Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0004762

Physical Location & Seq

Genomic Coordinates Reverse (-)

62876607 .. 62880749

Gene Structure 4143 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG420800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1149 bp

ATGGCGCCAAGGGCAACCAGAAACCAAAGTCCACCGTGCGATCCTGACGGAATGTTCGCCGGCATGGTCGTCTTTTTAGTCCACAATGGAGTCCAGAACCGTCGATTGCAGATTTGGAAGCAGAAACTGGTCCAAATGGGAGCCACTATAGAATTGCGAGTAACCAAAAATGTCACACACATATTGGCTATGAACCCAGAAGCCCTCTTGCAAGAAGTGGGCAGTGAGCGATTGGGTTTGTTTAAAGGAAGAGTTGTACTATATCAATGGCTACAGGATAGCTTGAGCTCAGGTGAAAAGGTACCTGAAGAATTGTACCTTGTGAATTTGGATGCTGACAAGTCTTCCAGTGATTACAATTCCACTGAAAATGAAACCCCAAATCCCAAAAAGACTAAACTCTCTCCTGAGAATTCACCTCACACTCCAAGCCCTAAAACCCCCAAAGCTCTAAATGAGGATCAGGTCACACCATTGCAGTCATCCTCACCCTACAGCCCACCTGATTTGAACAGCAACATAACTCAGATATTTGGAAAGCTTATCAATATTTATAGAGCCTTGGGCGATGACCGGAGATCTTTTAGCTATTACAAGGCTATACCTGTTATAGAGAGGTTGCCGTTCAAGATACAGAGTCAGGACCAAGTTAAAGGCTTACCTAACATTGGAAAGTCAATGCAAGACCATGTGGACATTGTATGTGGAGGATCATATAGACGCGGGAAAGCTTCTTGTGGGGATCTGGACATTATAATTACACATCCTGATGGAAAAAGTCATAGAGGCTTTTTACCAAAATACGTAAAGCATTTAAAGGATATGAAGTTTCTAAGGGAGGATCTGGTTTTCAGTACACACAGTGAGGAGGGTACTGATTCTGGTGTCGACACATATTTTGGGCTTTGCACATATCCTGGACGAGAGCTGCGCCACCGCATAGATATCAAGGTCTACCCACGGGAAATATATGCATTTGCGCTAATACATTGGACAGGCAATGATGTATTGAATAGGAGGTTGAGAGTTCTAGCCGAATCTAAAGGATTCCTACTTGATGATGATGGGCTATTTCCAGCTACACGGGGCTCTCTCGGTCAACGGATTATATCCATTTTGTTTGAGAACATTTTTACTTCTGTTAACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000724 GO:0000725 GO:0000726 GO:0003674 GO:0003824 GO:0003887 GO:0005488 GO:0006139 GO:0006259 GO:0006281 GO:0006284 GO:0006285 GO:0006287 GO:0006289 GO:0006302 GO:0006303 GO:0006310 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009314 GO:0009411 GO:0009416 GO:0009628 GO:0009987 GO:0010224 GO:0016740 GO:0016772 GO:0016779 GO:0016829 GO:0016835 GO:0018130 GO:0019438 GO:0030145 GO:0033554 GO:0034061 GO:0034641 GO:0034645 GO:0034654 GO:0043167 GO:0043169 GO:0043170 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0046483 GO:0046872 GO:0046914 GO:0050896 GO:0051575 GO:0051716 GO:0071704 GO:0071897 GO:0090304 GO:0097510 GO:0140097 GO:1901360 GO:1901362 GO:1901576

KEGG Pathways

Metabolic & Signaling

ko03410 ko03450 map03410 map03450

Pfam Domains

Protein Families

BRCT DNA_pol_B_palm DNA_pol_B_thumb DNA_pol_lambd_f HHH_8 LIM

Protein Analysis

382

Amino Acids

43.03

Weight (kDa)

8.69

Isoelectric Point (pI)

