Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1C

Orthogroup ID

OG0007525

Physical Location & Seq

Genomic Coordinates Forward (+)

2692547 .. 2696503

Gene Structure 3957 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1CG016800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 999 bp

ATGATGCCAGCCAAATCTAAAGATGTAGATCCAGGAACCCAGACTGTGTTGCAATCAAGTATGCAACCTTGGTGGCGTGGAGCGGGACATAGTTCGTCTTTTGGTGAAAGTGTTGTAGCATCGTCTTTGGGGGAACACGGTAACCGTTTTGTGATGAATGGCGCTATGCAGTCACAAGCTGATGCTGGAGCTAACTTCAAAAAAGATGTGCAGGCTACAATAGGATCACAGTCTGATGGGAATAGTGGACATGAAAACCAACAAATGAAAAGCACTTCCTCTGCAGTGGTTGCTAAATTGGGTGAACATCTTGATGCGAATTCACAAATGGAACTTGTTGGTCACTCAATTGTTTTGACATCATATCCATATTCAGATCCACAATACAGTGGGATGTTGAGTCATTATCGGCCACAAGCTATGGTGCCCCCTCAATTCTATGGCTTGCATCATGGTAGAATGCCCTTGCCCCTTGAAATGGAAGAGGAGCCTGTTTATGTAAATGCCAAGCAATACCATGGTATTTTGAGACGAAGACAGTCACGTGCTAAAGCTGAGCTTGAAAGGAAGCTTATAAAAGTTAGGAAGCCATATCTTCATGAGTCTCGTCACCAGCATGCGTTGAGGAGAGCAAGGGGTTGTGGAGGCCGTTTCCTTAATACGAAGAAGCAAGATGATAGTGATGCAAATTCCTCATCAGAAAAAACCATTAATTTGGATGCAAACTTTTCACCCAAATCTGCCAAATCTGGTTTTGAGTGCTTTCCTAATGATAGCAATGGCAATTTCGTTTCCTCCAATGTCCAGCAAGAAGGATCAGGTTCATGGTTCAGGACACTCAATAGCCACACACTCTCCAACGGTAATGGCAATGGCCATGTCCCGTCATCAACGTATCGTACAACATTTAATGACGGCAAGGAAGGTGTTTTCCTTGGTCAACAGAAGGAAACAATGCAGTTGAATGGATCCTCTCGTGGGGCCATTCACAGTAAATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003700 GO:0006355 GO:0007275 GO:0008150 GO:0009555 GO:0009790 GO:0009791 GO:0009793 GO:0009889 GO:0009890 GO:0009892 GO:0010154 GO:0010262 GO:0010468 GO:0010556 GO:0010558 GO:0010605 GO:0010629 GO:0019219 GO:0019222 GO:0022414 GO:0031323 GO:0031324 GO:0031326 GO:0031327 GO:0032501 GO:0032502 GO:0045892 GO:0045934 GO:0048229 GO:0048316 GO:0048519 GO:0048523 GO:0048608 GO:0048731 GO:0048856 GO:0050789 GO:0050794 GO:0051171 GO:0051172 GO:0051252 GO:0051253 GO:0055046 GO:0060255 GO:0061458 GO:0065007 GO:0080090 GO:0140110 GO:1902679 GO:1903506 GO:1903507 GO:2000112 GO:2000113 GO:2001141

KEGG Pathways

Metabolic & Signaling

ko04612 ko05152 map04612 map05152

Pfam Domains

Protein Families

CBFB_NFYA

Protein Analysis

332

Amino Acids

36.47

Weight (kDa)

9.3

Isoelectric Point (pI)

43.49

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CBFB_NFYA	PF02045	163 - 218	1.3e-26	CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B

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)

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Tree File

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Publication-ready

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Orthologous Genes (Group: OG0007525)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_7g01120 FvH4_7g01120 FvH4_7g01120
malus_domestica	MD02G1309800.v1.1 MD07G1011300.v1.1
prunus_persica	Prupe.2G014500_v2.0.a1
pyrus_communis	pycom07g00940
rosa_chinensis	RchiOBHm_Chr1g0316121 RchiOBHm_Chr1g0316201
rosa_laevigata	RLG00000030693
rosa_multiflora	Rmu_sc0002531.1_g000027 Rmu_sc0005919.1_g000009 Rmu_sc0005919.1_g000010
rosa_roxburghii	Rroxscaffold_4G00331120
rosa_rugosa	Rorug01G0009200 Rorug01G0009300 Rorug01G0009300 Rorug01G0009400 Rorug01G0009500 Rorug01G0009500
rosa_samantha	Rh1AG019200 Rh1BG014200 Rh1CG016800 Rh1DG013800
rosa_wichuraiana	Rw1G001250

