Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3B

Orthogroup ID

OG0013834

Physical Location & Seq

Genomic Coordinates Reverse (-)

26830188 .. 26832943

Gene Structure 2756 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3BG274600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1128 bp

ATGGCTGAGTACCCCTACTCATCAAATTTCTTCACAGGTCTCTTCAAATTCAACCCTCTTCTTCATCACCATCACCACCATGAATACCCTTTGATTTCAAACCCTCCTCCTCCTCCGCAACCACAACCTCAACCTCCCTATGCTCACAACTTCTTCAATATCAACTACAATCAGAACCACAACCAGTACTCTTCTTTTTACTCCAGCCAAACCACTCATCATCAACCCCCTTCTCCACCTCTCAGAGAAGCCCTCCCACTCCTTAACCGCTTAAGCCCAACAAAGCATCATGAAGACGAAGAACAAGAGCATGATCACCATCATGAGTACTACTCCTGTAGTACTGATCAAATGGATGTAGATGACAAGATCAGCAAACCGTACAACAAAGAAGACCATGGGGAAGATGATGAGGCTAGTGTGACTGTTGCACTGCACATAGGACTCCCGAGCCCTAGTGCAGCTGAAATGGCATCTGTGCTTTCTGCAGCTTCTTCTTCCTCAGAAATCAGCACAACTCATGACAAAGATCATGTTATTGGAGATCATGGTGATGATTCAACTGGGTACCCCATGAACAGATCATCGCTCAACAAGGGTCAGTATTGGATCCCAACTCCGTCACAGATTCTCATTGGTCCTACTCAATTCTCTTGCCCTGTCTGCTTCAAGACCTTCAACAGATACAATAACATGCAGATGCATATGTGGGGGCATGGATCTCAATACAGAAAAGGGCCCGAGTCTCTAAGAGGAACTCAACCTACAGGCATGCTTAGGCTTCCTTGCTATTGTTGCACACCAGGTTGCAGGAACAACATCGATCACCCGAGAGCGAAGCCCCTGAAAGACTTTAGAACCCTCCAAACACATTACAAGAGGAAGCATGGAATCAAGCCTTTCATGTGCAGAAAATGTGGCAAGGCATTTGCAGTGAGAGGAGATTGGAGAACCCACGAGAAGAATTGTGGCAAGCTTTGGTATTGCATTTGTGGCTCTGATTTTAAGCACAAGAGGTCTCTCAAAGATCATATCAAGGCTTTTGGGAATGGGCATGCAGCTTATGGAATTGATGGATTTGAAGAAGATGATGAGCCTGCATCTGAAGTTGAGCAAGATAATGATTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000902 GO:0000904 GO:0001709 GO:0003006 GO:0003674 GO:0003700 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006355 GO:0007275 GO:0008150 GO:0008152 GO:0009058 GO:0009653 GO:0009791 GO:0009812 GO:0009813 GO:0009826 GO:0009856 GO:0009860 GO:0009889 GO:0009908 GO:0009932 GO:0009987 GO:0010154 GO:0010468 GO:0010500 GO:0010556 GO:0016043 GO:0016049 GO:0019219 GO:0019222 GO:0022414 GO:0030154 GO:0031323 GO:0031326 GO:0032501 GO:0032502 GO:0032989 GO:0040007 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464 GO:0044706 GO:0045165 GO:0048367 GO:0048438 GO:0048467 GO:0048468 GO:0048588 GO:0048589 GO:0048608 GO:0048731 GO:0048856 GO:0048868 GO:0048869 GO:0050789 GO:0050794 GO:0051171 GO:0051252 GO:0051704 GO:0060255 GO:0060560 GO:0061458 GO:0065007 GO:0071704 GO:0071840 GO:0080090 GO:0090567 GO:0140110 GO:1901576 GO:1903506 GO:1990058 GO:2000112 GO:2001141

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

zf-C2H2

Protein Analysis

375

Amino Acids

42.85

Weight (kDa)

6.5

Isoelectric Point (pI)

51.31

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
zf-C2H2_STOP2_3rd	PF23115	263 - 297	1.3e-18	STOP2-like, C2H2-type zinc finger
C2CH-3rd_BIRD-IDD	PF22995	300 - 324	7.6e-12	BIRD-IDD transcription factor, third C2HC zinc finger

