Basic Information

Type: gene

Biological Identity

Species

arabidopsis_thaliana

Chromosome

Orthogroup ID

OG0005779

Physical Location & Seq

Genomic Coordinates Forward (+)

16760846 .. 16764276

Gene Structure 3431 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

AT5G41880.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1356 bp

ATGACGAGAGAGGAGACTGAAACCAGTGGAGAGGATATGATGATTGATGACCCAAAACCCAAAATCGAAAACGATTTCAATGTTCATTACCTCCGAATTTACTACGGAAATCTATTTCCTTACACTGATATTCACAAATGGCTTTCTTATGGGCACGATGGGAAACATCCTGGTTGTGATGAATATTACTTTGGTAGAAGAGAATTCTCGTTTACGCTTGAAAACGATGTTTATTTGCGGTATAAGTCTTTCAAGAATGCTTCACTTATGGAAGCTGCTATCAAATCGAATTTTCCATACAAGATTGATATTGGTGCTGTGTATAGCGTTGATCCGGATAAGAGACATGCATATGCTCAAAGTGGAACCAATTTGTTTACTCCAGTGGAGAGGGAGTTAGTCTTTGATATTGATATAACAGATTATGATGATGTTAGATACTGTTGTTCGGGAGCCGATGTTTGCTCCAAATGCTGGCCTTTAATGACAGTTGCTATCAAAGTCATTGATACTTCCTTAAGAGAGGATTTTGGTTTCAAACACATCCTCTGGGTCTTCAGTGGACGTCGTGGAGTTCACTGTTGGGTTTGTGATGCTAAAGCTCGAAGGTTGACTAATGAACAAAGATCAGCAGTTGCTGAATACTTTCGTGTTTATAAGGGAAATGAAAACAATGCAAAAAAGGTCGATCTGATGGGTCATTCTCTTCATCCGTTTCTTGCGAGATCATATGTGGACTTTATTAAGAGTTTCTTTGAGGGTGAGTTACAAGCAACTCAAAGTATATTCTCAAGCAAAGAAAAGTATGAGAAGATACTTGGGATGATTACAGATGAAGATATTCAAGCAGACCTCAGAGGAAAGTGGGAGAATTCTGCGAGATCATCTCTATCAGAAGAAGCCACCAGCCTTTTAAGGTGGGAACAACTTAAGAAAGCTCTTCAATCGAAGAGAAACAAGGCTCTATCACTGCGGACGTGCGTAGAAGAAATTGTCTTCACCTTTACGTATCCTCGAATTGATTTGGAGGTTTCAAAACAAATGAACCATTTGCTTAAGGCACCCTTCTGCGTCCATCCAAAAACAGGTCGTGTCTGTGTTCCTATTGACCCGAATAACTGTGATGAGTTTGATCCATTGGCAGTTCCAACTCTTTCACAGCTAATAGAAGAAATCAATTCCGGTGGCCTCAGAATGGACGTGGATGATGATGATTCAGATAGTAGTTTACTTGGGAAATCAATAAAGTTCTTCAGATCCTCATTCCTAGAACCCTTACTAAAATCATGCAAGGAAGAAATAGAGAGTTCATACAAAACCAAGATTGCTAAGACTAAGGATTCATTCAGCTGGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0000428 GO:0003674 GO:0003676 GO:0003677 GO:0003697 GO:0003824 GO:0003896 GO:0003899 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005657 GO:0005658 GO:0005694 GO:0006139 GO:0006259 GO:0006260 GO:0006261 GO:0006269 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030880 GO:0030894 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0032993 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043596 GO:0043601 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044454 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097159 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901363 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03030 map00230 map00240 map01100 map03030

Pfam Domains

Protein Families

DNA_primase_S

Protein Analysis

451

Amino Acids

52.07

Weight (kDa)

5.77

Isoelectric Point (pI)

45.66

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
DNA_primase_S	PF01896	135 - 370	2.1e-51	DNA primase small subunit

