Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0002257

Physical Location & Seq

Genomic Coordinates Reverse (-)

1700325 .. 1702488

Gene Structure 2164 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG025300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1062 bp

ATGTGCGGAGCTCACCGACTTCACAGTTCAAGGCATGAACGTTTGGTTCACTCTTCTTCGCAGCCGAAAATCACAGTTGAAGATTTCTCAAAGAAGCGGTCCATGGAACTTCGACTGCTCCATGGGATTGCTTATGGACATCCTTGGTTCGGTAGATGGGGGTACAGGTTTTGCCATGGAAGCTTTGGGGTTGCAGAAGAAACATATGAAAGAGCGCTTGATATTCTCAGCTCAATAGAGCTTGAAAAGATCATCCAAGATTTTAGTGACATGGAAGAGTGTGAAGAGCTGAAGAGAGTAATTCATTGCTACAAACATTGGAGCGAATCAAGCTTGGTTACAATCAAAGATCTTCTCAAATTTATGCTCACTGTCAAGGCTGGCTGTCCTGTGCAAAGAAAAGTCAGAAAACCGAAACCGCCTACTACTACTACTCTTTCATCCCTCCGGATCAAGTCCAAGCTGTTTACTGATGTTATTTCTCACAACCCCGGCAGACATCCTGCAAGAAGACTAAAGATGGCTGCAGATGCGATTGTGCATGTATTGAGAGAAAATGAAAAGAAAGGCTTTGTGAATGGTGAGATGGCCAGGCAAGATGTAAGAGATGCAGCTCTGTTGCATAGTAGAAGAAGAGGGTTGCCTATCAGAGATATAGGTTTGTTGGATAATGTACTGAGCAAGCTGGACAATGTGATTATTGGGAATCACATTGTCTGCCGCAAGCTGCATGCGATGCCTGGAATTAAGACTGGAATTAGGAAATATACCGTTCATGATCTTCTCGATGGAATCAAGTCCTTGGAACCTGAGAGAGAGTTACTTCTTCCATCACAAGCTCTAGTTCCTGATGTTTACAGTGATGTTCTTTACTTGTACAAGAATGTACTGTTGGGATATCCAGAATCCAAGTTGGTACAATTGGCTACTCAAGTGGTGTTGAACACCAAGTACTTTGTAAAGGAATATCGATTCGGGGATAAGGATGAGCAAGAGCAGTGCCTTGACATTCCTTTGCCAAGTATGACTGATAGTGCTAATCCTGCCGAGTCAGGAATCTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000212 GO:0000226 GO:0000228 GO:0000280 GO:0000785 GO:0000790 GO:0000791 GO:0003006 GO:0003674 GO:0003676 GO:0003677 GO:0003682 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005694 GO:0005719 GO:0006323 GO:0006355 GO:0006996 GO:0007010 GO:0007017 GO:0007049 GO:0007051 GO:0007059 GO:0007060 GO:0007140 GO:0007275 GO:0007276 GO:0008134 GO:0008150 GO:0009555 GO:0009889 GO:0009987 GO:0010032 GO:0010468 GO:0010556 GO:0016043 GO:0019219 GO:0019222 GO:0019953 GO:0022402 GO:0022412 GO:0022414 GO:0030154 GO:0030261 GO:0031323 GO:0031326 GO:0031974 GO:0031981 GO:0032501 GO:0032502 GO:0032504 GO:0033613 GO:0042393 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0043565 GO:0044422 GO:0044424 GO:0044427 GO:0044428 GO:0044446 GO:0044454 GO:0044464 GO:0044703 GO:0045132 GO:0048229 GO:0048232 GO:0048235 GO:0048285 GO:0048609 GO:0048856 GO:0048869 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0051276 GO:0051321 GO:0051704 GO:0055046 GO:0060255 GO:0065007 GO:0070013 GO:0070192 GO:0071103 GO:0071840 GO:0080090 GO:0097159 GO:0098813 GO:0140013 GO:1901363 GO:1903046 GO:1903506 GO:1990188 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PHD