54.25

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HHH_8	PF14716	171 - 232	1.1e-09	Helix-hairpin-helix domain
DNA_pol_B_palm	PF14792	224 - 321	8.1e-24	DNA polymerase beta palm
DNA_pol_B_thumb	PF14791	327 - 363	3.4e-08	DNA polymerase beta thumb

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: OG0004762)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G10520 AT1G10520
fragaria_vesca	FvH4_4g35010 FvH4_4g35030
malus_domestica	MD16G1086600.v1.1 MD16G1086700.v1.1
prunus_persica	Prupe.1G259900_v2.0.a1 Prupe.1G259900_v2.0.a1 Prupe.1G259900_v2.0.a1 Prupe.1G259900_v2.0.a1
pyrus_communis	pycom16g07470
rosa_chinensis	RchiOBHm_Chr4g0444541 RchiOBHm_Chr4g0444551
rosa_laevigata	RLG00000005822 RLG00000005825
rosa_multiflora	Rmu_sc0003839.1_g000005 Rmu_sc0012648.1_g000007
rosa_roxburghii	Rroxscaffold_5G00385000 Rroxscaffold_5G00385010
rosa_rugosa	Rorug04G0353500 Rorug04G0353600 Rorug04G0353700 Rorug04G0353800
rosa_samantha	Rh4AG413800 Rh4BG425500 Rh4CG439900 Rh4CG440200 Rh4DG420800 Rh4DG421100
rosa_wichuraiana	Rw4G035540 Rw4G035550