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0005779)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G41880
fragaria_vesca	FvH4_5g04460
malus_domestica	MD06G1105400.v1.1
prunus_persica	Prupe.5G117700_v2.0.a1
pyrus_communis	pycom06g09970
rosa_chinensis	RchiOBHm_Chr7g0195041
rosa_laevigata	RLG00000004150 RLG00000008501 RLG00000015305
rosa_multiflora	Rmu_sc0002246.1_g000003
rosa_roxburghii	Rroxscaffold_3G00260810
rosa_rugosa	Rorug07G0020100 Rorug07G0020200
rosa_samantha	Rh6BG025100 Rh6BG025600 Rh6BG025700 Rh6BG026500 Rh6BG026600 Rh6CG024600 Rh6DG024100 Rh6DG024400 Rh7AG147700 Rh7BG148300 Rh7CG152000
rosa_wichuraiana	Rw2G021680 Rw5G042100 Rw6G002490 Rw7G012610

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	657
AatII	GACGTC	1 cut(s)	568
AccB1I	GGYRCC	1 cut(s)	1060
AccB7I	CCANNNNNTGG	1 cut(s)	474
AccIII	TCCGGA	1 cut(s)	334
AciI	CCGC	2 cut(s)	238, 973
AclWI	GGATC	3 cut(s)	326, 1127, 1251
AcsI	RAATTY	4 cut(s)	96, 203, 289, 871
AcuI	CTGAAG	2 cut(s)	541, 1237
AcyI	GRCGYC	1 cut(s)	565
AfiI	CCNNNNNNNGG	3 cut(s)	474, 1085, 1195
AflII	CTTAAG	3 cut(s)	517, 929, 1055
AgsI	TTSAA	7 cut(s)	79, 221, 253, 538, 845, 944, 1035
AjiI	CACGTC	2 cut(s)	978, 1201
AjnI	CCWGG	1 cut(s)	169
AjuI	GAANNNNNNNTTGG	2 cut(s)	174, 206
AluBI	AGCT	5 cut(s)	275, 602, 938, 1162, 1350
AluI	AGCT	5 cut(s)	275, 602, 938, 1162, 1350
Alw26I	GTCTC	2 cut(s)	8, 337
AlwI	GGATC	3 cut(s)	326, 1127, 1251
AlwNI	CAGNNNCTG	1 cut(s)	638
Aor13HI	TCCGGA	1 cut(s)	334
AoxI	GGCC	2 cut(s)	476, 1186
ApeKI	GCWGC	1 cut(s)	275
ApoI	RAATTY	4 cut(s)	96, 203, 289, 871
Asp700I	GAANNNNTTC	2 cut(s)	645, 840
AsuHPI	GGTGA	2 cut(s)	773, 991
BaeGI	GKGCMC	1 cut(s)	156
BaeI	ACNNNNGTAYC	2 cut(s)	430, 463
BanI	GGYRCC	1 cut(s)	1060
BbsI	GAAGAC	2 cut(s)	547, 988
BbvI	GCAGC	1 cut(s)	262
BccI	CCATC	3 cut(s)	152, 688, 1083
BciT130I	CCWGG	1 cut(s)	171
BciVI	GTATCC	1 cut(s)	1020
BcoDI	GTCTC	2 cut(s)	8, 337
BfaI	CTAG	1 cut(s)	1268
BfrI	CTTAAG	3 cut(s)	517, 929, 1055
BfuI	GTATCC	1 cut(s)	1020
BisI	GCNGC	1 cut(s)	276
BlsI	GCNGC	1 cut(s)	277
Bme1390I	CCNGG	1 cut(s)	171
BmgBI	CACGTC	2 cut(s)	978, 1201
BmiI	GGNNCC	3 cut(s)	367, 454, 1062
BmrFI	CCNGG	1 cut(s)	171
BmsI	GCATC	1 cut(s)	583
BpiI	GAAGAC	2 cut(s)	547, 988
BplI	GAGNNNNNCTC	2 cut(s)	871, 903
BpmI	CTGGAG	1 cut(s)	366
BpuEI	CTTGAG	1 cut(s)	775