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	575
AccB1I	GGYRCC	1 cut(s)	424
AccBSI	CCGCTC	1 cut(s)	83
AciI	CCGC	1 cut(s)	83
AclWI	GGATC	6 cut(s)	23, 232, 371, 823, 963, 976
AcoI	YGGCCR	2 cut(s)	410, 874
AcsI	RAATTY	2 cut(s)	319, 688
AcvI	CACGTG	1 cut(s)	545
AfaI	GTAC	1 cut(s)	901
AfiI	CCNNNNNNNGG	2 cut(s)	478, 978
AgsI	TTSAA	4 cut(s)	199, 476, 563, 964
AjnI	CCWGG	1 cut(s)	31
AluBI	AGCT	6 cut(s)	179, 191, 419, 554, 559, 571
AluI	AGCT	6 cut(s)	179, 191, 419, 554, 559, 571
Alw26I	GTCTC	2 cut(s)	523, 609
AlwI	GGATC	6 cut(s)	23, 232, 371, 823, 963, 976
AoxI	GGCC	4 cut(s)	410, 646, 874, 981
ApoI	RAATTY	2 cut(s)	319, 688
AseI	ATTAAT	1 cut(s)	711
AspLEI	GCGC	1 cut(s)	164
AspS9I	GGNCC	1 cut(s)	981
AsuHPI	GGTGA	4 cut(s)	116, 314, 602, 723
BaeGI	GKGCMC	1 cut(s)	429
BalI	TGGCCA	1 cut(s)	876
BamHI	GGATCC	1 cut(s)	968
BanI	GGYRCC	1 cut(s)	424
BauI	CACGAG	1 cut(s)	975
BbrPI	CACGTG	1 cut(s)	545
BbsI	GAAGAC	1 cut(s)	541
BccI	CCATC	1 cut(s)	230
BceAI	ACGGC	2 cut(s)	633, 931
BciT130I	CCWGG	1 cut(s)	33
BcoDI	GTCTC	2 cut(s)	523, 609
BfmI	CTRYAG	1 cut(s)	282
BfoI	RGCGCY	1 cut(s)	165
BlpI	GCTNAGC	1 cut(s)	555
Bme1390I	CCNGG	1 cut(s)	33
BmgT120I	GGNCC	1 cut(s)	981
BmiI	GGNNCC	5 cut(s)	37, 426, 489, 970, 982
BmrFI	CCNGG	1 cut(s)	33
BmsI	GCATC	6 cut(s)	128, 172, 304, 457, 673, 709
BpiI	GAAGAC	1 cut(s)	541
BpmI	CTGGAG	1 cut(s)	207
Bpu1102I	GCTNAGC	1 cut(s)	555
BsaAI	YACGTR	1 cut(s)	545
BsaBI	GATNNNNATC	1 cut(s)	27
BsaJI	CCNNGG	3 cut(s)	68, 517, 934
BsaXI	ACNNNNNCTCC	2 cut(s)	839, 869
Bsc4I	CCNNNNNNNGG	2 cut(s)	478, 978
Bse3DI	GCAATG	2 cut(s)	784, 877
Bse8I	GATNNNNATC	1 cut(s)	27
BseBI	CCWGG	1 cut(s)	33
BseDI	CCNNGG	3 cut(s)	68, 517, 934
BseGI	GGATG	2 cut(s)	399, 724
BseJI	GATNNNNATC	1 cut(s)	27
BseLI	CCNNNNNNNGG	2 cut(s)	478, 978
BseMI	GCAATG	2 cut(s)	784, 877
BseMII	CTCAG	1 cut(s)	546
BseRI	GAGGAG	2 cut(s)	500, 640
BseSI	GKGCMC	1 cut(s)	429
BsgI	GTGCAG	1 cut(s)	230
BshFI	GGCC	4 cut(s)	412, 648, 876, 983
BshNI	GGYRCC	1 cut(s)	424
BslFI	GGGAC	2 cut(s)	99, 866
BslI	CCNNNNNNNGG	2 cut(s)	478, 978
BsmAI	GTCTC	2 cut(s)	523, 609
BsmBI	CGTCTC	1 cut(s)	523
BsmFI	GGGAC	2 cut(s)	99, 866