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	755
Acc65I	GGTACC	1 cut(s)	301
AccB1I	GGYRCC	2 cut(s)	4, 301
AccI	GTMKAC	2 cut(s)	888, 954
AccII	CGCG	1 cut(s)	723
AciI	CCGC	2 cut(s)	723, 937
AclWI	GGATC	5 cut(s)	35, 468, 718, 750, 849
AcsI	RAATTY	2 cut(s)	325, 412
AcuI	CTGAAG	1 cut(s)	327
AcyI	GRCGYC	1 cut(s)	5
AdeI	CACNNNGTG	1 cut(s)	863
AfaI	GTAC	5 cut(s)	258, 303, 317, 856, 874
AfiI	CCNNNNNNNGG	1 cut(s)	668
AgsI	TTSAA	3 cut(s)	511, 628, 1012
AjnI	CCWGG	1 cut(s)	916
AluBI	AGCT	8 cut(s)	282, 288, 449, 541, 588, 731, 928, 1079
AluI	AGCT	8 cut(s)	282, 288, 449, 541, 588, 731, 928, 1079
Alw21I	GWGCWC	1 cut(s)	290
AlwI	GGATC	5 cut(s)	35, 468, 718, 750, 849
AlwNI	CAGNNNCTG	1 cut(s)	127
ApeKI	GCWGC	1 cut(s)	928
ApoI	RAATTY	2 cut(s)	325, 412
ArsI	GACNNNNNNTTYG	4 cut(s)	38, 70, 881, 913
Asp718I	GGTACC	1 cut(s)	301
AspLEI	GCGC	3 cut(s)	7, 933, 982
AspS9I	GGNCC	2 cut(s)	130, 643
AsuHPI	GGTGA	3 cut(s)	305, 408, 480
AvaII	GGWCC	2 cut(s)	130, 643
BanI	GGYRCC	2 cut(s)	4, 301
BanII	GRGCYC	2 cut(s)	290, 1091
BbsI	GAAGAC	1 cut(s)	336
Bbv12I	GWGCWC	1 cut(s)	290
BbvI	GCAGC	1 cut(s)	915
BccI	CCATC	2 cut(s)	764, 1058
BceAI	ACGGC	1 cut(s)	607
BciT130I	CCWGG	1 cut(s)	918
BfaI	CTAG	1 cut(s)	1031
BfmI	CTRYAG	3 cut(s)	147, 272, 493
BfoI	RGCGCY	1 cut(s)	8
BglII	AGATCT	1 cut(s)	578
BisI	GCNGC	1 cut(s)	929
BlsI	GCNGC	1 cut(s)	930
Bme1390I	CCNGG	1 cut(s)	918
Bme18I	GGWCC	2 cut(s)	130, 643
BmgT120I	GGNCC	2 cut(s)	130, 643
BmiI	GGNNCC	3 cut(s)	6, 142, 303
BmrFI	CCNGG	1 cut(s)	918
BmsI	GCATC	1 cut(s)	322
BpiI	GAAGAC	1 cut(s)	336
Bpu10I	CCTNAGC	1 cut(s)	289
BpuEI	CTTGAG	1 cut(s)	304
BsaAI	YACGTR	1 cut(s)	805
BsaHI	GRCGYC	1 cut(s)	5
BsaJI	CCNNGG	3 cut(s)	8, 561, 959
BsaWI	WCCGGW	1 cut(s)	573
Bsc4I	CCNNNNNNNGG	1 cut(s)	668
Bse118I	RCCGGY	1 cut(s)	59
Bse1I	ACTGG	2 cut(s)	132, 348
Bse3DI	GCAATG	2 cut(s)	473, 1006
BseBI	CCWGG	1 cut(s)	918
BseDI	CCNNGG	3 cut(s)	8, 561, 959
BseGI	GGATG	3 cut(s)	337, 482, 763
BseLI	CCNNNNNNNGG	1 cut(s)	668
BseMI	GCAATG	2 cut(s)	473, 1006
BseMII	CTCAG	3 cut(s)	303, 399, 539
BseNI	ACTGG	2 cut(s)	132, 348
BseRI	GAGGAG	1 cut(s)	881
BseXI	GCAGC	1 cut(s)	915
Bsh1236I	CGCG	1 cut(s)	723
BshNI	GGYRCC	2 cut(s)	4, 301
BsiHKAI	GWGCWC	1 cut(s)	290
BsiSI	CCGG	2 cut(s)	60, 574
BslI	CCNNNNNNNGG	1 cut(s)	668
Bsp1286I	GDGCHC	2 cut(s)	290, 1091
Bsp143I	GATC	6 cut(s)	40, 460, 578, 710, 742, 841