Protein Analysis

353

Amino Acids

40.29

Weight (kDa)

9.09

Isoelectric Point (pI)

41.27

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
WHD_plant_repro	PF25874	166 - 245	3.1e-14	Winged helix-turn-helix domain in plant reproductive proteins

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: OG0002257)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G66170
fragaria_vesca	FvH4_1g29990 FvH4_1g29990 FvH4_1g29990 FvH4_6g02390
malus_domestica	MD09G1267100.v1.1 MD17G1254900.v1.1 MD17G1255100.v1.1 MD17G1260200.v1.1
prunus_persica	Prupe.3G164800_v2.0.a1
pyrus_communis	pycom12401g00150 pycom461g00270
rosa_chinensis	RchiOBHm_Chr3g0450161 RchiOBHm_Chr3g0492331
rosa_laevigata	RLG00000022781 RLG00000022872 RLG00000022874 RLG00000022875 RLG00000025750
rosa_multiflora	Rmu_co8200976.1_g000001 Rmu_sc0003156.1_g000026 Rmu_sc0010184.1_g000005 Rmu_sc0010184.1_g000015 Rmu_sc0020297.1_g000001
rosa_roxburghii	Rroxscaffold_3G00226630 Rroxscaffold_6G00392410 Rroxscaffold_6G00427920
rosa_rugosa	Rorug02G0625900 Rorug03G0253300
rosa_samantha	Rh2AG397300 Rh2CG383900 Rh3AG025300 Rh3AG303200 Rh3BG025900 Rh3BG339200 Rh3BG339300 Rh3CG024800 Rh3CG336400 Rh3DG025900 Rh3DG327500 Rh3DG338500
rosa_wichuraiana	Rw3G002030 Rw3G026750

