Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0011725

Physical Location & Seq

Genomic Coordinates Reverse (-)

60200498 .. 60203065

Gene Structure 2568 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG384700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1128 bp

ATGTCACAGACAATGGCACTGAATAGACTCGGTTCAATCTTTCTCGTCTTCTTTTTGTTGTCCTGTGTTGCTGTAATTGTCAACGCCGAAAATGATACTGCGGAAGATGAGTACTGGAAAGAACGAGCCGCTGTTGCTATGAAAATTGCCGAGGAATCTGTTCATCCAAATCCCCAGGAAGTTACCGAGGAGATCAATGCTGACGTACACGAGCTTATCATGGGGCAAAATAGCACGAAAAGGAAATTGAGAGGTTCCAAGGGATATGACGGTCCCTGCGAGGCCACCAACCCAATCGACGCATGCTGGCGGTGTGACCCTGATTGGGCCGACAATCGGGAGAAGATCGTCGATTGCGTCAAGGGTTTCGGCAAAAAGACTACCGGCGGCAAGGGTGGGCCCATCTACATTGTCACTGATGACTCAGATGACGACATTGTGAACCCTAAACCAGGAACCCTCCGCGACGCAGTGATCCAGAAAGGTCCTCTATGGATCATCTTTGAGCATAGCATGGTGATTCGTCTGCAACAAGAGCTGATGGTAACAAGTGACAAAACCATCGATGGTAGAGGAGCCAATGTTGTGATTGCCTTTGGTGGTGGTATCACTCTTCAGTATGTGAAAAATATCATCATCACGAACATTCACGTTAAGGACATTGAGTCCAAAGCCGGTGGTATGATCAGAGACTGCGTGAATCATTTTGGTTTTAGGACCAGGAGCGATGGCGATGGCATCTCCCTCTTCGGCGCTTCCAACGTCTGGATCGACCATGTTTCCATGGCGAGGTGCGACGACGGACTCATTGACGCTATCATGAGTTCCACTGCTATCACCATCTCCAACTCCCACTTCACTGACCACAACGAGGCAATGTTGTTCGGGGCAAGTAATAGCTACTCTCAAGACAAGATCATGCAAGTAACGGTCGCGTTCAACCACTTTGGGCAGGGGTTGATTCAGAGAATGCCAAGGTGCCGATTTGGATTCTTCCACGTGGTGAACAATGACTACACCCATTGGATAATGTATGCTATTGGTGGTAACATGAACCCTACCATCATCAGCCAGGGTAACAGGTACATTGCCCCTGAAAGCCATGTCGCAAAAGAGGTATGCAGTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0003824 GO:0008150 GO:0009664 GO:0009987 GO:0016043 GO:0016829 GO:0016835 GO:0016837 GO:0030570 GO:0045229 GO:0071554 GO:0071555 GO:0071669 GO:0071840

KEGG Pathways

Metabolic & Signaling

ko00040 ko02024 map00040 map02024

Pfam Domains

Protein Families

Pec_lyase_C Pec_lyase_N

Protein Analysis

375

Amino Acids

41.49

Weight (kDa)

5.54

Isoelectric Point (pI)

28.42

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Pec_lyase_N	PF04431	36 - 83	2.6e-13	Pectate lyase, N terminus
Pectate_lyase_4	PF00544	178 - 363	4e-19	Pectate lyase

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0011725)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G14420 AT2G02720
fragaria_vesca	FvH4_4g31900
malus_domestica	MD13G1078400.v1.1 MD16G1078000.v1.1 MD16G1078100.v1.1
prunus_persica	Prupe.1G268500_v2.0.a1 Prupe.1G268700_v2.0.a1
pyrus_communis	pycom13g06810 pycom16g06740 pycom16g06760
rosa_chinensis	RchiOBHm_Chr4g0440551
rosa_rugosa	Rorug04G0326600
rosa_samantha	Rh4AG378300 Rh4BG391000 Rh4CG405700 Rh4DG384700
rosa_wichuraiana	Rw4G032390 Rw4G032490