BsaAI	YACGTR	1 cut(s)	1008
BsaHI	GRCGYC	1 cut(s)	565
BsaWI	WCCGGW	2 cut(s)	334, 1181
BsaXI	ACNNNNNCTCC	4 cut(s)	380, 410, 444, 474
Bsc4I	CCNNNNNNNGG	3 cut(s)	474, 1085, 1195
Bse1I	ACTGG	2 cut(s)	24, 383
BseAI	TCCGGA	1 cut(s)	334
BseBI	CCWGG	1 cut(s)	171
BseGI	GGATG	6 cut(s)	166, 543, 709, 828, 1075, 1210
BseLI	CCNNNNNNNGG	3 cut(s)	474, 1085, 1195
BseMII	CTCAG	2 cut(s)	868, 1204
BseNI	ACTGG	2 cut(s)	24, 383
BseRI	GAGGAG	1 cut(s)	26
BseSI	GKGCMC	1 cut(s)	156
BseXI	GCAGC	1 cut(s)	262
BshFI	GGCC	2 cut(s)	478, 1188
BshNI	GGYRCC	1 cut(s)	1060
BsiSI	CCGG	2 cut(s)	335, 1182
BslI	CCNNNNNNNGG	3 cut(s)	474, 1085, 1195
BsmAI	GTCTC	2 cut(s)	8, 337
BsmI	GAATGC	1 cut(s)	262
BsnI	GGCC	2 cut(s)	478, 1188
Bsp1286I	GDGCHC	1 cut(s)	156
Bsp13I	TCCGGA	1 cut(s)	334
Bsp143I	GATC	7 cut(s)	331, 626, 688, 725, 881, 1132, 1256
BspACI	CCGC	2 cut(s)	238, 973
BspANI	GGCC	2 cut(s)	478, 1188
BspCNI	CTCAG	2 cut(s)	867, 1203
BspEI	TCCGGA	1 cut(s)	334
BspLI	GGNNCC	3 cut(s)	367, 454, 1062
BspPI	GGATC	3 cut(s)	326, 1127, 1251
BspQI	GCTCTTC	1 cut(s)	945
BspT107I	GGYRCC	1 cut(s)	1060
BspTI	CTTAAG	3 cut(s)	517, 929, 1055
BsrI	ACTGG	2 cut(s)	24, 383
BssMI	GATC	7 cut(s)	331, 626, 688, 725, 881, 1132, 1256
BssNI	GRCGYC	1 cut(s)	565
Bst2UI	CCWGG	1 cut(s)	171
Bst4CI	ACNGT	4 cut(s)	443, 490, 581, 1121
Bst6I	CTCTTC	4 cut(s)	193, 711, 944, 945
BstACI	GRCGYC	1 cut(s)	565
BstAFI	CTTAAG	3 cut(s)	517, 929, 1055
BstBAI	YACGTR	1 cut(s)	1008
BstC8I	GCNNGC	1 cut(s)	476
BstDEI	CTNAG	4 cut(s)	854, 1190, 1329, 1335
BstF5I	GGATG	6 cut(s)	166, 543, 709, 828, 1075, 1210
BstKTI	GATC	7 cut(s)	334, 629, 691, 728, 884, 1135, 1259
BstMAI	GTCTC	2 cut(s)	8, 337
BstMBI	GATC	7 cut(s)	331, 626, 688, 725, 881, 1132, 1256
BstMWI	GCNNNNNNNGC	1 cut(s)	471
BstNI	CCWGG	1 cut(s)	171
BstNSI	RCATGY	1 cut(s)	350
BstSCI	CCNGG	1 cut(s)	169
BstSLI	GKGCMC	1 cut(s)	156
BstSNI	TACGTA	1 cut(s)	1008
BstV1I	GCAGC	1 cut(s)	262
BstV2I	GAAGAC	2 cut(s)	547, 988
BstX2I	RGATCY	1 cut(s)	1256
BstYI	RGATCY	1 cut(s)	1256
BsuI	GTATCC	1 cut(s)	1020
BsuRI	GGCC	2 cut(s)	478, 1188
BtrI	CACGTC	2 cut(s)	978, 1201
BtsCI	GGATG	6 cut(s)	166, 543, 709, 828, 1075, 1210
BtsI	GCAGTG	1 cut(s)	968
BtsIMutI	CAGTG	6 cut(s)	31, 123, 390, 565, 577, 968
Cac8I	GCNNGC	1 cut(s)	476
CaiI	CAGNNNCTG	1 cut(s)	638
CseI	GACGC	1 cut(s)	1060