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: OG0013834)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G57670
fragaria_vesca	FvH4_6g23170
malus_domestica	MD12G1066400.v1.1 MD14G1066100.v1.1
prunus_persica	Prupe.7G067900_v2.0.a1
pyrus_communis	pycom12g05780 pycom14g05390
rosa_chinensis	RchiOBHm_Chr3g0481001
rosa_laevigata	RLG00000023434
rosa_multiflora	Rmu_sc0002927.1_g000032
rosa_roxburghii	Rroxscaffold_6G00400760
rosa_rugosa	Rorug03G0188900
rosa_samantha	Rh3AG239600 Rh3BG274600 Rh3CG270100 Rh3DG266200
rosa_wichuraiana	Rw0G018680

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	567
AccB1I	GGYRCC	1 cut(s)	567
AciI	CCGC	2 cut(s)	116, 268
AclWI	GGATC	3 cut(s)	604, 617, 727
AcsI	RAATTY	2 cut(s)	25, 47
AcuI	CTGAAG	1 cut(s)	1125
AfaI	GTAC	6 cut(s)	11, 188, 329, 343, 383, 569
AflII	CTTAAG	1 cut(s)	271
AgsI	TTSAA	8 cut(s)	46, 52, 99, 157, 561, 670, 679, 1082
AjnI	CCWGG	1 cut(s)	802
AluBI	AGCT	4 cut(s)	464, 491, 976, 1061
AluI	AGCT	4 cut(s)	464, 491, 976, 1061
Alw26I	GTCTC	3 cut(s)	44, 750, 1023
AlwI	GGATC	3 cut(s)	604, 617, 727
Ama87I	CYCGRG	3 cut(s)	448, 740, 829
AoxI	GGCC	1 cut(s)	737
ApaI	GGGCCC	1 cut(s)	741
ApeKI	GCWGC	3 cut(s)	461, 488, 1058
ApoI	RAATTY	2 cut(s)	25, 47
Asp718I	GGTACC	1 cut(s)	567
AspS9I	GGNCC	3 cut(s)	638, 737, 738
AsuHPI	GGTGA	5 cut(s)	59, 65, 308, 563, 818
AvaI	CYCGRG	3 cut(s)	448, 740, 829
AvaII	GGWCC	1 cut(s)	638
BaeGI	GKGCMC	1 cut(s)	741
BamHI	GGATCC	1 cut(s)	609
BanI	GGYRCC	1 cut(s)	567
BanII	GRGCYC	2 cut(s)	455, 741
BauI	CACGAG	1 cut(s)	956
BbsI	GAAGAC	2 cut(s)	300, 399
BbvI	GCAGC	3 cut(s)	473, 500, 1070
BccI	CCATC	3 cut(s)	78, 327, 1067
BciT130I	CCWGG	1 cut(s)	804
BclI	TGATCA	2 cut(s)	313, 346
BcoDI	GTCTC	3 cut(s)	44, 750, 1023
BfaI	CTAG	2 cut(s)	417, 456
BfmI	CTRYAG	3 cut(s)	337, 486, 765
BfrI	CTTAAG	1 cut(s)	271
BisI	GCNGC	3 cut(s)	462, 489, 1059
BlsI	GCNGC	3 cut(s)	463, 490, 1060
BmcAI	AGTACT	3 cut(s)	188, 329, 343
Bme1390I	CCNGG	1 cut(s)	804
Bme18I	GGWCC	1 cut(s)	638
BmeT110I	CYCGRG	3 cut(s)	448, 740, 829
BmgT120I	GGNCC	3 cut(s)	638, 737, 738
BmiI	GGNNCC	3 cut(s)	569, 611, 739
BmrFI	CCNGG	1 cut(s)	804
BmrI	ACTGGG	1 cut(s)	573
BmsI	GCATC	4 cut(s)	295, 482, 690, 1109
