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remove relative paths, add IRD functional annotation data files

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lmoncla committed Nov 15, 2019
1 parent bdd1de6 commit a8144ef7983bed7b1b519a47f70882969af699af

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Feature Identifier Sequence Feature Name Sequence Feature Length Variant Types Category Amino Acid Position Evidence Comments
Influenza A_M1_SF15 Influenza A_M1_nuclear-localization-signal-motif_101(5) 5 38 functional 101..105 UniProt: P03485 , -N/A-
Influenza A_M1_SF16 Influenza A_M1_transcription-inhibition-site_91(21) 21 211 functional 91..111 PMID: 8523532, This region has been found to be essential for anti-RNA synthesis activity, RNA binding, and oligomerization of M1.
Influenza A_M1_SF17 Influenza A_M1_membrane-binding-region_1(164) 164 1999 functional 1..164 UniProt: P03485 , -N/A-
Influenza A_M1_SF18 Influenza A_M1_RNP-binding-region_165(88) 88 1605 functional 165..252 UniProt: P03485 , PMID: 11222100, This C-terminal region binds to vRNP.
Influenza A_M1_SF19 Influenza A_M1_RNP-binding-region_1(76) 76 760 functional 1..76 PMID: 10438836, This N-terminal region binds to vRNP.
Influenza A_M1_SF20 Influenza A_M1_RNA-binding-domain_101(5) 5 38 functional 101..105 PMID: 9225034, This stretch of basic amino acids can bind to vRNA.
Influenza A_M1_SF21 Influenza A_M1_RNA-binding-domain_90(19) 19 180 functional 90..108 PMID: 10438836, -N/A-
Influenza A_M1_SF22 Influenza A_M1_RNA-binding-domain_135(31) 31 321 functional 135..165 PMID: 10438836, -N/A-
Influenza A_M1_SF23 Influenza A_M1_NS2/NEP-interaction-site_101(5) 5 38 functional 101..105 PMID: 12970177, This nuclear localization signal interacts with the C-terminus of NS2 (NEP).
Influenza A_M1_SF24 Influenza A_M1_lipid-binding-site_1(164) 164 1999 functional 1..164 PMID: 11222100, -N/A-
Influenza A_M1_SF25 Influenza A_M1_lipid-binding-site_62(7) 7 31 functional 62..68 PMID: 11222100, -N/A-
Influenza A_M1_SF26 Influenza A_M1_lipid-binding-site_114(20) 20 184 functional 114..133 PMID: PMID: 7288926, 11222100, -N/A-
Influenza A_M1_SF285 Influenza A_M1_determinants-of-virulence_148(15) 15 97 functional 148..162 PMID: 16731908, The putative zinc finger motif CCHH in the helix 9 of M1 plays a critical role in virulence in vivo in mice although it does not play an important role in virus growth in MDCK cells in cultures . The CCHH motif may be a contributory factor in virus virulence in a species-specific manner along with the remaining residues in the H9 region.
Influenza A_M1_SF286 Influenza A_M1_determinant-of-virulence_139(1) 1 8 functional 139 PMID: 10426210, All five mutations (T139A (and silent mutation: T121C) of M1, D538G in PB1, K482R (silent mutation: G912A) in PB2, N369I in NA and W47G in HA2) control virulence and replicative capacity in mice.The PB1 and PB2 mutations are shown to be host restrictive in changing the virus to a mouse specific strain.
Influenza A_M1_SF287 Influenza A_M1_determinants-of-virulence_30(2) 2 17 functional 30,215 PMID: 19117585, These two M1 residues contribute to differences in virulence of H5N1 avian influenza viruses in mice. Positions 30 and 215 are found in the N-terminal and C-terminal domains of M1 respectively.
Influenza A_M1_SF288 Influenza A_M1_determinant-of-virulence_155(1) 1 9 functional 155 PMID: 14573816, The Ala155Gly mutation in H9 is found to be lethal and is critical for the M1 protein function.
Influenza A_M1_SF289 Influenza A_M1_determinants-of-temperature-sensitivity_101(2) 2 18 functional 101,105 PMID: 15650216, 15331690, The R101S-R105S double mutation (substitution of Ser for Arg at either position 101 or position 105 of the RKLKR domain) is synergistic and results in temperature sensitivity as seen by reduced viral replication at a restrictive temperature. The double mutation is seen to be fully attenuated in mice.