CspCI	CAANNNNNGTGG	2 cut(s)	1165, 1200
CviAII	CATG	2 cut(s)	347, 1287
DdeI	CTNAG	4 cut(s)	854, 1190, 1329, 1335
DpnI	GATC	7 cut(s)	333, 628, 690, 727, 883, 1134, 1258
DpnII	GATC	7 cut(s)	331, 626, 688, 725, 881, 1132, 1256
Eam1104I	CTCTTC	4 cut(s)	193, 711, 944, 945
EarI	CTCTTC	4 cut(s)	193, 711, 944, 945
Eco105I	TACGTA	1 cut(s)	1008
Eco57I	CTGAAG	2 cut(s)	541, 1237
EcoRI	GAATTC	2 cut(s)	203, 871
EcoRII	CCWGG	1 cut(s)	169
EcoT22I	ATGCAT	1 cut(s)	352
FaeI	CATG	2 cut(s)	350, 1290
FalI	AAGNNNNNCTT	4 cut(s)	737, 769, 1049, 1081
FatI	CATG	2 cut(s)	346, 1286
FauNDI	CATATG	2 cut(s)	352, 730
Fnu4HI	GCNGC	1 cut(s)	276
FokI	GGATG	6 cut(s)	153, 530, 696, 835, 1062, 1217
Fsp4HI	GCNGC	1 cut(s)	276
FspBI	CTAG	1 cut(s)	1268
GluI	GCNGC	1 cut(s)	276
GsuI	CTGGAG	1 cut(s)	366
HaeIII	GGCC	2 cut(s)	478, 1188
HapII	CCGG	2 cut(s)	335, 1182
HgaI	GACGC	1 cut(s)	1060
Hin1I	GRCGYC	1 cut(s)	565
Hin1II	CATG	2 cut(s)	350, 1290
HincII	GTYRAC	1 cut(s)	612
HindII	GTYRAC	1 cut(s)	612
HinfI	GANTC	2 cut(s)	1214, 1340
HpaII	CCGG	2 cut(s)	335, 1182
HphI	GGTGA	2 cut(s)	773, 991
Hpy166II	GTNNAC	7 cut(s)	213, 378, 563, 577, 612, 736, 1229
Hpy188I	TCNGA	7 cut(s)	95, 693, 857, 895, 1193, 1219, 1256
Hpy188III	TCNNGA	3 cut(s)	253, 335, 450
Hpy8I	GTNNAC	7 cut(s)	213, 378, 563, 577, 612, 736, 1229
Hpy99I	CGWCG	1 cut(s)	570
HpyAV	CCTTC	2 cut(s)	600, 1075
HpyCH4III	ACNGT	4 cut(s)	443, 490, 581, 1121
HpyCH4IV	ACGT	4 cut(s)	565, 977, 1007, 1200
HpyCH4V	TGCA	3 cut(s)	350, 677, 1290
HpyF10VI	GCNNNNNNNGC	1 cut(s)	471
HpyF3I	CTNAG	4 cut(s)	854, 1190, 1329, 1335
HpySE526I	ACGT	4 cut(s)	565, 977, 1007, 1200
Hsp92I	GRCGYC	1 cut(s)	565
Hsp92II	CATG	2 cut(s)	350, 1290
Kpn2I	TCCGGA	1 cut(s)	334
Kzo9I	GATC	7 cut(s)	331, 626, 688, 725, 881, 1132, 1256
LguI	GCTCTTC	1 cut(s)	945
LmnI	GCTCC	2 cut(s)	452, 470
Lsp1109I	GCAGC	1 cut(s)	262
LweI	GCATC	1 cut(s)	583
MaeI	CTAG	1 cut(s)	1268
MaeII	ACGT	4 cut(s)	565, 977, 1007, 1200
MaeIII	GTNAC	1 cut(s)	765
MalI	GATC	7 cut(s)	333, 628, 690, 727, 883, 1134, 1258
MboI	GATC	7 cut(s)	331, 626, 688, 725, 881, 1132, 1256
MflI	RGATCY	1 cut(s)	1256
MhlI	GDGCHC	1 cut(s)	156
MluCI	AATT	8 cut(s)	96, 203, 289, 370, 871, 990, 1017, 1177
MmeI	TCCRAC	1 cut(s)	1172
Mph1103I	ATGCAT	1 cut(s)	352
MroI	TCCGGA	1 cut(s)	334
MroXI	GAANNNNTTC	2 cut(s)	645, 840