BmuI	ACTGGG	1 cut(s)	573
BpiI	GAAGAC	2 cut(s)	300, 399
BplI	GAGNNNNNCTC	4 cut(s)	237, 269, 317, 349
BpmI	CTGGAG	1 cut(s)	187
Bpu10I	CCTNAGC	1 cut(s)	776
Bsa29I	ATCGAT	1 cut(s)	822
BsaBI	GATNNNNATC	1 cut(s)	318
BsaI	GGTCTC	2 cut(s)	44, 1023
BsaJI	CCNNGG	1 cut(s)	397
Bse1I	ACTGG	2 cut(s)	184, 568
Bse8I	GATNNNNATC	1 cut(s)	318
BseBI	CCWGG	1 cut(s)	804
BseCI	ATCGAT	1 cut(s)	822
BseDI	CCNNGG	1 cut(s)	397
BseGI	GGATG	1 cut(s)	361
BseJI	GATNNNNATC	1 cut(s)	318
BseMII	CTCAG	2 cut(s)	256, 516
BseNI	ACTGG	2 cut(s)	184, 568
BseRI	GAGGAG	4 cut(s)	96, 99, 102, 954
BseSI	GKGCMC	1 cut(s)	741
BseXI	GCAGC	3 cut(s)	473, 500, 1070
BsgI	GTGCAG	3 cut(s)	419, 480, 928
BshFI	GGCC	1 cut(s)	739
BshNI	GGYRCC	1 cut(s)	567
BshVI	ATCGAT	1 cut(s)	822
BsiHKCI	CYCGRG	3 cut(s)	448, 740, 829
BsmAI	GTCTC	3 cut(s)	44, 750, 1023
BsnI	GGCC	1 cut(s)	739
Bso31I	GGTCTC	2 cut(s)	44, 1023
BsoBI	CYCGRG	3 cut(s)	448, 740, 829
Bsp120I	GGGCCC	1 cut(s)	737
Bsp1286I	GDGCHC	2 cut(s)	455, 741
Bsp19I	CCATGG	1 cut(s)	397
BspACI	CCGC	2 cut(s)	116, 268
BspANI	GGCC	1 cut(s)	739
BspCNI	CTCAG	2 cut(s)	255, 515
BspDI	ATCGAT	1 cut(s)	822
BspHI	TCATGA	3 cut(s)	289, 322, 520
BspLI	GGNNCC	3 cut(s)	569, 611, 739
BspMAI	CTGCAG	1 cut(s)	490
BspPI	GGATC	3 cut(s)	604, 617, 727
BspT107I	GGYRCC	1 cut(s)	567
BspTI	CTTAAG	1 cut(s)	271
BspTNI	GGTCTC	2 cut(s)	44, 1023
BsrI	ACTGG	2 cut(s)	184, 568
BssECI	CCNNGG	1 cut(s)	397
BssSI	CACGAG	1 cut(s)	956
BssT1I	CCWWGG	1 cut(s)	397
Bst2BI	CACGAG	1 cut(s)	956
Bst2UI	CCWGG	1 cut(s)	804
Bst4CI	ACNGT	2 cut(s)	381, 427
Bst6I	CTCTTC	3 cut(s)	47, 63, 196
BstAFI	CTTAAG	1 cut(s)	271
BstC8I	GCNNGC	4 cut(s)	773, 974, 1056, 1098
BstDEI	CTNAG	5 cut(s)	6, 242, 502, 749, 776
BstDSI	CCRYGG	1 cut(s)	397
BstF5I	GGATG	1 cut(s)	361
BstMAI	GTCTC	3 cut(s)	44, 750, 1023
BstMWI	GCNNNNNNNGC	4 cut(s)	470, 663, 795, 993
BstNI	CCWGG	1 cut(s)	804
BstNSI	RCATGY	3 cut(s)	697, 775, 1058
BstSCI	CCNGG	1 cut(s)	802
BstSFI	CTRYAG	3 cut(s)	337, 486, 765
BstSLI	GKGCMC	1 cut(s)	741
BstV1I	GCAGC	3 cut(s)	473, 500, 1070
BstV2I	GAAGAC	2 cut(s)	300, 399
BstX2I	RGATCY	2 cut(s)	609, 719
BstYI	RGATCY	2 cut(s)	609, 719
Bsu15I	ATCGAT	1 cut(s)	822
BsuRI	GGCC	1 cut(s)	739
BsuTUI	ATCGAT	1 cut(s)	822