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	978
AccB7I	CCANNNNNTGG	1 cut(s)	765
AccII	CGCG	2 cut(s)	465, 935
AciI	CCGC	5 cut(s)	101, 129, 310, 387, 463
AclWI	GGATC	3 cut(s)	469, 503, 776
AcuI	CTGAAG	1 cut(s)	599
AcvI	CACGTG	1 cut(s)	1000
AdeI	CACNNNGTG	1 cut(s)	1003
AfaI	GTAC	3 cut(s)	113, 207, 1085
AfiI	CCNNNNNNNGG	6 cut(s)	325, 336, 452, 765, 789, 871
AgsI	TTSAA	2 cut(s)	36, 940
AhdI	GACNNNNNGTC	1 cut(s)	664
AjnI	CCWGG	4 cut(s)	174, 451, 719, 1071
AjuI	GAANNNNNNNTTGG	2 cut(s)	839, 871
AluBI	AGCT	3 cut(s)	214, 538, 900
AluI	AGCT	3 cut(s)	214, 538, 900
Alw26I	GTCTC	1 cut(s)	684
AlwI	GGATC	3 cut(s)	469, 503, 776
AlwNI	CAGNNNCTG	1 cut(s)	693
AoxI	GGCC	3 cut(s)	282, 327, 398
ApaI	GGGCCC	1 cut(s)	402
Asp700I	GAANNNNTTC	1 cut(s)	159
AspLEI	GCGC	1 cut(s)	755
AspS9I	GGNCC	6 cut(s)	272, 327, 398, 399, 485, 717
AsuHPI	GGTGA	3 cut(s)	529, 829, 1015
AvaII	GGWCC	3 cut(s)	272, 485, 717
BaeGI	GKGCMC	1 cut(s)	402
BanI	GGYRCC	1 cut(s)	978
BanII	GRGCYC	1 cut(s)	402
BauI	CACGAG	1 cut(s)	209
BbrPI	CACGTG	1 cut(s)	1000
BbsI	GAAGAC	1 cut(s)	40
BccI	CCATC	8 cut(s)	410, 535, 560, 569, 722, 728, 848, 1070
BciT130I	CCWGG	4 cut(s)	176, 453, 721, 1073
BclI	TGATCA	1 cut(s)	684
BcoDI	GTCTC	1 cut(s)	684
BfoI	RGCGCY	1 cut(s)	756
BisI	GCNGC	2 cut(s)	129, 388
BlsI	GCNGC	2 cut(s)	130, 389
BmcAI	AGTACT	1 cut(s)	113
Bme1390I	CCNGG	4 cut(s)	176, 453, 721, 1073
Bme18I	GGWCC	3 cut(s)	272, 485, 717
BmeRI	GACNNNNNGTC	1 cut(s)	664
BmgT120I	GGNCC	6 cut(s)	272, 327, 398, 399, 485, 717
BmiI	GGNNCC	6 cut(s)	256, 274, 400, 457, 577, 980
BmrFI	CCNGG	4 cut(s)	176, 453, 721, 1073
BmsI	GCATC	1 cut(s)	747
BpiI	GAAGAC	1 cut(s)	40
BpuEI	CTTGAG	1 cut(s)	891
Bsa29I	ATCGAT	1 cut(s)	564
BsaAI	YACGTR	1 cut(s)	1000
BsaJI	CCNNGG	7 cut(s)	150, 174, 186, 258, 783, 974, 1072
BsaXI	ACNNNNNCTCC	2 cut(s)	567, 597
Bsc4I	CCNNNNNNNGG	6 cut(s)	325, 336, 452, 765, 789, 871
Bse118I	RCCGGY	2 cut(s)	383, 674
Bse1I	ACTGG	1 cut(s)	119
Bse3DI	GCAATG	2 cut(s)	882, 1086
BseBI	CCWGG	4 cut(s)	176, 453, 721, 1073
BseCI	ATCGAT	1 cut(s)	564