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccIII	TCCGGA	1 cut(s)	447
AciI	CCGC	4 cut(s)	6, 97, 419, 721
AclI	AACGTT	1 cut(s)	40
AclWI	GGATC	1 cut(s)	458
AcoI	YGGCCR	1 cut(s)	588
AcsI	RAATTY	1 cut(s)	359
AcuI	CTGAAG	1 cut(s)	311
AfaI	GTAC	6 cut(s)	164, 675, 878, 888, 918, 953
AfeI	AGCGCT	1 cut(s)	216
AfiI	CCNNNNNNNGG	1 cut(s)	149
AgsI	TTSAA	4 cut(s)	30, 80, 245, 943
AjnI	CCWGG	2 cut(s)	590, 739
AjuI	GAANNNNNNNTTGG	2 cut(s)	875, 907
Alw21I	GWGCWC	1 cut(s)	13
AlwI	GGATC	1 cut(s)	458
Aor13HI	TCCGGA	1 cut(s)	447
Aor51HI	AGCGCT	1 cut(s)	216
AoxI	GGCC	1 cut(s)	588
ApeKI	GCWGC	4 cut(s)	61, 524, 611, 727
ApoI	RAATTY	1 cut(s)	359
ArsI	GACNNNNNNTTYG	2 cut(s)	83, 115
AspLEI	GCGC	1 cut(s)	217
AspS9I	GGNCC	1 cut(s)	99
AsuC2I	CCSGG	1 cut(s)	492
AsuHPI	GGTGA	2 cut(s)	5, 593
AvaII	GGWCC	1 cut(s)	99
BalI	TGGCCA	1 cut(s)	590
BanII	GRGCYC	1 cut(s)	13
BbsI	GAAGAC	1 cut(s)	517
Bbv12I	GWGCWC	1 cut(s)	13
BbvI	GCAGC	4 cut(s)	73, 511, 623, 714
BccI	CCATC	5 cut(s)	150, 514, 580, 782, 838
BciT130I	CCWGG	2 cut(s)	592, 741
BcnI	CCSGG	1 cut(s)	492
BfaI	CTAG	1 cut(s)	842
BfmI	CTRYAG	1 cut(s)	525
BfoI	RGCGCY	1 cut(s)	218
BglII	AGATCT	1 cut(s)	349
BisI	GCNGC	5 cut(s)	62, 525, 612, 721, 728
BlsI	GCNGC	5 cut(s)	63, 526, 613, 722, 729
BmcAI	AGTACT	1 cut(s)	953
Bme1390I	CCNGG	3 cut(s)	492, 592, 741
Bme18I	GGWCC	1 cut(s)	99
BmgT120I	GGNCC	1 cut(s)	99
BmiI	GGNNCC	1 cut(s)	807
BmrFI	CCNGG	3 cut(s)	492, 592, 741
BmsI	GCATC	3 cut(s)	520, 598, 726
BpiI	GAAGAC	1 cut(s)	517
BpuEI	CTTGAG	1 cut(s)	915
BpuMI	CCSGG	1 cut(s)	492
Bsa29I	ATCGAT	1 cut(s)	970
BsaJI	CCNNGG	6 cut(s)	102, 121, 143, 175, 490, 801
BsaWI	WCCGGW	1 cut(s)	447
Bsc4I	CCNNNNNNNGG	1 cut(s)	149
Bse1I	ACTGG	1 cut(s)	757
Bse3DI	GCAATG	1 cut(s)	304
BseAI	TCCGGA	1 cut(s)	447
BseBI	CCWGG	2 cut(s)	592, 741
BseCI	ATCGAT	1 cut(s)	970
BseDI	CCNNGG	6 cut(s)	102, 121, 143, 175, 490, 801
BseGI	GGATG	5 cut(s)	139, 252, 440, 499, 991
BseLI	CCNNNNNNNGG	1 cut(s)	149
BseMI	GCAATG	1 cut(s)	304
BseMII	CTCAG	3 cut(s)	241, 668, 801
BseNI	ACTGG	1 cut(s)	757
BseXI	GCAGC	4 cut(s)	73, 511, 623, 714
BshFI	GGCC	1 cut(s)	590
BshVI	ATCGAT	1 cut(s)	970
BsiHKAI	GWGCWC	1 cut(s)	13
BsiSI	CCGG	2 cut(s)	448, 492
BslI	CCNNNNNNNGG	1 cut(s)	149
BsnI	GGCC	1 cut(s)	590
Bsp1286I	GDGCHC	1 cut(s)	13
Bsp13I	TCCGGA	1 cut(s)	447
Bsp1407I	TGTACA	1 cut(s)	876
Bsp143I	GATC	4 cut(s)	249, 349, 450, 778
