halophFGD

Basic Information

Locus ID: Ag3G00588

Species & Taxonomic ID: Apium graveolens & 4045

Genome Assembly: GCA_009905375.1

Short Name: HD1

Description: Belongs to the histone deacetylase family. HD Type 1 subfamily

Maps and Mapping Data

Chromosome	Start	End	Strand	ID
chr3	15969435	15979393	-	Ag3G00588

Protein Data

Protein Properties:

Theoretical pI	Molecular Weight	Instability Index	Aliphatic Index	GRAVY
5.25	56,229.36 Da	38.75	72.39	-0.53

Protein Domain:

Category	ID	Description	Start	End	Evalue/Score	InterPro ID
Pfam	PF00850	Histone deacetylase domain	36	324	3.8E-85	IPR023801
SUPERFAMILY	SSF52768	Arginase/deacetylase	17	381	3.69E-124	IPR023696
Gene3D	G3DSA:3.40.800.20	Histone deacetylase domain	15	388	5.6E-141	IPR037138
PIRSF	PIRSF037913	HDAC_I_euk	3	469	1.0E-212	IPR003084
PRINTS	PR01271	Histone deacetylase signature	38	55	7.3E-64	IPR003084
PRINTS	PR01271	Histone deacetylase signature	223	236	7.3E-64	IPR003084
PRINTS	PR01271	Histone deacetylase signature	102	119	7.3E-64	IPR003084
PRINTS	PR01271	Histone deacetylase signature	123	143	7.3E-64	IPR003084
PRINTS	PR01271	Histone deacetylase signature	71	89	7.3E-64	IPR003084
PRINTS	PR01271	Histone deacetylase signature	164	180	7.3E-64	IPR003084
PRINTS	PR01271	Histone deacetylase signature	240	258	7.3E-64	IPR003084
PRINTS	PR01270	Histone deacetylase superfamily signature	262	272	1.6E-23	IPR000286
PRINTS	PR01270	Histone deacetylase superfamily signature	145	168	1.6E-23	IPR000286
PRINTS	PR01270	Histone deacetylase superfamily signature	177	192	1.6E-23	IPR000286
MobiDBLite	mobidb-lite	consensus disorder prediction	477	494	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	477	501	-	-
MobiDBLite	mobidb-lite	consensus disorder prediction	383	407	-	-

Gene Ontology

Molecular Function:

GO:0004407 (histone deacetylase activity)

KEGG Pathway

KO Term:

K06067 (histone deacetylase 1/2 [EC:3.5.1.98])

Pathway:

ko04110 (Cell cycle) map04110 (Cell cycle) ko04213 (Longevity regulating pathway - multiple species) map04213 (Longevity regulating pathway - multiple species) ko04330 (Notch signaling pathway) map04330 (Notch signaling pathway)

Best hit

Source	Best Hit ID	Description
TAIR	AT4G38130.1	histone deacetylase 1. Encodes a histone deacetylase that enhances AtERF7-mediated transcriptional repression. Binds SIM3 and ERF7. Expressed in the nucleus in most tissues examined and throughout the life of the plant. Involved in jasmonic acid and ethylene dependent pathogen resistance. The sequence in GenBank has 17 AG dinucleotide repeats missing, which is also missing in Ler shotgun sequence from Cereon. Although it is annotated to be in Columbia, the GB sequence is probably not of Columbia origin. Plays a role in embryogenesis as mutants grown at higher temperatures display abnormalities in the organization of the root and shoot. Plant lines expressing an RNAi construct targeted against HDA19 shows some resistance to agrobacterium-mediated root transformation.
RefSeq	XP_017243742.1	PREDICTED: histone deacetylase 19-like [Daucus carota subsp. sativus]
Swiss-Prot	O22446	Histone deacetylase 19 OS=Arabidopsis thaliana OX=3702 GN=HDA19 PE=1 SV=2
TrEMBL	A0A165YVC9	Histone deacetylase OS=Daucus carota subsp. sativus OX=79200 GN=DCAR_013349 PE=3 SV=1