BseDI	CCNNGG	7 cut(s)	150, 174, 186, 258, 783, 974, 1072
BseGI	GGATG	1 cut(s)	163
BseLI	CCNNNNNNNGG	6 cut(s)	325, 336, 452, 765, 789, 871
BseMI	GCAATG	2 cut(s)	882, 1086
BseMII	CTCAG	1 cut(s)	438
BseNI	ACTGG	1 cut(s)	119
BseRI	GAGGAG	2 cut(s)	203, 588
BseSI	GKGCMC	1 cut(s)	402
Bsh1236I	CGCG	2 cut(s)	465, 935
Bsh1285I	CGRYCG	1 cut(s)	933
BshFI	GGCC	3 cut(s)	284, 329, 400
BshNI	GGYRCC	1 cut(s)	978
BshVI	ATCGAT	1 cut(s)	564
BsiEI	CGRYCG	1 cut(s)	933
BsiSI	CCGG	2 cut(s)	384, 675
BslFI	GGGAC	1 cut(s)	258
BslI	CCNNNNNNNGG	6 cut(s)	325, 336, 452, 765, 789, 871
BsmAI	GTCTC	1 cut(s)	684
BsmFI	GGGAC	1 cut(s)	258
BsmI	GAATGC	1 cut(s)	975
BsnI	GGCC	3 cut(s)	284, 329, 400
Bsp120I	GGGCCC	1 cut(s)	398
Bsp1286I	GDGCHC	1 cut(s)	402
Bsp143I	GATC	7 cut(s)	192, 345, 474, 495, 684, 768, 915
Bsp19I	CCATGG	1 cut(s)	783
BspACI	CCGC	5 cut(s)	101, 129, 310, 387, 463
BspANI	GGCC	3 cut(s)	284, 329, 400
BspCNI	CTCAG	1 cut(s)	437
BspDI	ATCGAT	1 cut(s)	564
BspFNI	CGCG	2 cut(s)	465, 935
BspHI	TCATGA	1 cut(s)	819
BspLI	GGNNCC	6 cut(s)	256, 274, 400, 457, 577, 980
BspPI	GGATC	3 cut(s)	469, 503, 776
BspT107I	GGYRCC	1 cut(s)	978
BsrDI	GCAATG	2 cut(s)	882, 1086
BsrFI	RCCGGY	2 cut(s)	383, 674
BsrI	ACTGG	1 cut(s)	119
BssAI	RCCGGY	2 cut(s)	383, 674
BssECI	CCNNGG	7 cut(s)	150, 174, 186, 258, 783, 974, 1072
BssMI	GATC	7 cut(s)	192, 345, 474, 495, 684, 768, 915
BssSI	CACGAG	1 cut(s)	209
BssT1I	CCWWGG	3 cut(s)	258, 783, 974
Bst2BI	CACGAG	1 cut(s)	209
Bst2UI	CCWGG	4 cut(s)	176, 453, 721, 1073
Bst4CI	ACNGT	2 cut(s)	272, 931
Bst6I	CTCTTC	2 cut(s)	618, 752
BstBAI	YACGTR	1 cut(s)	1000
BstC8I	GCNNGC	2 cut(s)	304, 308
BstDEI	CTNAG	1 cut(s)	424
BstDSI	CCRYGG	1 cut(s)	783
BstENI	CCTNNNNNAGG	1 cut(s)	450
BstF5I	GGATG	1 cut(s)	163
BstFNI	CGCG	2 cut(s)	465, 935
BstH2I	RGCGCY	1 cut(s)	756
BstHHI	GCGC	1 cut(s)	755
BstKTI	GATC	7 cut(s)	195, 348, 477, 498, 687, 771, 918
BstMAI	GTCTC	1 cut(s)	684
BstMBI	GATC	7 cut(s)	192, 345, 474, 495, 684, 768, 915
BstMCI	CGRYCG	1 cut(s)	933
BstMWI	GCNNNNNNNGC	2 cut(s)	134, 535
BstNI	CCWGG	4 cut(s)	176, 453, 721, 1073
BstNSI	RCATGY	1 cut(s)	306