BtgI	CCRYGG	1 cut(s)	397
BtgZI	GCGATG	1 cut(s)	570
BtsCI	GGATG	1 cut(s)	361
BtsI	GCAGTG	2 cut(s)	431, 939
BtsIMutI	CAGTG	2 cut(s)	431, 939
Cac8I	GCNNGC	4 cut(s)	773, 974, 1056, 1098
CciI	TCATGA	3 cut(s)	289, 322, 520
Cfr13I	GGNCC	3 cut(s)	638, 737, 738
ClaI	ATCGAT	1 cut(s)	822
CsiI	ACCWGGT	1 cut(s)	802
Csp6I	GTAC	6 cut(s)	10, 187, 328, 342, 382, 568
CviQI	GTAC	6 cut(s)	10, 187, 328, 342, 382, 568
DdeI	CTNAG	5 cut(s)	6, 242, 502, 749, 776
Eam1104I	CTCTTC	3 cut(s)	47, 63, 196
EarI	CTCTTC	3 cut(s)	47, 63, 196
Eco130I	CCWWGG	1 cut(s)	397
Eco24I	GRGCYC	2 cut(s)	455, 741
Eco31I	GGTCTC	2 cut(s)	44, 1023
Eco47I	GGWCC	1 cut(s)	638
Eco57I	CTGAAG	1 cut(s)	1125
Eco88I	CYCGRG	3 cut(s)	448, 740, 829
EcoO109I	RGGNCCY	1 cut(s)	737
EcoRII	CCWGG	1 cut(s)	802
EcoT14I	CCWWGG	1 cut(s)	397
EcoT22I	ATGCAT	1 cut(s)	705
EcoT38I	GRGCYC	2 cut(s)	455, 741
ErhI	CCWWGG	1 cut(s)	397
FauNDI	CATATG	1 cut(s)	705
FbaI	TGATCA	2 cut(s)	313, 346
Fnu4HI	GCNGC	3 cut(s)	462, 489, 1059
FokI	GGATG	1 cut(s)	368
FriOI	GRGCYC	2 cut(s)	455, 741
Fsp4HI	GCNGC	3 cut(s)	462, 489, 1059
FspBI	CTAG	2 cut(s)	417, 456
GluI	GCNGC	3 cut(s)	462, 489, 1059
GsuI	CTGGAG	1 cut(s)	187
HaeIII	GGCC	1 cut(s)	739
HindIII	AAGCTT	1 cut(s)	974
HinfI	GANTC	5 cut(s)	444, 557, 628, 743, 891
HphI	GGTGA	5 cut(s)	59, 65, 308, 563, 818
Hpy188I	TCNGA	5 cut(s)	174, 245, 505, 1000, 1105
Hpy188III	TCNNGA	5 cut(s)	290, 323, 448, 521, 670
HpyAV	CCTTC	2 cut(s)	240, 685
HpyCH4III	ACNGT	2 cut(s)	381, 427
HpyF10VI	GCNNNNNNNGC	4 cut(s)	470, 663, 795, 993
HpyF3I	CTNAG	5 cut(s)	6, 242, 502, 749, 776
KpnI	GGTACC	1 cut(s)	571
Ksp22I	TGATCA	2 cut(s)	313, 346
Lsp1109I	GCAGC	3 cut(s)	473, 500, 1070
LweI	GCATC	4 cut(s)	295, 482, 690, 1109
MabI	ACCWGGT	1 cut(s)	802
MaeI	CTAG	2 cut(s)	417, 456
MaeIII	GTNAC	2 cut(s)	421, 621
MflI	RGATCY	2 cut(s)	609, 719
MhlI	GDGCHC	2 cut(s)	455, 741
MluCI	AATT	5 cut(s)	25, 47, 647, 964, 1068
MlyI	GAGTC	2 cut(s)	438, 752
Mph1103I	ATGCAT	1 cut(s)	705
MseI	TTAA	4 cut(s)	264, 272, 1005, 1126
MslI	CAYNNNNRTG	4 cut(s)	78, 321, 552, 698
MspA1I	CMGCKG	1 cut(s)	464
MspCI	CTTAAG	1 cut(s)	271
MspR9I	CCNGG	1 cut(s)	804
MvaI	CCWGG	1 cut(s)	804
MwoI	GCNNNNNNNGC	4 cut(s)	470, 663, 795, 993