MseI	TTAA	6 cut(s)	482, 518, 744, 914, 930, 1056
MslI	CAYNNNNRTG	1 cut(s)	351
MspA1I	CMGCKG	1 cut(s)	1350
MspCI	CTTAAG	3 cut(s)	517, 929, 1055
MspI	CCGG	2 cut(s)	335, 1182
MspR9I	CCNGG	1 cut(s)	171
Mva1269I	GAATGC	1 cut(s)	262
MvaI	CCWGG	1 cut(s)	171
MwoI	GCNNNNNNNGC	1 cut(s)	471
NdeI	CATATG	2 cut(s)	352, 730
NdeII	GATC	7 cut(s)	331, 626, 688, 725, 881, 1132, 1256
NlaIII	CATG	2 cut(s)	350, 1290
NlaIV	GGNNCC	3 cut(s)	367, 454, 1062
NsiI	ATGCAT	1 cut(s)	352
NspI	RCATGY	1 cut(s)	350
PciSI	GCTCTTC	1 cut(s)	945
PctI	GAATGC	1 cut(s)	262
PdmI	GAANNNNTTC	2 cut(s)	645, 840
PfeI	GAWTC	2 cut(s)	1214, 1340
PflMI	CCANNNNNTGG	1 cut(s)	474
PkrI	GCNGC	1 cut(s)	277
Ppu21I	YACGTR	1 cut(s)	1008
PsiI	TTATAA	1 cut(s)	657
Psp6I	CCWGG	1 cut(s)	169
PspGI	CCWGG	1 cut(s)	169
PspN4I	GGNNCC	3 cut(s)	367, 454, 1062
PstNI	CAGNNNCTG	1 cut(s)	638
PsuI	RGATCY	1 cut(s)	1256
PvuII	CAGCTG	1 cut(s)	1350
RseI	CAYNNNNRTG	1 cut(s)	351
SapI	GCTCTTC	1 cut(s)	945
SaqAI	TTAA	6 cut(s)	482, 518, 744, 914, 930, 1056
SatI	GCNGC	1 cut(s)	276
Sau3AI	GATC	7 cut(s)	331, 626, 688, 725, 881, 1132, 1256
ScrFI	CCNGG	1 cut(s)	171
SduI	GDGCHC	1 cut(s)	156
SfaNI	GCATC	1 cut(s)	583
SmiMI	CAYNNNNRTG	1 cut(s)	351
SmlI	CTYRAG	4 cut(s)	517, 790, 929, 1055
SmoI	CTYRAG	4 cut(s)	517, 790, 929, 1055
SnaBI	TACGTA	1 cut(s)	1008
Sse9I	AATT	8 cut(s)	96, 203, 289, 370, 871, 990, 1017, 1177
SsiI	CCGC	2 cut(s)	238, 973
SspI	AATATT	1 cut(s)	185
SspMI	CTAG	1 cut(s)	1268
StyD4I	CCNGG	1 cut(s)	169
TaaI	ACNGT	4 cut(s)	443, 490, 581, 1121
TaiI	ACGT	4 cut(s)	568, 980, 1010, 1203
TaqI	TCGA	6 cut(s)	66, 287, 604, 687, 947, 1015
TasI	AATT	8 cut(s)	96, 203, 289, 370, 871, 990, 1017, 1177
TfiI	GAWTC	2 cut(s)	1214, 1340
Tru1I	TTAA	6 cut(s)	482, 518, 744, 914, 930, 1056
Tru9I	TTAA	6 cut(s)	482, 518, 744, 914, 930, 1056
TscAI	CASTG	6 cut(s)	31, 130, 390, 565, 584, 975
TseI	GCWGC	1 cut(s)	275
TspDTI	ATGAA	9 cut(s)	74, 195, 633, 681, 698, 849, 1058, 1299, 1332
TspGWI	ACGGA	2 cut(s)	120, 702
TspRI	CASTG	6 cut(s)	31, 130, 390, 565, 584, 975
Van91I	CCANNNNNTGG	1 cut(s)	474
Vha464I	CTTAAG	3 cut(s)	517, 929, 1055
XapI	RAATTY	4 cut(s)	96, 203, 289, 871
XceI	RCATGY	1 cut(s)	350
XmnI	GAANNNNTTC	2 cut(s)	645, 840
XspI	CTAG	1 cut(s)	1268
ZraI	GACGTC	1 cut(s)	566
Zsp2I	ATGCAT	1 cut(s)	352

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.