BstSCI	CCNGG	4 cut(s)	174, 451, 719, 1071
BstSLI	GKGCMC	1 cut(s)	402
BstUI	CGCG	2 cut(s)	465, 935
BstV2I	GAAGAC	1 cut(s)	40
Bsu15I	ATCGAT	1 cut(s)	564
BsuRI	GGCC	3 cut(s)	284, 329, 400
BsuTUI	ATCGAT	1 cut(s)	564
BtgI	CCRYGG	1 cut(s)	783
BtgZI	GCGATG	2 cut(s)	741, 747
BtsCI	GGATG	1 cut(s)	163
BtsI	GCAGTG	2 cut(s)	477, 828
BtsIMutI	CAGTG	5 cut(s)	17, 414, 477, 828, 858
Cac8I	GCNNGC	2 cut(s)	304, 308
CaiI	CAGNNNCTG	1 cut(s)	693
CciI	TCATGA	1 cut(s)	819
CfoI	GCGC	1 cut(s)	755
Cfr10I	RCCGGY	2 cut(s)	383, 674
Cfr13I	GGNCC	6 cut(s)	272, 327, 398, 399, 485, 717
ClaI	ATCGAT	1 cut(s)	564
CseI	GACGC	4 cut(s)	308, 346, 476, 821
Csp6I	GTAC	3 cut(s)	112, 206, 1084
CspCI	CAANNNNNGTGG	2 cut(s)	658, 693
CviAII	CATG	9 cut(s)	220, 303, 514, 776, 784, 820, 919, 1051, 1103
CviQI	GTAC	3 cut(s)	112, 206, 1084
DdeI	CTNAG	1 cut(s)	424
DpnI	GATC	7 cut(s)	194, 347, 476, 497, 686, 770, 917
DpnII	GATC	7 cut(s)	192, 345, 474, 495, 684, 768, 915
DraIII	CACNNNGTG	1 cut(s)	1003
DriI	GACNNNNNGTC	1 cut(s)	664
Eam1104I	CTCTTC	2 cut(s)	618, 752
Eam1105I	GACNNNNNGTC	1 cut(s)	664
EarI	CTCTTC	2 cut(s)	618, 752
Eco130I	CCWWGG	3 cut(s)	258, 783, 974
Eco24I	GRGCYC	1 cut(s)	402
Eco47I	GGWCC	3 cut(s)	272, 485, 717
Eco57I	CTGAAG	1 cut(s)	599
Eco72I	CACGTG	1 cut(s)	1000
EcoNI	CCTNNNNNAGG	1 cut(s)	450
EcoO109I	RGGNCCY	1 cut(s)	485
EcoRII	CCWGG	4 cut(s)	174, 451, 719, 1071
EcoT14I	CCWWGG	3 cut(s)	258, 783, 974
EcoT38I	GRGCYC	1 cut(s)	402
ErhI	CCWWGG	3 cut(s)	258, 783, 974
FaeI	CATG	9 cut(s)	223, 306, 517, 779, 787, 823, 922, 1054, 1106
FaqI	GGGAC	1 cut(s)	258
FatI	CATG	9 cut(s)	219, 302, 513, 775, 783, 819, 918, 1050, 1102
FbaI	TGATCA	1 cut(s)	684
Fnu4HI	GCNGC	2 cut(s)	129, 388
FokI	GGATG	1 cut(s)	150
FriOI	GRGCYC	1 cut(s)	402
Fsp4HI	GCNGC	2 cut(s)	129, 388
GlaI	GCGC	1 cut(s)	754
GluI	GCNGC	2 cut(s)	129, 388
HaeII	RGCGCY	1 cut(s)	756
HaeIII	GGCC	3 cut(s)	284, 329, 400
HapII	CCGG	2 cut(s)	384, 675
HgaI	GACGC	4 cut(s)	308, 346, 476, 821
HhaI	GCGC	1 cut(s)	755
Hin1II	CATG	9 cut(s)	223, 306, 517, 779, 787, 823, 922, 1054, 1106