BspACI	CCGC	2 cut(s)	723, 937
BspCNI	CTCAG	3 cut(s)	302, 400, 538
BspFNI	CGCG	1 cut(s)	723
BspLI	GGNNCC	3 cut(s)	6, 142, 303
BspPI	GGATC	5 cut(s)	35, 468, 718, 750, 849
BspT107I	GGYRCC	2 cut(s)	4, 301
BsrDI	GCAATG	2 cut(s)	473, 1006
BsrFI	RCCGGY	1 cut(s)	59
BsrI	ACTGG	2 cut(s)	132, 348
BssAI	RCCGGY	1 cut(s)	59
BssECI	CCNNGG	3 cut(s)	8, 561, 959
BssMI	GATC	6 cut(s)	40, 460, 578, 710, 742, 841
BssNI	GRCGYC	1 cut(s)	5
BssT1I	CCWWGG	2 cut(s)	8, 561
Bst2UI	CCWGG	1 cut(s)	918
Bst4CI	ACNGT	3 cut(s)	36, 101, 863
Bst6I	CTCTTC	1 cut(s)	244
BstACI	GRCGYC	1 cut(s)	5
BstBAI	YACGTR	1 cut(s)	805
BstC8I	GCNNGC	1 cut(s)	61
BstDEI	CTNAG	4 cut(s)	289, 408, 525, 833
BstDSI	CCRYGG	1 cut(s)	959
BstF5I	GGATG	3 cut(s)	337, 482, 763
BstFNI	CGCG	1 cut(s)	723
BstH2I	RGCGCY	1 cut(s)	8
BstHHI	GCGC	3 cut(s)	7, 933, 982
BstKTI	GATC	6 cut(s)	43, 463, 581, 713, 745, 844
BstMBI	GATC	6 cut(s)	40, 460, 578, 710, 742, 841
BstMWI	GCNNNNNNNGC	1 cut(s)	11
BstNI	CCWGG	1 cut(s)	918
BstSCI	CCNGG	1 cut(s)	916
BstSFI	CTRYAG	3 cut(s)	147, 272, 493
BstSNI	TACGTA	1 cut(s)	805
BstUI	CGCG	1 cut(s)	723
BstV1I	GCAGC	1 cut(s)	915
BstV2I	GAAGAC	1 cut(s)	336
BstX2I	RGATCY	3 cut(s)	578, 742, 841
BstYI	RGATCY	3 cut(s)	578, 742, 841
BtgI	CCRYGG	1 cut(s)	959
BtgZI	GCGATG	1 cut(s)	582
BtsCI	GGATG	3 cut(s)	337, 482, 763
BtsI	GCAGTG	1 cut(s)	229
BtsIMutI	CAGTG	4 cut(s)	229, 355, 363, 868
Cac8I	GCNNGC	1 cut(s)	61
CaiI	CAGNNNCTG	1 cut(s)	127
CfoI	GCGC	3 cut(s)	7, 933, 982
Cfr10I	RCCGGY	1 cut(s)	59
Cfr13I	GGNCC	2 cut(s)	130, 643
CseI	GACGC	1 cut(s)	729
Csp6I	GTAC	5 cut(s)	257, 302, 316, 855, 873
CspCI	CAANNNNNGTGG	2 cut(s)	489, 524
CviAII	CATG	2 cut(s)	64, 689
CviQI	GTAC	5 cut(s)	257, 302, 316, 855, 873
DdeI	CTNAG	4 cut(s)	289, 408, 525, 833
DinI	GGCGCC	1 cut(s)	6
DpnI	GATC	6 cut(s)	42, 462, 580, 712, 744, 843
DpnII	GATC	6 cut(s)	40, 460, 578, 710, 742, 841
DraI	TTTAAA	2 cut(s)	244, 816
DraIII	CACNNNGTG	1 cut(s)	863
Eam1104I	CTCTTC	1 cut(s)	244
EarI	CTCTTC	1 cut(s)	244
Ecl136II	GAGCTC	1 cut(s)	288
Eco105I	TACGTA	1 cut(s)	805
Eco130I	CCWWGG	2 cut(s)	8, 561
Eco24I	GRGCYC	2 cut(s)	290, 1091
Eco32I	GATATC	1 cut(s)	946
Eco47I	GGWCC	2 cut(s)	130, 643
Eco53kI	GAGCTC	1 cut(s)	288
Eco57I	CTGAAG	1 cut(s)	327
EcoICRI	GAGCTC	1 cut(s)	288
EcoRI	GAATTC	1 cut(s)	412
EcoRII	CCWGG	1 cut(s)	916
EcoRV	GATATC	1 cut(s)	946
EcoT14I	CCWWGG	2 cut(s)	8, 561