Expression

BioProject	Accession	TPM	Cultivar	Tissue	Development Stage	Sample Name	Description
PRJNA723697	SRX10692252	17.215052	Shengqin NO.2	seed	S1-1	S1-1	initial formation stage (S1)
PRJNA723697	SRX10692254	8.385539	Shengqin NO.2	seed	S1-3	S1-3	initial formation stage (S1)
PRJNA723697	SRX10692255	21.57206	Shengqin NO.2	seed	S3-1	S3-1	middle development stage (S3)
PRJNA723697	SRX10692256	23.992718	Shengqin NO.2	seed	S3-2	S3-2	middle development stage (S3)
PRJNA723697	SRX10692257	20.508816	Shengqin NO.2	seed	S3-3	S3-3	middle development stage (S3)
PRJNA723697	SRX10692258	30.727661	Shengqin NO.2	seed	S5-1	S5-1	maturation stage (S5)
PRJNA723697	SRX10692259	18.582588	Shengqin NO.2	seed	S5-2	S5-2	maturation stage (S5)
PRJNA723697	SRX10692260	15.048993	Shengqin NO.2	seed	S5-3	S5-3	maturation stage (S5)
PRJNA884666	SRX17729272	12.120281	celery	anther		W99A-r1	male sterile lineÂ
PRJNA884666	SRX17729273	10.848354	celery	anther		W99A-r2	male sterile lineÂ
PRJNA884666	SRX17729274	13.365452	celery	anther		W99A-r3	male sterile lineÂ
PRJNA884666	SRX17729275	11.350434	celery	anther		W99B-r1	maintainer line
PRJNA884666	SRX17729276	12.663939	celery	anther		W99B-r2	maintainer line
PRJNA884666	SRX17729277	15.76953	celery	anther		W99B-r3	maintainer line
PRJNA884180	SRX17743889	7.89529	var. secalinum Yablochny	collenchyma		Col_S1_rep1-1
PRJNA884180	SRX17748056	8.288359	var. secalinum Yablochny	collenchyma		Col_S1_rep3	biological replicate 3
PRJNA884180	SRX17748057	5.922427	var. secalinum Yablochny	collenchyma		Col_S1_rep4	biological replicate 4
PRJNA884180	SRX17748678	10.542645	var. secalinum Yablochny	parenchyma		Par_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748679	7.789987	var. secalinum Yablochny	parenchyma		Par_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748680	9.27781	var. secalinum Yablochny	parenchyma		Par_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748681	9.591521	var. secalinum Yablochny	parenchyma		Par_S1_rep4	Biological replicate 4
PRJNA884180	SRX17748898	9.872186	var. secalinum Yablochny	vascular bundle		Vas_S1_rep1	Biological replicate 1
PRJNA884180	SRX17748899	8.872107	var. secalinum Yablochny	vascular bundle		Vas_S1_rep2	Biological replicate 2
PRJNA884180	SRX17748900	8.609244	var. secalinum Yablochny	vascular bundle		Vas_S1_rep3	Biological replicate 3
PRJNA884180	SRX17748901	9.460497	var. secalinum Yablochny	vascular bundle		Vas_S1_rep4	Biological replicate 4
PRJNA884180	SRX17749129	6.847898	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep1	Biological replicate 1
PRJNA884180	SRX17749130	7.359785	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep2	Biological replicate 2
PRJNA884180	SRX17749131	7.412537	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep3	Biological replicate 3
PRJNA884180	SRX17749132	6.54956	var. secalinum Yablochny	part of the celery petiole without collenchyma strands		Collenchyma-free_S1_rep4	Biological replicate 4
PRJNA1124269	SRX24936411	14.818298		leaf		CK1	replicate=biological replicate1
PRJNA1124269	SRX24936412	8.817537		leaf		CK2	replicate=biological replicate2
PRJNA1124269	SRX24936413	7.5199		leaf		CK3	replicate=biological replicate3
PRJNA1124269	SRX24936414	35.390987		leaf		D1	replicate=biological replicate1
PRJNA1124269	SRX24936415	23.947712		leaf		D2	replicate=biological replicate2
PRJNA1124269	SRX24936416	29.086044		leaf		D3	replicate=biological replicate3
PRJNA1124269	SRX24936417	14.137533		leaf		MD1	replicate=biological replicate1
PRJNA1124269	SRX24936418	12.546839		leaf		MD2	replicate=biological replicate2
PRJNA1124269	SRX24936419	13.61713		leaf		MD3	replicate=biological replicate3
PRJNA387092	SRX2833309	2.735895	shanghaihuangxin	leaf	leaves between 0.5 and 1 cm in breadth, folded;	stage 2
PRJNA387092	SRX2833321	4.287056	shanghaihuangxin	leaf	leaves between 2and 2.5 cm in breadth, nearly unfolded, with clear stem exten-sion	stage 5
PRJNA387092	SRX2833323	6.063976	shanghaihuangxin	leaf	leaves >3 cm, unfolded, with clearstem extension	stage 7
PRJNA543957	SRX5879598	6.070001	Zhangzhou lvqing	stem		Se3	100 ppm Na2SeO4
PRJNA543957	SRX5879599	4.147964	Zhangzhou lvqing	stem		Se2	100 ppm Na2SeO4
PRJNA543957	SRX5879600	10.71729	Zhangzhou lvqing	stem		Mock2	mock
PRJNA543957	SRX5879601	5.700439	Zhangzhou lvqing	stem		Mock1	mock
PRJNA543957	SRX5879602	4.856371	Zhangzhou lvqing	stem		Se1	100 ppm Na2SeO4
PRJNA543957	SRX5879603	8.039699	Zhangzhou lvqing	stem		Mock3	mock
PRJNA609149	SRX7815917	13.737015	Jinnan Shiqin	flower bud	early flower bud	early flower bud
PRJNA609149	SRX7815918	13.861556	Jinnan Shiqin	flower bud	middle flower bud	middle flower bud
PRJNA609149	SRX7815919	15.064875	Jinnan Shiqin	flower bud	early flowering period	early flowering period