Hin6I	GCGC	1 cut(s)	753
HinP1I	GCGC	1 cut(s)	753
HincII	GTYRAC	1 cut(s)	82
HindII	GTYRAC	1 cut(s)	82
HinfI	GANTC	9 cut(s)	27, 155, 422, 520, 665, 700, 804, 961, 990
HpaII	CCGG	2 cut(s)	384, 675
HphI	GGTGA	3 cut(s)	529, 829, 1015
Hpy166II	GTNNAC	4 cut(s)	82, 208, 442, 1006
Hpy188I	TCNGA	3 cut(s)	427, 689, 966
Hpy188III	TCNNGA	6 cut(s)	338, 478, 640, 766, 820, 908
Hpy8I	GTNNAC	4 cut(s)	82, 208, 442, 1006
Hpy99I	CGWCG	5 cut(s)	302, 353, 470, 800, 803
HpyCH4III	ACNGT	2 cut(s)	272, 931
HpyCH4IV	ACGT	4 cut(s)	204, 651, 762, 999
HpyCH4V	TGCA	3 cut(s)	529, 922, 1122
HpyF10VI	GCNNNNNNNGC	2 cut(s)	134, 535
HpyF3I	CTNAG	1 cut(s)	424
HpySE526I	ACGT	4 cut(s)	204, 651, 762, 999
Hsp92II	CATG	9 cut(s)	223, 306, 517, 779, 787, 823, 922, 1054, 1106
HspAI	GCGC	1 cut(s)	753
Ksp22I	TGATCA	1 cut(s)	684
Kzo9I	GATC	7 cut(s)	192, 345, 474, 495, 684, 768, 915
LmnI	GCTCC	2 cut(s)	575, 723
LweI	GCATC	1 cut(s)	747
MaeII	ACGT	4 cut(s)	204, 651, 762, 999
MaeIII	GTNAC	9 cut(s)	3, 181, 314, 412, 544, 551, 925, 1046, 1076
MalI	GATC	7 cut(s)	194, 347, 476, 497, 686, 770, 917
MboI	GATC	7 cut(s)	192, 345, 474, 495, 684, 768, 915
MboII	GAAGA	6 cut(s)	40, 116, 355, 605, 739, 985
MhlI	GDGCHC	1 cut(s)	402
MluCI	AATT	3 cut(s)	75, 144, 245
MlyI	GAGTC	4 cut(s)	21, 416, 674, 798
MmeI	TCCRAC	2 cut(s)	783, 870
MroXI	GAANNNNTTC	1 cut(s)	159
MseI	TTAA	2 cut(s)	654, 1126
MspA1I	CMGCKG	1 cut(s)	131
MspI	CCGG	2 cut(s)	384, 675
MspR9I	CCNGG	4 cut(s)	176, 453, 721, 1073
Mva1269I	GAATGC	1 cut(s)	975
MvaI	CCWGG	4 cut(s)	176, 453, 721, 1073
MvnI	CGCG	2 cut(s)	465, 935
MwoI	GCNNNNNNNGC	2 cut(s)	134, 535
NcoI	CCATGG	1 cut(s)	783
NdeII	GATC	7 cut(s)	192, 345, 474, 495, 684, 768, 915
NlaIII	CATG	9 cut(s)	223, 306, 517, 779, 787, 823, 922, 1054, 1106
NlaIV	GGNNCC	6 cut(s)	256, 274, 400, 457, 577, 980
NmeAIII	GCCGAG	1 cut(s)	175
NmuCI	GTSAC	4 cut(s)	3, 314, 412, 551
NspI	RCATGY	1 cut(s)	306
PaeI	GCATGC	1 cut(s)	306
PagI	TCATGA	1 cut(s)	819
PcsI	WCGNNNNNNNCGW	3 cut(s)	276, 354, 768
PctI	GAATGC	1 cut(s)	975
PdmI	GAANNNNTTC	1 cut(s)	159
PfeI	GAWTC	5 cut(s)	155, 520, 700, 961, 990
