 6.0 +2. Tmhmm 2.0c +3. Samtools 1.16.1 +4. Localizer 1.0.5 +5. DeepLoc 2.0 + + + +### Installation of SignalP 6.0 +``` +# create and activate a python virtual environment +python -m venv signalp6_env +source signalp6_env/bin/activate + +# register for signalp use here to obtain the software +https://services.healthtech.dtu.dk/services/SignalP-6.0/ + +#install SignalP +tar -zxvf signalp-6.0h.fast.tar.gz +cd signalp6_fast/ +pip install signalp-6-package/ + +#it installs with numpy 2, which is incorrect, so had to run this. +pip install numpy==1.24.3 + +#This code stores the installation path of the signalp module in the variable SIGNALP_DIR, so that you can use this path in further shell commands. +SIGNALP_DIR=$(python3 -c "import signalp; import os; print(os.path.dirname(signalp.__file__))" ) +``` + +### Run Signalp 6.0 +``` +#softlink your proteins +ln -s /work/gif3/masonbrink/Baum/01_ReannotateAllSCNGenomes/42_Fix67CDSs/TN10FinalManualAnnotation_proteins.fasta + +#run signalp 6 in a compute node +echo "source signalp6_env/bin/activate; signalp6 --fastafile TN10FinalManualAnnotation_proteins.fasta --organism euk --output_dir Signalp6_out --format txt --mode fast --model_dir signalp6_fast/signalp-6-package/models/" >signalp.sh +``` + +Excerpt of results from Signalp 6.0. We want to get the fasta names that are secreted and the last position of the cleavage site. +``` +# SignalP-6.0 Organism: Eukarya Timestamp: 20240910112251 +# ID Prediction OTHER SP(Sec/SPI) CS Position +Hg_chrom1_TN10mRNA_1 gene=Hg_chrom1_TN10gene_1 OTHER 1.000000 0.000000 +Hg_chrom1_TN10mRNA_2 gene=Hg_chrom1_TN10gene_2 OTHER 1.000000 0.000001 +Hg_chrom1_TN10mRNA_3 gene=Hg_chrom1_TN10gene_3 OTHER 1.000000 0.000000 +Hg_chrom1_TN10mRNA_4 gene=Hg_chrom1_TN10gene_4 OTHER 1.000000 0.000003 +Hg_chrom1_TN10mRNA_5 gene=Hg_chrom1_TN10gene_5 OTHER 1.000000 0.000023 +Hg_chrom1_TN10mRNA_6 gene=Hg_chrom1_TN10gene_6 OTHER 1.000000 0.000006 +Hg_chrom1_TN10mRNA_7 gene=Hg_chrom1_TN10gene_7 OTHER 1.000000 0.000000 +Hg_chrom1_TN10mRNA_8 gene=Hg_chrom1_TN10gene_8 OTHER 0.999587 0.000437 +Hg_chrom1_TN10mRNA_9 gene=Hg_chrom1_TN10gene_9 OTHER 1.000000 0.000006 +Hg_chrom1_TN10mRNA_10 gene=Hg_chrom1_TN10gene_10 OTHER 1.000000 0.000000 +Hg_chrom1_TN10mRNA_11 gene=Hg_chrom1_TN10gene_11 SP 0.000243 0.999714 CS pos: 19-20. Pr: 0.9780 +Hg_chrom1_TN10mRNA_12 gene=Hg_chrom1_TN10gene_12 OTHER 1.000000 0.000000 +Hg_chrom1_TN10mRNA_13 gene=Hg_chrom1_TN10gene_13 SP 0.000200 0.999755 CS pos: 19-20. Pr: 0.9861 +Hg_chrom1_TN10mRNA_14 gene=Hg_chrom1_TN10gene_14 OTHER 0.976381 0.023633 +Hg_chrom1_TN10mRNA_15 gene=Hg_chrom1_TN10gene_15 OTHER 1.000000 0.000039 +Hg_chrom1_TN10mRNA_16 gene=Hg_chrom1_TN10gene_16 OTHER 1.000000 0.000000 +Hg_chrom1_TN10mRNA_17 gene=Hg_chrom1_TN10gene_17 OTHER 1.000000 0.000000 +Hg_chrom1_TN10mRNA_18 gene=Hg_chrom1_TN10gene_18 OTHER 1.000000 0.000000 +Hg_chrom1_TN10mRNA_19 gene=Hg_chrom1_TN10gene_19 OTHER 0.844543 0.155449 +Hg_chrom1_TN10mRNA_20 gene=Hg_chrom1_TN10gene_20 OTHER 1.000000 0.000005 +Hg_chrom1_TN10mRNA_21 gene=Hg_chrom1_TN10gene_21 SP 0.000452 0.999497 CS pos: 25-26. Pr: 0.9702 +continued ... +``` + + +### Identify secreted proteins in signalp6 results and remove signal peptide for transmembrane domain prediction +``` +# create a faidx index of our proteins to subtract the signal peptide from the fasta of secreted proteins +ml samtools;samtools faidx TN10FinalManualAnnotation_proteins.fasta + +# this gets the signalp results file and the protein lengths in the same order +awk '$2=="SP"{print $1"\t"$7}' Signalp6_out/prediction_results.txt|sed -e 's/\.//g' -e 's/-/\t/g' |awk -F"\t" '{print "samtools faidx TN10FinalManualAnnotation_proteins.fasta "$1":"$3"- >>SignalPeptidesSubtracted6.fasta"}' >ExtractSignalPContainingProts6.sh + +sh ExtractSignalPContainingProts6.sh +``` + +**Excerpt from SignalPeptidesSubtracted6.fasta** +``` +>Hg_chrom1_TN10mRNA_11:20- +HDQQLRSENLGDVAAKDHRATGGDTLPKYSKDQLHQRAQKIGEAKTAEHQQQNFQNAVAD +QQQHQAAAPSAFKVENAVGHDNQEQQQKAAEHLENKFVASGTKSKLMNTDARKNVHEQQQ +QQAVGQQAVQQRTDELRQHLEQPSTSAIEGDQQRHARVYVVKQVAAEPIFNSNAEQPEAE +EFNAGRKLNKDMGNELLRPVYLNDNNRFATAARIVSKVFGGHYYEQQQQQRQFQYQRGYG +SNKMGQPEQGEQFENAETRQQRVQFSGKNGQTELVLDNLNQHQQQQYNNNMGKDSQSFKS +ERLDNSRGMQRVQEHQQQQQNKLGQDSRVILGDLQQQKLEQDNARTFQGEQQQQQKQKLE +QGNSRTFQGEQQQKLEQDSMRTFQGEQQQKLEQDSMRTFQGEQQHQQKEQHEIQQFEQQE +NKQQEPSLALERARLEELRIKERARVAKLEAERQARLVEIQARERQAKLEAEMRVRNVEN +RVRQAKLEAEARANQAILEAKVRQAERRARLGHGGGFADASEELQKDEQQAQQRQQQQLL +EQPQINTPQQLRENVAQPIVAAPVVAVAGVH. +>Hg_chrom1_TN10mRNA_13:20- +AHQQQLGTPVIGGICKLDTPDVHIGGKQTQFFLRCEPNTDSAQGEGVWVVKSRHAGSTAA +KIPAAAVVSQQEIEQGEQNSQKIAATKQISSYVCDLVSDAVEHGYCSTSENCLQPVYTDR +TAFLQCDPTSRRWTKKHCQSGFNFDFERQACIAHTAKMSHHFRQFPTQVLPHSQRGGGIV +CTFAQCSVADPCNVGSCNNGYCCTAAVGSMPKAVLPISTNKTISSGNSNNIAKPLSPPSS +TIAVSASETVPPIPSILVIELNNNNNHNDDVIEYDQLRLNDIPSTLIGHISSNSQPMPTI +FDHCSSGFHSPIRCGGTSGGECPVGLICELATRFCCPFPPKKLKRKSTSTNSGGIGGVVG +TTATGNWAQSLVPNGAKVVRRRTALRRHGRFERSFFSSFCCVPAAEQLLIDANDNETPEQ +QLNMFICPTGAPALGPCSPGYCVAPLQCAGALCCAPPAPVMAPPPPIAYACPGGLPALGP +CIGGRCAAPAICASPSNVCCAQPSVPTAIPATVCPDGTQAAGACVNGQCGAGFTCNQGLC +CTNSSQTPRCLDGSQSIGACIQGRCGTGYTCTTGNICCPSQLNLCPPGQTSVGQAVNGRC +PAGYTNFNGQCCGPQSAQSQVSCSVEDSFGRCDSNQQCAEPGYACDVANNWCCPQVIGDA +IGPCIQGEGGNRLCPEGYACVGEGEGQCFRLDTGTCAPEEQSGPCAPDGTCPPGYECIEG +FCCQTDAGGANPAAAALRLFHQRRRRRRASASSSAFLKMINYDRGSRQPTQNRNSKK. +>Hg_chrom1_TN10mRNA_21:26- +TISTAFSQFLRNYFNDEVEKNIARRDLGTDGSFGGGKGRIKAKKRPVIFVHGLTNLAGEL +DYVRRLFREKGGYRDSELYATTYGYGMKGWKWLRDAMKCDHVKMIRIMIRAITQFTHSSQ +AILGGVCVDTEEQLGPPLTHLVHTFIGVGGANREAVHLCRLFEWAMPCNPVNGMRCHSQF +LYDINSNVGYEATTRIFVIRSMDDGTVGTRDCEGRSVSAIDGQNDEIVLRNYSHQMVIFG +TGEQQLKLLTF. +``` + +# Install and run Tmhmm to identify transmembrane domains +``` +#Download and extract tmhmm from here. +https://services.healthtech.dtu.dk/services/TMHMM-2.0/ + +add this to your ~/.bashrc +#export PATH="/path/to/your/tmhmm-2.0c/bin/:$PATH" + +#run tmhmm +tmhmm SignalPeptidesSubtracted6.fasta >SignalPeptidesSubtracted6.tmhmmout +``` + +**Excerpt of the results from Tmhmm** +``` +# Hg_chrom1_TN10mRNA_11:20- Length: 571 +# Hg_chrom1_TN10mRNA_11:20- Number of predicted TMHs: 0 +# Hg_chrom1_TN10mRNA_11:20- Exp number of AAs in TMHs: 0.00222 +# Hg_chrom1_TN10mRNA_11:20- Exp number, first 60 AAs: 0 +# Hg_chrom1_TN10mRNA_11:20- Total prob of N-in: 0.00112 +Hg_chrom1_TN10mRNA_11:20- TMHMM2.0 outside 1 571 +# Hg_chrom1_TN10mRNA_13:20- Length: 777 +# Hg_chrom1_TN10mRNA_13:20- Number of predicted TMHs: 0 +# Hg_chrom1_TN10mRNA_13:20- Exp number of AAs in TMHs: 0.01067 +# Hg_chrom1_TN10mRNA_13:20- Exp number, first 60 AAs: 0.00038 +# Hg_chrom1_TN10mRNA_13:20- Total prob of N-in: 0.00040 +Hg_chrom1_TN10mRNA_13:20- TMHMM2.0 outside 1 777 +# Hg_chrom1_TN10mRNA_21:26- Length: 251 +# Hg_chrom1_TN10mRNA_21:26- Number of predicted TMHs: 0 +# Hg_chrom1_TN10mRNA_21:26- Exp number of AAs in TMHs: 0.02999 +# Hg_chrom1_TN10mRNA_21:26- Exp number, first 60 AAs: 0.02192 +# Hg_chrom1_TN10mRNA_21:26- Total prob of N-in: 0.01958 +Hg_chrom1_TN10mRNA_21:26- TMHMM2.0 outside 1 251 +# Hg_chrom1_TN10mRNA_25:23- Length: 2168 +# Hg_chrom1_TN10mRNA_25:23- Number of predicted TMHs: 0 +# Hg_chrom1_TN10mRNA_25:23- Exp number of AAs in TMHs: 30.69038 +# Hg_chrom1_TN10mRNA_25:23- Exp number, first 60 AAs: 0.01395 +# Hg_chrom1_TN10mRNA_25:23- Total prob of N-in: 0.00072 +continued ... +``` + +# Subcellular Localization +Here we are using two distinct subcellular localization predictors. Each of these two software's uses a different approach to identifying the cellular compartment localization. + + +| Feature | Localizer | DeepLoc | +|--------------------------|--------------------------------------------|------------------------------------------| +| **Focus** | Plant-specific, focused on chloroplast, mitochondrion, and nucleus. | General eukaryotic protein localization across 10 compartments. | +| **Subcellular compartments** | Chloroplast, mitochondrion, nucleus. | Nucleus, cytoplasm, extracellular, mitochondrion, ER, Golgi, lysosome/vacuole, peroxisome, plasma membrane, chloroplast. | +| **Methodology** | Rule-based predictions using known motifs/signals. | Deep learning model (RNN) based on sequence data. | +| **Organism specificity** | Plant