BsmI	GAATGC	1 cut(s)	465
BsnI	GGCC	4 cut(s)	412, 648, 876, 983
Bsp1286I	GDGCHC	1 cut(s)	429
Bsp143I	GATC	5 cut(s)	28, 224, 376, 815, 968
Bsp1720I	GCTNAGC	1 cut(s)	555
Bsp19I	CCATGG	1 cut(s)	517
BspACI	CCGC	1 cut(s)	83
BspANI	GGCC	4 cut(s)	412, 648, 876, 983
BspCNI	CTCAG	1 cut(s)	547
BspHI	TCATGA	1 cut(s)	598
BspLI	GGNNCC	5 cut(s)	37, 426, 489, 970, 982
BspMAI	CTGCAG	1 cut(s)	286
BspPI	GGATC	6 cut(s)	23, 232, 371, 823, 963, 976
BspT107I	GGYRCC	1 cut(s)	424
BsrBI	CCGCTC	1 cut(s)	83
BsrDI	GCAATG	2 cut(s)	784, 877
BssECI	CCNNGG	3 cut(s)	68, 517, 934
BssMI	GATC	5 cut(s)	28, 224, 376, 815, 968
BssSI	CACGAG	1 cut(s)	975
BssT1I	CCWWGG	3 cut(s)	68, 517, 934
Bst2BI	CACGAG	1 cut(s)	975
Bst2UI	CCWGG	1 cut(s)	33
Bst4CI	ACNGT	8 cut(s)	46, 140, 146, 231, 389, 540, 863, 992
Bst6I	CTCTTC	1 cut(s)	477
BstAPI	GCANNNNNTGC	1 cut(s)	290
BstBAI	YACGTR	1 cut(s)	545
BstC8I	GCNNGC	4 cut(s)	9, 213, 446, 618
BstDEI	CTNAG	1 cut(s)	555
BstDSI	CCRYGG	1 cut(s)	517
BstEII	GGTNACC	1 cut(s)	140
BstF5I	GGATG	2 cut(s)	399, 724
BstH2I	RGCGCY	1 cut(s)	165
BstHHI	GCGC	1 cut(s)	164
BstKTI	GATC	5 cut(s)	31, 227, 379, 818, 971
BstMAI	GTCTC	2 cut(s)	523, 609
BstMBI	GATC	5 cut(s)	28, 224, 376, 815, 968
BstMWI	GCNNNNNNNGC	1 cut(s)	290
BstNI	CCWGG	1 cut(s)	33
BstNSI	RCATGY	1 cut(s)	620
BstPI	GGTNACC	1 cut(s)	140
BstSCI	CCNGG	1 cut(s)	31
BstSFI	CTRYAG	1 cut(s)	282
BstSLI	GKGCMC	1 cut(s)	429
BstV2I	GAAGAC	1 cut(s)	541
BstX2I	RGATCY	3 cut(s)	28, 376, 968
BstXI	CCANNNNNNTGG	1 cut(s)	715
BstYI	RGATCY	3 cut(s)	28, 376, 968
BsuRI	GGCC	4 cut(s)	412, 648, 876, 983
BtgI	CCRYGG	1 cut(s)	517
BtsCI	GGATG	2 cut(s)	399, 724
BtsI	GCAGTG	1 cut(s)	291
BtsIMutI	CAGTG	2 cut(s)	291, 394
Cac8I	GCNNGC	4 cut(s)	9, 213, 446, 618
CciI	TCATGA	1 cut(s)	598
CfoI	GCGC	1 cut(s)	164
Cfr13I	GGNCC	1 cut(s)	981
Csp6I	GTAC	1 cut(s)	900
CspCI	CAANNNNNGTGG	2 cut(s)	53, 88
CviAII	CATG	7 cut(s)	251, 452, 518, 599, 617, 825, 878
CviQI	GTAC	1 cut(s)	900
DdeI	CTNAG	1 cut(s)	555
DpnI	GATC	5 cut(s)	30, 226, 378, 817, 970
DpnII	GATC	5 cut(s)	28, 224, 376, 815, 968
EaeI	YGGCCR	2 cut(s)	410, 874
Eam1104I	CTCTTC	1 cut(s)	477