Influenza A_M1_SF290 Influenza A_M1_determinant-of-replication_139(1) 1 8 functional 139 PMID: 10426210, All five mutations (T139A (and silent mutation: T121C) of M1, D538G in PB1, K482R (silent mutation: G912A) in PB2, N369I in NA and W47G in HA2) control virulence and replicative capacity in mice.The PB1 and PB2 mutations are shown to be host restrictive in changing the virus to a mouse specific strain.
Influenza A_M1_SF291 Influenza A_M1_determinants-of-replication_101(2) 2 18 functional 101,105 PMID: 15650216, 15331690, The R101S-R105S double mutation (substitution of Ser for Arg at either position 101 or position 105 of the RKLKR domain) is synergistic and results in temperature sensitivity as seen by reduced viral replication at a restrictive temperature. The double mutation is seen to be fully attenuated in mice.
Influenza A_M1_SF307 Influenza A_M1_Determinants-of-morphology_30(3) 3 37 functional 30,207,209 PMID:23209789, Key to spherical morphology. Substitution of any one of these residues with the corresponding TR swine residues causes transition to a filamentous morphology.
Influenza A_M1_SF308 Influenza A_M1_Determinants-of-budding_30(3) 3 37 functional 30,207,209 PMID:23209789, Making M1 protein sufficient for virus-like particle production, indicating a unique feature of the pH1N1 M1 protein to induce and complete budding at the plasma membrane by itself.
Influenza A_M1_SF309 Influenza A_M1_Determinants-of-virus-production_30(4) 4 70 functional 30,142,207,209 PMID:23209789, Single replacement of either one of the residue in M1 protein reduces overall viral production as well as growth kinetics.
Influenza A_M1_SF323 Influenza A_M1_determinant-of-virulence_30(2) 2 15 functional 30,215 PMID:19117585, Introduction of Asn30Asp and Thr215Ala substitutions in the A/duck/Guangxi/53/2002 backbone conferred increased virulence in mice indicated by survival rate.
Influenza A_M1_SF324 Influenza A_M1_determinant-of-virulence_139(1) 1 7 functional 139 PMID:8879138, PMID:10426210 , The mouse adapted A/Fort Monmouth/1/47 virus contained Thr139Ala substitution that conferred increased virulence as indicated by measuring median lethal dose in mice and increased viral yield in lungs of mice and MDCK cells.
Influenza A_M1_SF325 Influenza A_M1_replication-efficiency_139(1) 1 7 functional 139 PMID:8879138, PMID:10426210 , The mouse adapted A/Fort Monmouth/1/47 virus contained Thr139Ala substitution that conferred increased virulence as indicated by measuring median lethal dose in mice and increased viral yield in lungs of mice and MDCK cells.
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Feature Identifier Sequence Feature Name Sequence Feature Length Variant Types Category Amino Acid Position Evidence Comments
Influenza A_M2_SF11 Influenza A_M2_viral-assembly-and-morhogenesis-site_74(6) 6 106 sequence alteration 74..79 PMID: 16699003, These residues play a role in play a role in virion morphogenesis and affect viral infectivity
Influenza A_M2_SF13 Influenza A_M2_CRAC-motif_46(15) 15 474 functional 46..60 PMID: 15221235, This is the 'cholesterol recognition consensus (CRAC) motif' found downstream of the transmembrane domain in the cytoplasmic tail region and also possess the C50 palmitoylation site. It is involved in M2 cholesterol binding.
Influenza A_M2_SF15 Influenza A_M2_determinant-of-host-range-specificity_11(5) 5 172 functional 11,14,16,18,20 PMID: 15777646, At positions 11, 14, 16, 18 and 20, Weybridge possesses Thr, Gly, Glu, Ser and Ser, whereas WSN possesses Ile, Glu, Gly, Arg and Asn, respectively.
Influenza A_M2_SF16 Influenza A_M2_determinant-of-amantadine-resistance_26(1) 1 12 functional 26 PMID: 15673732, This residue is one of the critical amino acid occuring within the transmembrane domain of M2 protein. Substitution at this residue results in loss of sensitivity to M2 inhibitor drugs.