proteins. | General eukaryotes, including plants. | +| **Prediction accuracy** | Focuses on high accuracy for three compartments. | Predicts across a broad range of compartments using neural networks. | +| **Ease of interpretation**| Results are interpretable based on known localization signals. | Predictions from a neural network may be harder to interpret. | +| **Input format** | Protein sequences (FASTA). | Protein sequences (FASTA). | +| **Publication** | Sperschneider et al. (2017). | Almagro Armenteros et al. (2017). | + + +### Localizer +Localizer is a highly specialized software for plants and only predicts chlorplast, mitochondrial, and nuclear localization using known motifs/signals. + +**Install Localizer** +``` +git clone https://github.com/JanaSperschneider/LOCALIZER.git +tar -xvf LOCALIZER-1.0.5.tar.gz +cd LOCALIZER-1.0.5/Scripts + + +python -m venv localizer +source localizer/bin/activate + +tar xvf emboss-latest.tar.gz +cd EMBOSS-6.5.7/ +./configure +make +cd ../ +unzip weka-3-6-12.zip + +# added this to my ~/.bashrc +#export PATH="/work/gif3/masonbrink/Baum/01_ReannotateAllSCNGenomes/39_localizer/LOCALIZER/Scripts/:$PATH" +``` +### Run Localizer 1.0.5 +``` +echo "source localizer/bin/activate; LOCALIZER.py -e -M -o SP6Out -i SignalPeptidesSubtracted6.fasta ">localizerSP6.sh +``` + +**Excerpt of results from Localizer** +``` +# ----------------- +# LOCALIZER 1.0.5 Predictions (-e mode) +# ----------------- +Identifier Chloroplast Mitochondria Nucleus +Hg_chrom1_TN10mRNA_1003:25-587 Y (0.964 | 62-86) - Y (RKRNRRLSASSVHRRRRHS,RRNCNEKLCNFTQETKRWR) +Hg_chrom1_TN10mRNA_1006:26-1143 - - Y (KWRRRNNGNKKGERSKKEKRRP) +Hg_chrom1_TN10mRNA_1028:26-246 - - Y (APAPHSQRKEKQGKKEKAKSSSSSSSAEEEEKKHRKKGNGRQIVKHFGKGKKKD) +Hg_chrom1_TN10mRNA_102:19-109 - - - +Hg_chrom1_TN10mRNA_1045:36-353 - - - +Hg_chrom1_TN10mRNA_1046:24-361 - - - +Hg_chrom1_TN10mRNA_105:30-452 - - - +Hg_chrom1_TN10mRNA_1069:30-355 - - - +Hg_chrom1_TN10mRNA_1090:22-475 - - Y (KKGKIGGFLIQKIQRQRRQ) +Hg_chrom1_TN10mRNA_1092:44-1224 - - - +Hg_chrom1_TN10mRNA_1097:25-161 - - - +Hg_chrom1_TN10mRNA_1108:25-397 - - - +Hg_chrom1_TN10mRNA_1115:30-4744 - - Y (PKPS) +Hg_chrom1_TN10mRNA_1116:23-494 - - - +Hg_chrom1_TN10mRNA_112:24-315 - - Y (RKIMQQTNAKKAFKK,KKGDKLKPKKPPAKNAPEAPVTGKSKAEEKGQEKEEKKGTTDKKEAGAEKKKKEL) +Hg_chrom1_TN10mRNA_113:26-479 - - - +Hg_chrom1_TN10mRNA_1150:30-127 Y (1.0 | 5-45) - Y (RRIPKMSRTEKRKLL,KRHRATAQSDNRARRI,KGRKRKRTDGRQKRHRA) +Hg_chrom1_TN10mRNA_1154:27-652 - - - +Hg_chrom1_TN10mRNA_1157:25-598 - - Y (RKSK,PANKRRC) +Continued ... +``` + +### DEEPLOC 2.0 +DeepLoc is a general tool for eukaryotic protein localization, covering a much wider range of subcellular compartments using advanced