Bsp19I	CCATGG	3 cut(s)	102, 121, 175
BspACI	CCGC	4 cut(s)	6, 97, 419, 721
BspANI	GGCC	1 cut(s)	590
BspCNI	CTCAG	3 cut(s)	240, 669, 802
BspDI	ATCGAT	1 cut(s)	970
BspEI	TCCGGA	1 cut(s)	447
BspHI	TCATGA	1 cut(s)	775
BspLI	GGNNCC	1 cut(s)	807
BspMAI	CTGCAG	1 cut(s)	529
BspPI	GGATC	1 cut(s)	458
BspQI	GCTCTTC	1 cut(s)	279
BsrDI	GCAATG	1 cut(s)	304
BsrGI	TGTACA	1 cut(s)	876
BsrI	ACTGG	1 cut(s)	757
BssECI	CCNNGG	6 cut(s)	102, 121, 143, 175, 490, 801
BssMI	GATC	4 cut(s)	249, 349, 450, 778
BssT1I	CCWWGG	5 cut(s)	102, 121, 143, 175, 801
Bst2UI	CCWGG	2 cut(s)	592, 741
Bst4CI	ACNGT	6 cut(s)	26, 76, 373, 772, 860, 891
Bst6I	CTCTTC	5 cut(s)	58, 270, 279, 287, 628
BstAPI	GCANNNNNTGC	1 cut(s)	736
BstAUI	TGTACA	1 cut(s)	876
BstC8I	GCNNGC	4 cut(s)	382, 683, 725, 732
BstDEI	CTNAG	3 cut(s)	227, 677, 810
BstDSI	CCRYGG	3 cut(s)	102, 121, 175
BstF5I	GGATG	5 cut(s)	139, 252, 440, 499, 991
BstH2I	RGCGCY	1 cut(s)	218
BstHHI	GCGC	1 cut(s)	217
BstKTI	GATC	4 cut(s)	252, 352, 453, 781
BstMBI	GATC	4 cut(s)	249, 349, 450, 778
BstMWI	GCNNNNNNNGC	5 cut(s)	180, 330, 530, 736, 1043
BstNI	CCWGG	2 cut(s)	592, 741
BstNSI	RCATGY	2 cut(s)	545, 734
BstSCI	CCNGG	3 cut(s)	490, 590, 739
BstSFI	CTRYAG	1 cut(s)	525
BstV1I	GCAGC	4 cut(s)	73, 511, 623, 714
BstV2I	GAAGAC	1 cut(s)	517
BstX2I	RGATCY	1 cut(s)	349
BstYI	RGATCY	1 cut(s)	349
Bsu15I	ATCGAT	1 cut(s)	970
BsuRI	GGCC	1 cut(s)	590
BsuTUI	ATCGAT	1 cut(s)	970
BtgI	CCRYGG	3 cut(s)	102, 121, 175
BtgZI	GCGATG	1 cut(s)	749
BtsCI	GGATG	5 cut(s)	139, 252, 440, 499, 991
BtsI	GCAGTG	1 cut(s)	1004
BtsIMutI	CAGTG	3 cut(s)	369, 865, 1004
Cac8I	GCNNGC	4 cut(s)	382, 683, 725, 732
CciI	TCATGA	1 cut(s)	775
CfoI	GCGC	1 cut(s)	217
Cfr13I	GGNCC	1 cut(s)	99
ClaI	ATCGAT	1 cut(s)	970
Csp6I	GTAC	6 cut(s)	163, 674, 877, 887, 917, 952
CviAII	CATG	8 cut(s)	35, 103, 122, 176, 271, 542, 731, 776
CviQI	GTAC	6 cut(s)	163, 674, 877, 887, 917, 952
DdeI	CTNAG	3 cut(s)	227, 677, 810
DpnI	GATC	4 cut(s)	251, 351, 452, 780
DpnII	GATC	4 cut(s)	249, 349, 450, 778
EaeI	YGGCCR	1 cut(s)	588
Eam1104I	CTCTTC	5 cut(s)	58, 270, 279, 287, 628
EarI	CTCTTC	5 cut(s)	58, 270, 279, 287, 628
Ecl136II	GAGCTC	1 cut(s)	11
Eco130I	CCWWGG	5 cut(s)	102, 121, 143, 175, 801
Eco24I	GRGCYC	1 cut(s)	13
Eco32I	GATATC	1 cut(s)	899
Eco47I	GGWCC	1 cut(s)	99
Eco47III	AGCGCT	1 cut(s)	216
Eco53kI	GAGCTC	1 cut(s)	11
Eco57I	CTGAAG	1 cut(s)	311