Network

🔍 Co-expression Network

🔍 Protein-Protein Interaction Network

Orthology

Family	Species	Count	Orthologous Genes
Acanthaceae	Avicennia marina	3	jg22524, jg27523, jg37594
Aizoaceae	Mesembryanthemum crystallinum	3	gene_19483, gene_19885, gene_6783
Amaranthaceae	Atriplex hortensis	3	Ah000539, Ah006577, Ah031725
Amaranthaceae	Beta vulgaris	2	BVRB_5g117920, BVRB_9g218010
Amaranthaceae	Salicornia bigelovii	6	Sbi_jg11170, Sbi_jg19334, Sbi_jg285, Sbi_jg36223 ... Sbi_jg43890, Sbi_jg46144
Amaranthaceae	Salicornia europaea	3	Seu_jg18031, Seu_jg20484, Seu_jg4316
Amaranthaceae	Suaeda aralocaspica	3	GOSA_00013848, GOSA_00014885, GOSA_00022160
Amaranthaceae	Suaeda glauca	8	Sgl25357, Sgl30533, Sgl55158, Sgl60408, Sgl65464, Sgl65465 ... Sgl65498, Sgl69819
Amaranthaceae	Chenopodium album	9	gene:ENSEOMG00000006091, gene:ENSEOMG00000010777 ... gene:ENSEOMG00000014298, gene:ENSEOMG00000020239, gene:ENSEOMG00000024764, gene:ENSEOMG00000024994, gene:ENSEOMG00000030047, gene:ENSEOMG00000042795, gene:ENSEOMG00000051056
Amaranthaceae	Chenopodium quinoa	6	CQ.Regalona.r1.2AG0000590, CQ.Regalona.r1.2BG0001900 ... CQ.Regalona.r1.4AG0013200, CQ.Regalona.r1.4BG0015480, CQ.Regalona.r1.5AG0023500, CQ.Regalona.r1.5BG0025000
Anacardiaceae	Pistacia vera	3	pistato.v30057020, pistato.v30107170, pistato.v30139780
Apiaceae	Apium graveolens	5	Ag10G00121, Ag11G03444, Ag11G04365, Ag3G00588, Ag5G00708
Arecaceae	Cocos nucifera	5	COCNU_06G001220, COCNU_14G000530, COCNU_14G005740 ... COCNU_15G000030, scaffold016592G000080
Arecaceae	Phoenix dactylifera	6	gene-LOC103706146, gene-LOC103708153, gene-LOC103709297 ... gene-LOC103721325, gene-LOC103721589, gene-LOC113462888
Asparagaceae	Asparagus officinalis	5	AsparagusV1_01.2263.V1.1, AsparagusV1_01.2685.V1.1 ... AsparagusV1_02.853.V1.1, AsparagusV1_02.854.V1.1, AsparagusV1_03.3063.V1.1
Asteraceae	Flaveria trinervia	3	Ftri12G29285, Ftri2G21553, FtriNA33547
Brassicaceae	Arabidopsis thaliana	4	AT3G44680.1, AT4G38130.1, AT5G35600.1, AT5G63110.1
Brassicaceae	Eutrema salsugineum	3	Thhalv10002540m.g.v1.0, Thhalv10005608m.g.v1.0 ... Thhalv10025146m.g.v1.0
Brassicaceae	Schrenkiella parvula	4	Sp2g26240.v2.2, Sp5g13800.v2.2, Sp5g16560.v2.2 ... Sp7g37620.v2.2
Brassicaceae	Brassica nigra	8	BniB01g060620.2N, BniB06g011560.2N, BniB07g042070.2N ... BniB07g062040.2N, BniB08g057690.2N, BniB08g061490.2N, BniB08g061500.2N, BniB08g061510.2N
Casuarinaceae	Casuarina equisetifolia	4	Ceq01G1913, Ceq03G1442, Ceq05G1765, Ceq09G0007
Casuarinaceae	Casuarina glauca	4	Cgl01G2080, Cgl03G1577, Cgl05G1756, Cgl09G0006
Cymodoceaceae	Cymodocea nodosa	4	gene.Cymno07g00140, gene.Cymno07g07130, gene.Cymno09g05450 ... gene.Cymno11g05370