EcoT22I	ATGCAT	1 cut(s)	976
EcoT38I	GRGCYC	2 cut(s)	290, 1091
EgeI	GGCGCC	1 cut(s)	6
EheI	GGCGCC	1 cut(s)	6
ErhI	CCWWGG	2 cut(s)	8, 561
FaeI	CATG	2 cut(s)	67, 692
FatI	CATG	2 cut(s)	63, 688
FauI	CCCGC	1 cut(s)	716
FblI	GTMKAC	2 cut(s)	888, 954
Fnu4HI	GCNGC	1 cut(s)	929
FokI	GGATG	3 cut(s)	344, 469, 750
FriOI	GRGCYC	2 cut(s)	290, 1091
Fsp4HI	GCNGC	1 cut(s)	929
FspBI	CTAG	1 cut(s)	1031
GlaI	GCGC	3 cut(s)	6, 932, 981
GluI	GCNGC	1 cut(s)	929
HaeII	RGCGCY	1 cut(s)	8
HapII	CCGG	2 cut(s)	60, 574
HgaI	GACGC	1 cut(s)	729
HhaI	GCGC	3 cut(s)	7, 933, 982
Hin1I	GRCGYC	1 cut(s)	5
Hin1II	CATG	2 cut(s)	67, 692
Hin6I	GCGC	3 cut(s)	5, 931, 980
HinP1I	GCGC	3 cut(s)	5, 931, 980
HincII	GTYRAC	3 cut(s)	889, 1100, 1144
HindII	GTYRAC	3 cut(s)	889, 1100, 1144
HindIII	AAGCTT	2 cut(s)	539, 729
HinfI	GANTC	5 cut(s)	90, 637, 878, 1037, 1047
HpaI	GTTAAC	1 cut(s)	1144
HpaII	CCGG	2 cut(s)	60, 574
HphI	GGTGA	3 cut(s)	305, 408, 480
Hpy166II	GTNNAC	8 cut(s)	32, 82, 694, 857, 889, 955, 1100, 1144
Hpy188I	TCNGA	1 cut(s)	528
Hpy188III	TCNNGA	7 cut(s)	44, 94, 407, 628, 641, 746, 767
Hpy8I	GTNNAC	8 cut(s)	32, 82, 694, 857, 889, 955, 1100, 1144
Hpy99I	CGWCG	1 cut(s)	105
HpyCH4III	ACNGT	3 cut(s)	36, 101, 863
HpyCH4IV	ACGT	1 cut(s)	804
HpyCH4V	TGCA	6 cut(s)	109, 211, 478, 682, 909, 974
HpyF10VI	GCNNNNNNNGC	1 cut(s)	11
HpyF3I	CTNAG	4 cut(s)	289, 408, 525, 833
HpySE526I	ACGT	1 cut(s)	804
Hsp92I	GRCGYC	1 cut(s)	5
Hsp92II	CATG	2 cut(s)	67, 692
HspAI	GCGC	3 cut(s)	5, 931, 980
KasI	GGCGCC	1 cut(s)	4
KpnI	GGTACC	1 cut(s)	305
KroI	GCCGGC	1 cut(s)	59
KroNI	GCCGGC	1 cut(s)	61
KspAI	GTTAAC	1 cut(s)	1144
Kzo9I	GATC	6 cut(s)	40, 460, 578, 710, 742, 841
LmnI	GCTCC	1 cut(s)	140
Lsp1109I	GCAGC	1 cut(s)	915
LweI	GCATC	1 cut(s)	322
MaeI	CTAG	1 cut(s)	1031
MaeII	ACGT	1 cut(s)	804
MaeIII	GTNAC	3 cut(s)	160, 172, 466
MalI	GATC	6 cut(s)	42, 462, 580, 712, 744, 843
MboI	GATC	6 cut(s)	40, 460, 578, 710, 742, 841
MboII	GAAGA	3 cut(s)	261, 320, 336
MflI	RGATCY	3 cut(s)	578, 742, 841
MhlI	GDGCHC	2 cut(s)	290, 1091
MluCI	AATT	6 cut(s)	152, 311, 325, 358, 412, 756
Mly113I	GGCGCC	1 cut(s)	5
MlyI	GAGTC	2 cut(s)	99, 646
Mph1103I	ATGCAT	1 cut(s)	976
MroNI	GCCGGC	1 cut(s)	59
MseI	TTAA	4 cut(s)	243, 651, 815, 1143
MslI	CAYNNNNRTG	1 cut(s)	768
MspI	CCGG	2 cut(s)	60, 574
MspR9I	CCNGG	1 cut(s)	918
MvaI	CCWGG	1 cut(s)	918