PflMI	CCANNNNNTGG	1 cut(s)	765
PkrI	GCNGC	2 cut(s)	130, 389
PleI	GAGTC	4 cut(s)	21, 416, 673, 798
PmaCI	CACGTG	1 cut(s)	1000
PmlI	CACGTG	1 cut(s)	1000
PpsI	GAGTC	4 cut(s)	21, 416, 673, 798
Ppu21I	YACGTR	1 cut(s)	1000
PpuMI	RGGWCCY	1 cut(s)	485
Psp5II	RGGWCCY	1 cut(s)	485
Psp6I	CCWGG	4 cut(s)	174, 451, 719, 1071
PspCI	CACGTG	1 cut(s)	1000
PspGI	CCWGG	4 cut(s)	174, 451, 719, 1071
PspN4I	GGNNCC	6 cut(s)	256, 274, 400, 457, 577, 980
PspOMI	GGGCCC	1 cut(s)	398
PspPI	GGNCC	6 cut(s)	272, 327, 398, 399, 485, 717
PspPPI	RGGWCCY	1 cut(s)	485
PsrI	GAACNNNNNNTAC	2 cut(s)	998, 1030
PstNI	CAGNNNCTG	1 cut(s)	693
RsaI	GTAC	3 cut(s)	113, 207, 1085
RsaNI	GTAC	3 cut(s)	112, 206, 1084
SaqAI	TTAA	2 cut(s)	654, 1126
SatI	GCNGC	2 cut(s)	129, 388
Sau3AI	GATC	7 cut(s)	192, 345, 474, 495, 684, 768, 915
Sau96I	GGNCC	6 cut(s)	272, 327, 398, 399, 485, 717
ScaI	AGTACT	1 cut(s)	113
SchI	GAGTC	4 cut(s)	21, 416, 674, 798
ScrFI	CCNGG	4 cut(s)	176, 453, 721, 1073
SduI	GDGCHC	1 cut(s)	402
SfaNI	GCATC	1 cut(s)	747
SinI	GGWCC	3 cut(s)	272, 485, 717
SmlI	CTYRAG	1 cut(s)	906
SmoI	CTYRAG	1 cut(s)	906
SphI	GCATGC	1 cut(s)	306
Sse9I	AATT	3 cut(s)	75, 144, 245
SsiI	CCGC	5 cut(s)	101, 129, 310, 387, 463
StyD4I	CCNGG	4 cut(s)	174, 451, 719, 1071
StyI	CCWWGG	3 cut(s)	258, 783, 974
TaaI	ACNGT	2 cut(s)	272, 931
TaiI	ACGT	4 cut(s)	207, 654, 765, 1002
TaqI	TCGA	4 cut(s)	297, 351, 564, 771
TasI	AATT	3 cut(s)	75, 144, 245
TatI	WGTACW	1 cut(s)	111
TauI	GCSGC	2 cut(s)	131, 390
TfiI	GAWTC	5 cut(s)	155, 520, 700, 961, 990
Tru1I	TTAA	2 cut(s)	654, 1126
Tru9I	TTAA	2 cut(s)	654, 1126
TscAI	CASTG	5 cut(s)	24, 421, 477, 835, 865
TseFI	GTSAC	4 cut(s)	3, 314, 412, 551
Tsp45I	GTSAC	4 cut(s)	3, 314, 412, 551
TspDTI	ATGAA	3 cut(s)	152, 155, 1067
TspGWI	ACGGA	1 cut(s)	816
TspRI	CASTG	5 cut(s)	24, 421, 477, 835, 865
Van91I	CCANNNNNTGG	1 cut(s)	765
VpaK11BI	GGWCC	3 cut(s)	272, 485, 717
XagI	CCTNNNNNAGG	1 cut(s)	450
XceI	RCATGY	1 cut(s)	306
XmnI	GAANNNNTTC	1 cut(s)	159
ZrmI	AGTACT	1 cut(s)	113

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