EcoICRI	GAGCTC	1 cut(s)	11
EcoRII	CCWGG	2 cut(s)	590, 739
EcoRV	GATATC	1 cut(s)	899
EcoT14I	CCWWGG	5 cut(s)	102, 121, 143, 175, 801
EcoT38I	GRGCYC	1 cut(s)	13
ErhI	CCWWGG	5 cut(s)	102, 121, 143, 175, 801
FaeI	CATG	8 cut(s)	38, 106, 125, 179, 274, 545, 734, 779
FalI	AAGNNNNNCTT	2 cut(s)	554, 586
FatI	CATG	8 cut(s)	34, 102, 121, 175, 270, 541, 730, 775
FauNDI	CATATG	1 cut(s)	205
Fnu4HI	GCNGC	5 cut(s)	62, 525, 612, 721, 728
FokI	GGATG	5 cut(s)	126, 239, 427, 486, 998
FriOI	GRGCYC	1 cut(s)	13
Fsp4HI	GCNGC	5 cut(s)	62, 525, 612, 721, 728
FspBI	CTAG	1 cut(s)	842
GlaI	GCGC	1 cut(s)	216
GluI	GCNGC	5 cut(s)	62, 525, 612, 721, 728
HaeII	RGCGCY	1 cut(s)	218
HaeIII	GGCC	1 cut(s)	590
HapII	CCGG	2 cut(s)	448, 492
HhaI	GCGC	1 cut(s)	217
Hin1II	CATG	8 cut(s)	38, 106, 125, 179, 274, 545, 734, 779
Hin6I	GCGC	1 cut(s)	215
HinP1I	GCGC	1 cut(s)	215
HindIII	AAGCTT	2 cut(s)	181, 331
HinfI	GANTC	7 cut(s)	326, 706, 792, 905, 972, 1049, 1056
HpaII	CCGG	2 cut(s)	448, 492
HphI	GGTGA	2 cut(s)	5, 593
Hpy166II	GTNNAC	3 cut(s)	49, 468, 856
Hpy188I	TCNGA	2 cut(s)	407, 650
Hpy188III	TCNNGA	6 cut(s)	448, 776, 785, 848, 902, 1053
Hpy8I	GTNNAC	3 cut(s)	49, 468, 856
HpyCH4III	ACNGT	6 cut(s)	26, 76, 373, 772, 860, 891
HpyCH4IV	ACGT	1 cut(s)	40
HpyCH4V	TGCA	8 cut(s)	194, 394, 506, 527, 541, 611, 622, 730
HpyF10VI	GCNNNNNNNGC	5 cut(s)	180, 330, 530, 736, 1043
HpyF3I	CTNAG	3 cut(s)	227, 677, 810
HpySE526I	ACGT	1 cut(s)	40
Hsp92II	CATG	8 cut(s)	38, 106, 125, 179, 274, 545, 734, 779
HspAI	GCGC	1 cut(s)	215
Kpn2I	TCCGGA	1 cut(s)	447
Kzo9I	GATC	4 cut(s)	249, 349, 450, 778
LguI	GCTCTTC	1 cut(s)	279
LmnI	GCTCC	3 cut(s)	8, 123, 321
Lsp1109I	GCAGC	4 cut(s)	73, 511, 623, 714
LweI	GCATC	3 cut(s)	520, 598, 726
MaeI	CTAG	1 cut(s)	842
MaeII	ACGT	1 cut(s)	40
MaeIII	GTNAC	3 cut(s)	266, 337, 819
MalI	GATC	4 cut(s)	251, 351, 452, 780
MboI	GATC	4 cut(s)	249, 349, 450, 778
MfeI	CAATTG	1 cut(s)	920
MflI	RGATCY	1 cut(s)	349
MhlI	GDGCHC	1 cut(s)	13
MlsI	TGGCCA	1 cut(s)	590
MluCI	AATT	5 cut(s)	300, 359, 744, 756, 920
MluNI	TGGCCA	1 cut(s)	590
MlyI	GAGTC	1 cut(s)	1058
MmeI	TCCRAC	1 cut(s)	645
MnlI	CCTC	2 cut(s)	455, 629
Mox20I	TGGCCA	1 cut(s)	590
MroI	TCCGGA	1 cut(s)	447
MscI	TGGCCA	1 cut(s)	590
MseI	TTAA	1 cut(s)	747
Msp20I	TGGCCA	1 cut(s)	590
MspI	CCGG	2 cut(s)	448, 492
MspR9I	CCNGG	3 cut(s)	492, 592, 741
MunI	CAATTG	1 cut(s)	920