deep learning techniques. It is more flexible but less focused on specific plant biology needs compared to Localizer. The software will provide different predictions based on whether you've removed the signal peptide in your protein, so here I am going to predict on my truncated proteins and proteins that were unmodified. + + +**Install Deeploc** +``` +You will need to register for this software and they will send you a download link +https://services.healthtech.dtu.dk/services/DeepLoc-2.0/ + +tar -zxvf deeploc-2.0.All.tar.gz +cd deeploc2_package +pip install . --user + +``` +### Run deeploc2 -- 2 runs: one on subtracted SP proteins, and one on unmodified proteins. +``` +deeploc2 -f SignalPeptidesSubtracted6.fasta -o Signap6Accurate -m Accurate -d cuda +deeploc2 -f TN10FinalManualAnnotation_proteins.fasta -o AllProteins -m Accurate -d cuda +``` +**Excerpt of results from Deeploc 2.0** +``` +Protein_ID,Localizations,Signals,Cytoplasm,Nucleus,Extracellular,Cell membrane,Mitochondrion,Plastid,Endoplasmic reticulum,Lysosome/Vacuole,Golgi apparatus,Peroxisome +Hg_chrom1_TN10mRNA_1,Nucleus,Nuclear localization signal,0.4494999945163727,0.6108999848365784,0.1216999962925911,0.07580000162124634,0.3386000096797943,0.008999999612569809,0.13439999520778656,0.048700001090765,0.042399998754262924,0.005799999926239252 +Hg_chrom1_TN10mRNA_2,Cytoplasm,Nuclear localization signal,0.7009999752044678,0.4546999931335449,0.09380000084638596,0.39579999446868896,0.09120000153779984,0.017500000074505806,0.05480000004172325,0.024700000882148743,0.02889999933540821,0.011900000274181366 +Hg_chrom1_TN10mRNA_3,Cytoplasm|Nucleus,Nuclear localization signal,0.5720000267028809,0.7562000155448914,0.03790000081062317,0.12630000710487366,0.052400000393390656,0.016200000420212746,0.029400000348687172,0.016100000590085983,0.03009999915957451,0.009100000374019146 +Hg_chrom1_TN10mRNA_4,Nucleus,,0.4250999987125397,0.451200008392334,0.24070000648498535,0.14259999990463257,0.20229999721050262,0.03359999880194664,0.11720000207424164,0.06080000102519989,0.04450000077486038,0.05620000138878822 +Hg_chrom1_TN10mRNA_5,Cytoplasm,Nuclear localization signal,0.5914000272750854,0.37220001220703125,0.13279999792575836,0.15309999883174896,0.16269999742507935,0.054999999701976776,0.09549999982118607,0.11569999903440475,0.07930000126361847,0.01510000042617321 +Continued ... +``` + +### Create feature lists for each mRNA +I always create a excel chart for each feature of a gene, so it is nice to have a tabular list of gene name "\t" feature. In this case I have the Signalp 6 secretion score and the number of transmembrane domains after the signal peptide is cleaved from the protein. +``` +#Signalp scores for those that are