Dunaliellaceae	Dunaliella salina	3	Dusal.0001s00049.v1.0, Dusal.0020s00020.v1.0 ... Dusal.0591s00004.v1.0
Hydrocharitaceae	Thalassia testudinum	3	gene.Thate02g16210, gene.Thate04g01140, gene.Thate09g05930
Malvaceae	Hibiscus hamabo Siebold & Zucc.	1	nbisL1-mrna-9405
Nitrariaceae	Nitraria sibirica	3	evm.TU.LG08.477, evm.TU.LG09.725, evm.TU.LG10.683
Plantaginaceae	Plantago ovata	5	Pov_00012250, Pov_00014185, Pov_00015850, Pov_00033780 ... Pov_00037523
Plumbaginaceae	Limonium bicolor	3	Lb3G19854, Lb4G25722, Lb6G31512
Poaceae	Echinochloa crus-galli	14	AH06.2118, AH07.828, AH09.893, BH02.2235, BH05.1650 ... BH06.1934, BH07.973, BH08.1152, BH09.963, CH02.2390, CH06.2161, CH07.718, CH08.1280, CH09.1079
Poaceae	Eleusine coracana subsp. coracana	12	gene-QOZ80_1AG0022330, gene-QOZ80_1BG0072590 ... gene-QOZ80_2AG0106100, gene-QOZ80_2AG0135470, gene-QOZ80_2BG0159570, gene-QOZ80_4AG0318680, gene-QOZ80_4BG0350150, gene-QOZ80_6AG0543680, gene-QOZ80_6BG0497030, gene-QOZ80_8AG0626910, gene-QOZ80_8BG0655760, gene-QOZ80_8BG0666260
Poaceae	Hordeum vulgare	6	HORVU.MOREX.r3.2HG0165820.1, HORVU.MOREX.r3.4HG0346510.1 ... HORVU.MOREX.r3.5HG0495300.1.CDS1, HORVU.MOREX.r3.6HG0578170.1, HORVU.MOREX.r3.6HG0578930.1, HORVU.MOREX.r3.7HG0715600.1
Poaceae	Lolium multiflorum	7	gene-QYE76_006558, gene-QYE76_021568, gene-QYE76_034637 ... gene-QYE76_043452, gene-QYE76_048251, gene-QYE76_053498, gene-QYE76_053706
Poaceae	Oryza coarctata	9	Oco01G013450, Oco02G013610, Oco03G005620, Oco04G005800 ... Oco07G005150, Oco11G011780, Oco12G011860, Oco15G006670, Oco16G006490
Poaceae	Oryza sativa	9	LOC_Os01g40350.1, LOC_Os01g40400.1, LOC_Os02g12350.1 ... LOC_Os02g12380.1, LOC_Os04g33480.1, LOC_Os06g38470.1, LOC_Os08g25570.1, LOC_Os11g09370.1, LOC_Os11g09418.1
Poaceae	Paspalum vaginatum	6	gene-BS78_03G176400, gene-BS78_04G085200 ... gene-BS78_05G109800, gene-BS78_06G083400, gene-BS78_07G107000, gene-BS78_10G175800
Poaceae	Puccinellia tenuiflora	8	Pt_Chr0202019, Pt_Chr0302847, Pt_Chr0302917, Pt_Chr0303060 ... Pt_Chr0303072, Pt_Chr0400554, Pt_Chr0405914, Pt_Chr0701390
Poaceae	Sporobolus alterniflorus	15	Chr02G016840, Chr05G017190, Chr06G028580, Chr06G032690 ... Chr06G032730, Chr0G019720, Chr0G029240, Chr10G017040, Chr11G005410, Chr15G019840, Chr15G024070, Chr16G012960, Chr17G012380, Chr23G013680, Chr29G007510
Poaceae	Thinopyrum elongatum	7	Tel2E01G520900, Tel2E01G521000, Tel3E01G198400 ... Tel5E01G471700, Tel6E01G359200, Tel6E01G363200, Tel7E01G612000
Poaceae	Triticum dicoccoides	9	gene_TRIDC2AG042390, gene_TRIDC2BG045510 ... gene_TRIDC5AG044140, gene_TRIDC6AG026100, gene_TRIDC6AG026730, gene_TRIDC6BG032360, gene_TRIDC6BG032740, gene_TRIDC7AG051150, gene_TRIDC7BG042690