EarI	CTCTTC	1 cut(s)	477
Eco130I	CCWWGG	3 cut(s)	68, 517, 934
Eco72I	CACGTG	1 cut(s)	545
Eco91I	GGTNACC	1 cut(s)	140
EcoO65I	GGTNACC	1 cut(s)	140
EcoRI	GAATTC	1 cut(s)	319
EcoRII	CCWGG	1 cut(s)	31
EcoT14I	CCWWGG	3 cut(s)	68, 517, 934
ErhI	CCWWGG	3 cut(s)	68, 517, 934
Esp3I	CGTCTC	1 cut(s)	523
FaeI	CATG	7 cut(s)	254, 455, 521, 602, 620, 828, 881
FalI	AAGNNNNNCTT	2 cut(s)	543, 575
FaqI	GGGAC	2 cut(s)	99, 866
FatI	CATG	7 cut(s)	250, 451, 517, 598, 616, 824, 877
FauI	CCCGC	1 cut(s)	76
FokI	GGATG	2 cut(s)	406, 731
GlaI	GCGC	1 cut(s)	163
GsuI	CTGGAG	1 cut(s)	207
HaeII	RGCGCY	1 cut(s)	165
HaeIII	GGCC	4 cut(s)	412, 648, 876, 983
HhaI	GCGC	1 cut(s)	164
Hin1II	CATG	7 cut(s)	254, 455, 521, 602, 620, 828, 881
Hin6I	GCGC	1 cut(s)	162
HinP1I	GCGC	1 cut(s)	162
HincII	GTYRAC	1 cut(s)	941
HindII	GTYRAC	1 cut(s)	941
HindIII	AAGCTT	1 cut(s)	569
HinfI	GANTC	2 cut(s)	400, 602
HphI	GGTGA	4 cut(s)	116, 314, 602, 723
Hpy166II	GTNNAC	3 cut(s)	248, 305, 941
Hpy188I	TCNGA	3 cut(s)	235, 376, 700
Hpy188III	TCNNGA	3 cut(s)	311, 599, 832
Hpy8I	GTNNAC	3 cut(s)	248, 305, 941
HpyAV	CCTTC	3 cut(s)	806, 917, 940
HpyCH4III	ACNGT	8 cut(s)	46, 140, 146, 231, 389, 540, 863, 992
HpyCH4IV	ACGT	2 cut(s)	544, 893
HpyCH4V	TGCA	9 cut(s)	52, 64, 169, 211, 284, 448, 686, 722, 958
HpyF10VI	GCNNNNNNNGC	1 cut(s)	290
HpyF3I	CTNAG	1 cut(s)	555
HpySE526I	ACGT	2 cut(s)	544, 893
Hsp92II	CATG	7 cut(s)	254, 455, 521, 602, 620, 828, 881
HspAI	GCGC	1 cut(s)	162
Kzo9I	GATC	5 cut(s)	28, 224, 376, 815, 968
LmnI	GCTCC	3 cut(s)	80, 188, 487
LweI	GCATC	6 cut(s)	128, 172, 304, 457, 673, 709
MaeII	ACGT	2 cut(s)	544, 893
MaeIII	GTNAC	5 cut(s)	140, 171, 341, 540, 608
MalI	GATC	5 cut(s)	30, 226, 378, 817, 970
MbiI	CCGCTC	1 cut(s)	83
MboI	GATC	5 cut(s)	28, 224, 376, 815, 968
MboII	GAAGA	4 cut(s)	494, 546, 587, 676
MfeI	CAATTG	1 cut(s)	348
MflI	RGATCY	3 cut(s)	28, 376, 968
MhlI	GDGCHC	1 cut(s)	429
MlsI	TGGCCA	1 cut(s)	876
MluCI	AATT	7 cut(s)	296, 319, 348, 434, 688, 712, 784
MluNI	TGGCCA	1 cut(s)	876
MlyI	GAGTC	2 cut(s)	409, 611
MmeI	TCCRAC	1 cut(s)	882
MnlI	CCTC	8 cut(s)	289, 441, 478, 618, 638, 703, 805, 982