MvnI	CGCG	1 cut(s)	723
MwoI	GCNNNNNNNGC	1 cut(s)	11
NaeI	GCCGGC	1 cut(s)	61
NarI	GGCGCC	1 cut(s)	5
NdeII	GATC	6 cut(s)	40, 460, 578, 710, 742, 841
NgoMIV	GCCGGC	1 cut(s)	59
NlaIII	CATG	2 cut(s)	67, 692
NlaIV	GGNNCC	3 cut(s)	6, 142, 303
NmuCI	GTSAC	2 cut(s)	172, 466
NsiI	ATGCAT	1 cut(s)	976
PdiI	GCCGGC	1 cut(s)	61
PfeI	GAWTC	3 cut(s)	878, 1037, 1047
PfoI	TCCNGGA	1 cut(s)	916
PkrI	GCNGC	1 cut(s)	930
PleI	GAGTC	2 cut(s)	98, 645
PluTI	GGCGCC	1 cut(s)	8
PpsI	GAGTC	2 cut(s)	98, 645
Ppu21I	YACGTR	1 cut(s)	805
PsiI	TTATAA	1 cut(s)	755
Psp124BI	GAGCTC	1 cut(s)	290
Psp6I	CCWGG	1 cut(s)	916
PspGI	CCWGG	1 cut(s)	916
PspN4I	GGNNCC	3 cut(s)	6, 142, 303
PspPI	GGNCC	2 cut(s)	130, 643
PstNI	CAGNNNCTG	1 cut(s)	127
PsuI	RGATCY	3 cut(s)	578, 742, 841
RsaI	GTAC	5 cut(s)	258, 303, 317, 856, 874
RsaNI	GTAC	5 cut(s)	257, 302, 316, 855, 873
RseI	CAYNNNNRTG	1 cut(s)	768
SacI	GAGCTC	1 cut(s)	290
SalI	GTCGAC	1 cut(s)	887
SaqAI	TTAA	4 cut(s)	243, 651, 815, 1143
SatI	GCNGC	1 cut(s)	929
Sau3AI	GATC	6 cut(s)	40, 460, 578, 710, 742, 841
Sau96I	GGNCC	2 cut(s)	130, 643
SchI	GAGTC	2 cut(s)	99, 646
ScrFI	CCNGG	1 cut(s)	918
SduI	GDGCHC	2 cut(s)	290, 1091
SfaNI	GCATC	1 cut(s)	322
SfcI	CTRYAG	3 cut(s)	147, 272, 493
SfoI	GGCGCC	1 cut(s)	6
SinI	GGWCC	2 cut(s)	130, 643
SmiMI	CAYNNNNRTG	1 cut(s)	768
SmlI	CTYRAG	1 cut(s)	283
SmoI	CTYRAG	1 cut(s)	283
SnaBI	TACGTA	1 cut(s)	805
Sse9I	AATT	6 cut(s)	152, 311, 325, 358, 412, 756
SsiI	CCGC	2 cut(s)	723, 937
SspDI	GGCGCC	1 cut(s)	4
SspI	AATATT	1 cut(s)	550
SspMI	CTAG	1 cut(s)	1031
SstI	GAGCTC	1 cut(s)	290
StyD4I	CCNGG	1 cut(s)	916
StyI	CCWWGG	2 cut(s)	8, 561
TaaI	ACNGT	3 cut(s)	36, 101, 863
TaiI	ACGT	1 cut(s)	807
TaqI	TCGA	2 cut(s)	103, 888
TaqII	GACCGA	1 cut(s)	1085
TasI	AATT	6 cut(s)	152, 311, 325, 358, 412, 756
TatI	WGTACW	2 cut(s)	256, 854
TfiI	GAWTC	3 cut(s)	878, 1037, 1047
Tru1I	TTAA	4 cut(s)	243, 651, 815, 1143
Tru9I	TTAA	4 cut(s)	243, 651, 815, 1143
TscAI	CASTG	4 cut(s)	229, 355, 370, 868
TseFI	GTSAC	2 cut(s)	172, 466
TseI	GCWGC	1 cut(s)	928
Tsp45I	GTSAC	2 cut(s)	172, 466
TspDTI	ATGAA	3 cut(s)	206, 387, 839
TspGWI	ACGGA	2 cut(s)	63, 1117
TspRI	CASTG	4 cut(s)	229, 355, 370, 868
VpaK11BI	GGWCC	2 cut(s)	130, 643
XapI	RAATTY	2 cut(s)	325, 412
XmiI	GTMKAC	2 cut(s)	888, 954
XspI	CTAG	1 cut(s)	1031
Zsp2I	ATGCAT	1 cut(s)	976

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