MvaI	CCWGG	2 cut(s)	592, 741
MwoI	GCNNNNNNNGC	5 cut(s)	180, 330, 530, 736, 1043
NciI	CCSGG	1 cut(s)	492
NcoI	CCATGG	3 cut(s)	102, 121, 175
NdeI	CATATG	1 cut(s)	205
NdeII	GATC	4 cut(s)	249, 349, 450, 778
NlaIII	CATG	8 cut(s)	38, 106, 125, 179, 274, 545, 734, 779
NlaIV	GGNNCC	1 cut(s)	807
NmuCI	GTSAC	1 cut(s)	266
NspI	RCATGY	2 cut(s)	545, 734
PaeI	GCATGC	1 cut(s)	734
PagI	TCATGA	1 cut(s)	775
PciSI	GCTCTTC	1 cut(s)	279
PfeI	GAWTC	6 cut(s)	326, 706, 792, 905, 972, 1056
PkrI	GCNGC	5 cut(s)	63, 526, 613, 722, 729
PleI	GAGTC	1 cut(s)	1057
PpsI	GAGTC	1 cut(s)	1057
Psp124BI	GAGCTC	1 cut(s)	13
Psp1406I	AACGTT	1 cut(s)	40
Psp6I	CCWGG	2 cut(s)	590, 739
PspGI	CCWGG	2 cut(s)	590, 739
PspN4I	GGNNCC	1 cut(s)	807
PspPI	GGNCC	1 cut(s)	99
PsrI	GAACNNNNNNTAC	2 cut(s)	935, 967
PstI	CTGCAG	1 cut(s)	529
PsuI	RGATCY	1 cut(s)	349
RsaI	GTAC	6 cut(s)	164, 675, 878, 888, 918, 953
RsaNI	GTAC	6 cut(s)	163, 674, 877, 887, 917, 952
SacI	GAGCTC	1 cut(s)	13
SapI	GCTCTTC	1 cut(s)	279
SaqAI	TTAA	1 cut(s)	747
SatI	GCNGC	5 cut(s)	62, 525, 612, 721, 728
Sau3AI	GATC	4 cut(s)	249, 349, 450, 778
Sau96I	GGNCC	1 cut(s)	99
ScaI	AGTACT	1 cut(s)	953
SchI	GAGTC	1 cut(s)	1058
ScrFI	CCNGG	3 cut(s)	492, 592, 741
SduI	GDGCHC	1 cut(s)	13
SfaNI	GCATC	3 cut(s)	520, 598, 726
SfcI	CTRYAG	1 cut(s)	525
SinI	GGWCC	1 cut(s)	99
SmlI	CTYRAG	1 cut(s)	930
SmoI	CTYRAG	1 cut(s)	930
SphI	GCATGC	1 cut(s)	734
Sse9I	AATT	5 cut(s)	300, 359, 744, 756, 920
SsiI	CCGC	4 cut(s)	6, 97, 419, 721
SspMI	CTAG	1 cut(s)	842
SstI	GAGCTC	1 cut(s)	13
StyD4I	CCNGG	3 cut(s)	490, 590, 739
StyI	CCWWGG	5 cut(s)	102, 121, 143, 175, 801
TaaI	ACNGT	6 cut(s)	26, 76, 373, 772, 860, 891
TaiI	ACGT	1 cut(s)	43
TaqI	TCGA	3 cut(s)	112, 786, 970
TasI	AATT	5 cut(s)	300, 359, 744, 756, 920
TatI	WGTACW	4 cut(s)	673, 876, 886, 951
TauI	GCSGC	1 cut(s)	723
TfiI	GAWTC	6 cut(s)	326, 706, 792, 905, 972, 1056
Tru1I	TTAA	1 cut(s)	747
Tru9I	TTAA	1 cut(s)	747
TscAI	CASTG	3 cut(s)	376, 865, 1004
TseFI	GTSAC	1 cut(s)	266
TseI	GCWGC	4 cut(s)	61, 524, 611, 727
Tsp45I	GTSAC	1 cut(s)	266
TspDTI	ATGAA	6 cut(s)	51, 222, 293, 429, 573, 764
TspRI	CASTG	3 cut(s)	376, 865, 1004
VpaK11BI	GGWCC	1 cut(s)	99
XapI	RAATTY	1 cut(s)	359
XceI	RCATGY	2 cut(s)	545, 734
XcmI	CCANNNNNNNNNTGG	1 cut(s)	182
XspI	CTAG	1 cut(s)	842
ZrmI	AGTACT	1 cut(s)	953

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