Poaceae	Triticum aestivum	17	TraesCS2A02G293200.1, TraesCS2B02G309700.1 ... TraesCS2D02G291000.1, TraesCS4A02G213200.1, TraesCS4B02G102600.1, TraesCS4D02G100000.1, TraesCS5A02G295000.1.cds1, TraesCS5D02G302400.1.cds1, TraesCS6A02G181100.1, TraesCS6A02G184100.2, TraesCS6B02G210200.1, TraesCS6B02G212600.3, TraesCS6D02G168400.1, TraesCS6D02G171000.1, TraesCS7A02G365600.3, TraesCS7B02G261800.1, TraesCS7D02G356800.1
Poaceae	Zea mays	5	Zm00001eb084120_P001, Zm00001eb177560_P001 ... Zm00001eb205290_P002, Zm00001eb240210_P002, Zm00001eb385490_P002
Poaceae	Zoysia japonica	6	nbis-gene-10152, nbis-gene-33394, nbis-gene-41135 ... nbis-gene-43327, nbis-gene-50929, nbis-gene-7754
Poaceae	Zoysia macrostachya	6	Zma_g12442, Zma_g12544, Zma_g21219, Zma_g22831, Zma_g30745 ... Zma_g32986
Portulacaceae	Portulaca oleracea	6	evm.TU.LG02.983, evm.TU.LG03.1890, evm.TU.LG06.1364 ... evm.TU.LG09.981, evm.TU.LG11.704, evm.TU.LG14.175
Posidoniaceae	Posidonia oceanica	3	gene.Posoc04g11550, gene.Posoc04g20140, gene.Posoc05g22720
Rhizophoraceae	Bruguiera sexangula	3	evm.TU.Scaffold_11_RagTag.1064 ... evm.TU.Scaffold_13_RagTag.463, evm.TU.Scaffold_1_RagTag.2410
Rhizophoraceae	Carallia pectinifolia	3	nbisL1-mrna-14738, nbisL1-mrna-30643, nbisL1-mrna-5161
Rhizophoraceae	Ceriops tagal	3	nbisL1-mrna-5033, nbisL1-mrna-7463, nbisL1-mrna-8164
Rhizophoraceae	Ceriops zippeliana	3	nbisL1-mrna-12622, nbisL1-mrna-21034, nbisL1-mrna-3171
Rhizophoraceae	Kandelia candel	3	evm.TU.utg000010l.138, evm.TU.utg000015l.242 ... evm.TU.utg000016l.3
Rhizophoraceae	Kandelia obovata	3	Maker00008887, Maker00015452, Maker00017258
Rhizophoraceae	Rhizophora apiculata	4	nbisL1-mrna-18551, nbisL1-mrna-4161, nbisL1-mrna-4562 ... nbisL1-mrna-720
Rhizophoraceae	Rhizophora mangle	4	nbisL1-mrna-22153, nbisL1-mrna-22535, nbisL1-mrna-22536 ... nbisL1-mrna-8699
Salicaceae	Populus euphratica	4	populus_peu00125, populus_peu08383, populus_peu28698 ... populus_peu30123
Solanaceae	Lycium barbarum	3	gene-LOC132600547, gene-LOC132601610, gene-LOC132609445
Solanaceae	Solanum chilense	4	SOLCI001597500, SOLCI002971200, SOLCI004502400 ... SOLCI006985000
Solanaceae	Solanum pennellii	4	gene-LOC107004476, gene-LOC107014089, gene-LOC107020997 ... gene-LOC107031546
Tamaricaceae	Reaumuria soongarica	5	STRG.8613_chr06_-, STRG.8616_chr06_-, gene_10424, gene_14351 ... gene_820
Tamaricaceae	Tamarix chinensis	5	TC01G2597, TC03G2708, TC08G2504, TC09G2116, TC09G2122
Zosteraceae	Zostera marina	4	Zosma01g01880.v3.1, Zosma04g24440.v3.1, Zosma06g10000.v3.1 ... Zosma06g18840.v3.1