Influenza A_M2_SF17 Influenza A_M2_determinant-of-amantadine-resistance_27(1) 1 15 functional 27 PMID: 15673732, It is shown that single-amino-acid substitution at this position within the transmembrane domain of M2 produces amantadine resistance in Influenza viruses
Influenza A_M2_SF18 Influenza A_M2_determinant-of-amantadine-resistance_30(1) 1 13 functional 30 PMID: 15673732, It is shown that single-amino-acid substitution at this position within the transmembrane domain of M2 produces amantadine resistance in Influenza viruses
Influenza A_M2_SF19 Influenza A_M2_determinant-of-amantadine-resistance_31(1) 1 14 functional 31 PMID: 15673732, It is shown that single-amino-acid substitution at this position within the transmembrane domain of M2 produces amantadine resistance in Influenza viruses
Influenza A_M2_SF20 Influenza A_M2_determinant-of-amantadine-resistance_34(1) 1 9 functional 34 PMID: 15673732, It is shown that single-amino-acid substitution at this position within the transmembrane domain of M2 produces amantadine resistance in Influenza viruses
Influenza A_M2_SF103 Influenza A_M2_determinant-of-virulence_50(1) 1 14 functional 50 PMID: 19553312, The viruses lacking the palmitoylation site at this residue have been shown to cause a modest reduction in virulence in vivo (mouse models) although the effect is not seen tissue culture cells.
Influenza A_M2_SF104 Influenza A_M2_determinants-of-infectivity_74(6) 6 98 functional 74..79 PMID: 16699003, The amino acids 74 to 79 of the M2 tail play a role in virion morphogenesis and affect viral infectivity.
Influenza A_M2_SF108 Influenza A_M2_determinant-of-transmission_16(1) 1 12 sequence alteration 16 PMID: 22132146, A16G substitution leads to enhanced transmission in humans
Influenza A_M2_SF109 Influenza A_M2_determinant-of-transmission_55(1) 1 14 sequence alteration 55 PMID: 22132146, C55F substitution leads to enhanced transmission in humans
Influenza A_M2_SF110 Influenza A_M2_determinant-of-drug-resistance_31(1) 1 14 sequence alteration 31 PMID: 22132146, 31N confers resistance to Adamantane
Influenza A_M2_SF111 Influenza A_M2_determinant-of-drug-resistance_26(1) 1 11 sequence alteration 26 PMID: 16456087, PMID: 15673732, 26F confers resistance to Adamantane
Influenza A_M2_SF112 Influenza A_M2_determinant-of-drug-resistance_27(1) 1 14 sequence alteration 27 PMID: 16456087, PMID: 15673732, 27A confers resistance to Adamantane
Influenza A_M2_SF113 Influenza A_M2_determinant-of-drug-resistance_30(1) 1 14 sequence alteration 30 PMID: 16456087, PMID: 15673732, 30T confers resistance to Adamantane
Influenza A_M2_SF114 Influenza A_M2_determinant-of-drug-resistance_34(1) 1 9 sequence alteration 34 PMID: 16456087, PMID: 15673732, 34E confers resistance to Adamantane
Influenza A_M2_SF118 Influenza A_M2_antiviral-activity_26(1) 1 10 functional 26 PMID:20834097, PMID:15673732 , Introduction of Leu26Phe substitution in the WSN/1933 backbone conferred decreased sensitivity to amantadine as indicated by plaque reduction assay in MDBK cells and reduced plaque sizes.
Influenza A_M2_SF119 Influenza A_M2_antiviral-activity_34(1) 1 8 functional 34 PMID:15673732, Introduction of Gly34Glu substitution in the WSN/1933 backbone conferred decreased sensitivity to amantadine as indicated by plaque reduction assay.
Influenza A_M2_SF120 Influenza A_M2_antiviral-activity_27(1) 1 13 functional 27 PMID:20834097, PMID:15673732, PMID:16703504, PMID:16081121 , Introduction of Val27Ala substitution in the A/Chicken/Hong Kong/YU250/03 backbone conferred decreased sensitivity to amantadine.
Influenza A_M2_SF121 Influenza A_M2_Antiviral-activity_31(1) 1 13 functional 31 PMID: 20834097; 16703504; 2723453; 17897729; 17431677; 15659762; 17494553; 16081121 , A/Chicken/Hebei/108/2002 isolate with Ser31Asn substitution conferred decreased sensitivity to amantadine and rimantadine in MDCK cells using plaque assay.
Influenza A_M2_SF122 Influenza A_M2_Antiviral-activity_31(1) 1 13 functional 31 PMID: 20834097; 16703504; 2723453; 17897729; 17431677; 15659762; 17494553; 16081121 , A/Chicken/Hebei/108/2002 isolate with Ser31Asn substitution conferred decreased sensitivity to amantadine and rimantadine in MDCK cells using plaque assay.
Influenza A_M2_AVD_SF1 Influenza A_M2_antiviral-binding-site_2RLF_40(5) 5 34 functional 40..41,43..45 PMID: 18235503, Rimantadine Binding Site
Influenza A_M2_AVD_SF2 Influenza A_M2_antiviral-binding-site_2LJC_30(2) 2 24 functional 30..31 PMID: 22078564, Rimantadine Binding Site

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