Mox20I	TGGCCA	1 cut(s)	876
MscI	TGGCCA	1 cut(s)	876
MseI	TTAA	3 cut(s)	657, 711, 909
MslI	CAYNNNNRTG	2 cut(s)	312, 615
Msp20I	TGGCCA	1 cut(s)	876
MspR9I	CCNGG	1 cut(s)	33
MunI	CAATTG	1 cut(s)	348
Mva1269I	GAATGC	1 cut(s)	465
MvaI	CCWGG	1 cut(s)	33
MwoI	GCNNNNNNNGC	1 cut(s)	290
NcoI	CCATGG	1 cut(s)	517
NdeII	GATC	5 cut(s)	28, 224, 376, 815, 968
NlaIII	CATG	7 cut(s)	254, 455, 521, 602, 620, 828, 881
NlaIV	GGNNCC	5 cut(s)	37, 426, 489, 970, 982
NmuCI	GTSAC	4 cut(s)	171, 341, 540, 608
NspI	RCATGY	1 cut(s)	620
PaeI	GCATGC	1 cut(s)	620
PagI	TCATGA	1 cut(s)	598
PctI	GAATGC	1 cut(s)	465
PfoI	TCCNGGA	1 cut(s)	31
PleI	GAGTC	2 cut(s)	408, 610
PmaCI	CACGTG	1 cut(s)	545
PmlI	CACGTG	1 cut(s)	545
PpsI	GAGTC	2 cut(s)	408, 610
Ppu21I	YACGTR	1 cut(s)	545
PshBI	ATTAAT	1 cut(s)	711
PsiI	TTATAA	1 cut(s)	575
Psp6I	CCWGG	1 cut(s)	31
PspCI	CACGTG	1 cut(s)	545
PspEI	GGTNACC	1 cut(s)	140
PspGI	CCWGG	1 cut(s)	31
PspN4I	GGNNCC	5 cut(s)	37, 426, 489, 970, 982
PspPI	GGNCC	1 cut(s)	981
PstI	CTGCAG	1 cut(s)	286
PsuI	RGATCY	3 cut(s)	28, 376, 968
RsaI	GTAC	1 cut(s)	901
RsaNI	GTAC	1 cut(s)	900
RseI	CAYNNNNRTG	2 cut(s)	312, 615
SaqAI	TTAA	3 cut(s)	657, 711, 909
Sau3AI	GATC	5 cut(s)	28, 224, 376, 815, 968
Sau96I	GGNCC	1 cut(s)	981
SchI	GAGTC	2 cut(s)	409, 611
ScrFI	CCNGG	1 cut(s)	33
SduI	GDGCHC	1 cut(s)	429
SfaNI	GCATC	6 cut(s)	128, 172, 304, 457, 673, 709
SfcI	CTRYAG	1 cut(s)	282
SmiMI	CAYNNNNRTG	2 cut(s)	312, 615
SphI	GCATGC	1 cut(s)	620
Sse9I	AATT	7 cut(s)	296, 319, 348, 434, 688, 712, 784
SsiI	CCGC	1 cut(s)	83
StyD4I	CCNGG	1 cut(s)	31
StyI	CCWWGG	3 cut(s)	68, 517, 934
TaaI	ACNGT	8 cut(s)	46, 140, 146, 231, 389, 540, 863, 992
TaiI	ACGT	2 cut(s)	547, 896
TasI	AATT	7 cut(s)	296, 319, 348, 434, 688, 712, 784
Tru1I	TTAA	3 cut(s)	657, 711, 909
Tru9I	TTAA	3 cut(s)	657, 711, 909
TscAI	CASTG	2 cut(s)	291, 394
TseFI	GTSAC	4 cut(s)	171, 341, 540, 608
Tsp45I	GTSAC	4 cut(s)	171, 341, 540, 608
TspDTI	ATGAA	5 cut(s)	170, 267, 281, 587, 813
TspRI	CASTG	2 cut(s)	291, 394
VspI	ATTAAT	1 cut(s)	711
XapI	RAATTY	2 cut(s)	319, 688
XceI	RCATGY	1 cut(s)	620

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