NcoI	CCATGG	1 cut(s)	397
NdeI	CATATG	1 cut(s)	705
NlaIV	GGNNCC	3 cut(s)	569, 611, 739
NmuCI	GTSAC	2 cut(s)	421, 621
NsiI	ATGCAT	1 cut(s)	705
NspI	RCATGY	3 cut(s)	697, 775, 1058
PaeI	GCATGC	2 cut(s)	775, 1058
PagI	TCATGA	3 cut(s)	289, 322, 520
PfeI	GAWTC	3 cut(s)	557, 628, 891
PkrI	GCNGC	3 cut(s)	463, 490, 1060
PleI	GAGTC	2 cut(s)	438, 751
PpsI	GAGTC	2 cut(s)	438, 751
Psp6I	CCWGG	1 cut(s)	802
PspGI	CCWGG	1 cut(s)	802
PspN4I	GGNNCC	3 cut(s)	569, 611, 739
PspOMI	GGGCCC	1 cut(s)	737
PspPI	GGNCC	3 cut(s)	638, 737, 738
PsrI	GAACNNNNNNTAC	2 cut(s)	748, 780
PstI	CTGCAG	1 cut(s)	490
PsuI	RGATCY	2 cut(s)	609, 719
PvuII	CAGCTG	1 cut(s)	464
RsaI	GTAC	6 cut(s)	11, 188, 329, 343, 383, 569
RsaNI	GTAC	6 cut(s)	10, 187, 328, 342, 382, 568
RseI	CAYNNNNRTG	4 cut(s)	78, 321, 552, 698
SaqAI	TTAA	4 cut(s)	264, 272, 1005, 1126
SatI	GCNGC	3 cut(s)	462, 489, 1059
Sau96I	GGNCC	3 cut(s)	638, 737, 738
ScaI	AGTACT	3 cut(s)	188, 329, 343
SchI	GAGTC	2 cut(s)	438, 752
ScrFI	CCNGG	1 cut(s)	804
SduI	GDGCHC	2 cut(s)	455, 741
SexAI	ACCWGGT	1 cut(s)	802
SfaNI	GCATC	4 cut(s)	295, 482, 690, 1109
SfcI	CTRYAG	3 cut(s)	337, 486, 765
SinI	GGWCC	1 cut(s)	638
SmiMI	CAYNNNNRTG	4 cut(s)	78, 321, 552, 698
SmlI	CTYRAG	1 cut(s)	271
SmoI	CTYRAG	1 cut(s)	271
SphI	GCATGC	2 cut(s)	775, 1058
Sse9I	AATT	5 cut(s)	25, 47, 647, 964, 1068
SsiI	CCGC	2 cut(s)	116, 268
SspMI	CTAG	2 cut(s)	417, 456
StyD4I	CCNGG	1 cut(s)	802
StyI	CCWWGG	1 cut(s)	397
TaaI	ACNGT	2 cut(s)	381, 427
TaqI	TCGA	1 cut(s)	822
TasI	AATT	5 cut(s)	25, 47, 647, 964, 1068
TatI	WGTACW	3 cut(s)	186, 327, 341
TfiI	GAWTC	3 cut(s)	557, 628, 891
Tru1I	TTAA	4 cut(s)	264, 272, 1005, 1126
Tru9I	TTAA	4 cut(s)	264, 272, 1005, 1126
TscAI	CASTG	2 cut(s)	438, 939
TseFI	GTSAC	2 cut(s)	421, 621
TseI	GCWGC	3 cut(s)	461, 488, 1058
Tsp45I	GTSAC	2 cut(s)	421, 621
TspDTI	ATGAA	5 cut(s)	53, 96, 306, 590, 892
TspGWI	ACGGA	1 cut(s)	609
TspRI	CASTG	2 cut(s)	438, 939
Vha464I	CTTAAG	1 cut(s)	271
VpaK11BI	GGWCC	1 cut(s)	638
XapI	RAATTY	2 cut(s)	25, 47
XceI	RCATGY	3 cut(s)	697, 775, 1058
XspI	CTAG	2 cut(s)	417, 456
ZrmI	AGTACT	3 cut(s)	188, 329, 343
Zsp2I	ATGCAT	1 cut(s)	705

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