secreted + less Signalp6_out/prediction_results.txt |awk '$2=="SP" {print $2"\t"$4}' >signalp6Scores.tab + +#Number of transmembrane domains in each secreted protein +grep "Number of predicted" SignalPeptidesSubtracted6.tmhmmout |sed 's/:/\t/g' |awk '{print $2"\t"$8}' >Signalp6Tmhmm.tab + +#subcellular localization Localizer for secreted proteins +less SP6Out/Results.txt |awk 'NR>4' |awk -F"\t" '{if(substr($2,1,1)=="Y") {print $1"\tChloroplast",$2} else if(substr($3,1,1)=="Y" ) {print $1"\tMitochondria",$3} else if(substr($4,1,1)=="Y") {print $1"\tNucleus",$4} else {next;}}' |sed 's/:/\t/g' |awk '{print $1"\t"$3}' >LocalizerSP6.tab + +#subcellular localization Deeploc secreted proteins +cat Signap6Accurate/results_20240910-133321.csv Signap5Accurate/results_20240910-133354.csv |sed 's/,/\t/g' |cut -f 1,2,3 |sed 's/:/\t/g' |cut -f 1,3,4,5 |sed 's/\t/#/1' |sed 's/\t/ /g' |sed 's/#/\t/g' >SecretedProteinsDeepLoc.tab + +#subcellular localization Deeploc non-secreted proteins +cat AllProteins/results_20240910-142450.csv Signap5Accurate/results_20240910-133354.csv |sed 's/,/\t/g' |cut -f 1,2,3 |sed 's/:/\t/g' |cut -f 1,3,4,5 |sed 's/\t/#/1' |sed 's/\t/ /g' |sed 's/#/\t/g' >AllOtherProteinsDeepLoc.tab +``` +| mRNA_Names | Gene_Names | SignalPv6.0_Scores | Transmembrane_Domain_Counts| Localizer 1.0.5 | DeepLoc2.0 Secreted | DeepLoc2.0 All Proteins | +|-------------------------|-------------------------|-------------------|-------------------------------------------------------|------------------|------------------------------------------|-------------------------------------------------------| +| Hg_chrom1_TN10mRNA_1 | Hg_chrom1_TN10gene_1 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_10 | Hg_chrom1_TN10gene_10 | 0.000 | #N/A | #N/A | #N/A | #N/A | +| Hg_chrom1_TN10mRNA_100 | Hg_chrom1_TN10gene_96 | 0.000 | #N/A | #N/A | #N/A | Signal peptide|Transmembrane domain | +| Hg_chrom1_TN10mRNA_1000 | Hg_chrom1_TN10gene_956 | 0.000 | #N/A | #N/A | #N/A | Transmembrane domain | +| Hg_chrom1_TN10mRNA_1001 | Hg_chrom1_TN10gene_957 | 0.499 | #N/A | #N/A | #N/A | Signal peptide | +| Hg_chrom1_TN10mRNA_1002 | Hg_chrom1_TN10gene_958 | 0.006 | #N/A | #N/A | #N/A | #N/A | +| Hg_chrom1_TN10mRNA_1003 | Hg_chrom1_TN10gene_959 | 0.999 | 0 | Chloroplast | Extracellular Signal peptide | Signal peptide | +| Hg_chrom1_TN10mRNA_1004 | Hg_chrom1_TN10gene_960 | 0.000 | #N/A | #N/A | #N/A | #N/A | +| Hg_chrom1_TN10mRNA_1005 | Hg_chrom1_TN10gene_960 | 0.000 | #N/A | #N/A | #N/A | Nuclear export signal | +| Hg_chrom1_TN10mRNA_1006 | Hg_chrom1_TN10gene_961 | 1.000 | 1 | Nucleus | Golgi apparatus Signal peptide|Transmembrane domain | Signal peptide|Transmembrane domain | +| Hg_chrom1_TN10mRNA_1007 | Hg_chrom1_TN10gene_962 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_1008 | Hg_chrom1_TN10gene_963 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal|Nuclear export signal | +| Hg_chrom1_TN10mRNA_1009 | Hg_chrom1_TN10gene_964 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_101 | Hg_chrom1_TN10gene_97 | 0.000 | #N/A | #N/A | #N/A | #N/A | +| Hg_chrom1_TN10mRNA_1010 | Hg_chrom1_TN10gene_963 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_1011 | Hg_chrom1_TN10gene_965 | 0.000 | #N/A | #N/A | #N/A | #N/A | +| Hg_chrom1_TN10mRNA_1012 | Hg_chrom1_TN10gene_966 | 0.000 | #N/A | #N/A | #N/A | Signal peptide | +| Hg_chrom1_TN10mRNA_1013 | Hg_chrom1_TN10gene_967 | 0.427 | #N/A | #N/A | Cytoplasm Nuclear localization signal | Signal peptide | +| Hg_chrom1_TN10mRNA_1014 | Hg_chrom1_TN10gene_968 | 0.000 | #N/A | #N/A | #N/A | Signal peptide|Transmembrane domain | +| Hg_chrom1_TN10mRNA_1015 | Hg_chrom1_TN10gene_969 | 0.000 | #N/A | #N/A | #N/A | #N/A | +| Hg_chrom1_TN10mRNA_1016 | Hg_chrom1_TN10gene_970 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_1017 | Hg_chrom1_TN10gene_971 | 0.162 | #N/A | #N/A | #N/A | #N/A | +| Hg_chrom1_TN10mRNA_1018 | Hg_chrom1_TN10gene_972 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_1019 | Hg_chrom1_TN10gene_973 | 0.000 | #N/A | #N/A | #N/A | Signal peptide|Transmembrane domain | +| Hg_chrom1_TN10mRNA_102 | Hg_chrom1_TN10gene_98 | 0.997 | 0 | #N/A | Nucleus | Signal peptide | +| Hg_chrom1_TN10mRNA_1020 | Hg_chrom1_TN10gene_974 | 0.000 | #N/A | #N/A | #N/A | Transmembrane domain | +| Hg_chrom1_TN10mRNA_1021 | Hg_chrom1_TN10gene_975 | 0.000 | #N/A | #N/A | #N/A | Signal peptide|Transmembrane domain | +| Hg_chrom1_TN10mRNA_1022 | Hg_chrom1_TN10gene_976 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_1023 | Hg_chrom1_TN10gene_977 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_1024 | Hg_chrom1_TN10gene_978 | 0.000 | #N/A | #N/A | #N/A | Nuclear export signal | +| Hg_chrom1_TN10mRNA_1025 | Hg_chrom1_TN10gene_979 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_1026 | Hg_chrom1_TN10gene_979 | 0.000 | #N/A | #N/A | #N/A | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_1027 | Hg_chrom1_TN10gene_980 | 0.000 | #N/A | #N/A | #N/A | #N/A | +| Hg_chrom1_TN10mRNA_1028 | Hg_chrom1_TN10gene_981 | 0.981 | 0 | Nucleus | Cytoplasm|Nucleus|Cell membrane | Nuclear localization signal | +| Hg_chrom1_TN10mRNA_1029 | Hg_chrom1_TN10gene_982 | 0.000 | #N/A | #N/A | #N/A | Signal peptide|Transmembrane domain | +| Hg_chrom1_TN10mRNA_103 | Hg_chrom1_TN10gene_99 | 0.000 | #N/A | #N/A | #N/A | Nuclear export signal | + + +[Back to the Assembly and Annotation Index page](annotation_and_assembly_index.md) \ No newline at end of file