Rh5CG042300
MADS Family

MADS-box transcription factor

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5C
OG0017997
Physical Location & Seq
Forward (+)
2929824 .. 2930394
571 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5CG042300.1

Sequence Viewer

Length: 447 bp
ATGGGTACCGGAAAGAAGAAAATTGACATAGAGCCGATCACCGACTATCAGTCTCGCATGGTGGCCTTCACCAGGAGACGAACAGGTCTCTTCAAAAAAGCCCAGAAGCTAGCAGAAATGTCTGGTTCATCCATCGCCATTGCTGTGATCTCCGAGACCGGTCAACCTTACCTCCATGGCTCTCCTTCCTTGCTTGAACGAGTTCTTGCCTCCAAAGCCTCTTCCTCCACAGTTACTGGCTCTTCTACCACTAAAGCTGACGCTGGTTCTTCCACCACCACCGCCACTACAGGATCTTTAGAAAGATTTAACGCTGGGGTGAACTCTCAGATTGAAGCTTGTACCACTCTGGAAGAAGCAGAGAGTTTGAAAAGGAAATTGTTGGAAATCAAAAAGAGGGCGGACGATAAACTTTCTGGAAGTGATCTTCAATTTGTTCTTAATTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko04011 ko04111 map04011 map04111
Pfam Domains
Protein Families
SRF-TF

Protein Analysis

148

Amino Acids

15.8

Weight (kDa)

9.44

Isoelectric Point (pI)

51.44

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
SRF-TF PF00319 12 - 57 9.8e-14 SRF-type transcription factor (DNA-binding and dimerisation domain)
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0017997)

Species Orthologous Gene IDs
fragaria_vesca FvH4_3g02880
rosa_chinensis RchiOBHm_Chr5g0004451
rosa_laevigata RLG00000031227
rosa_multiflora Rmu_sc0000433.1_g000010 Rmu_sc0002453.1_g000004
rosa_roxburghii Rroxscaffold_1G00071100
rosa_rugosa Rorug04G0411700
rosa_samantha Rh5AG039100 Rh5BG038100 Rh5CG042300 Rh5DG037700

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 84
Acc65I GGTACC 1 cut(s) 5
AccB1I GGYRCC 1 cut(s) 5
AciI CCGC 2 cut(s) 282, 401
AclWI GGATC 1 cut(s) 301
AfaI GTAC 2 cut(s) 7, 343
AfiI CCNNNNNNNGG 1 cut(s) 72
AgeI ACCGGT 1 cut(s) 158
AgsI TTSAA 5 cut(s) 94, 197, 335, 370, 431
AhdI GACNNNNNGTC 1 cut(s) 49
AjnI CCWGG 1 cut(s) 71
AluBI AGCT 3 cut(s) 109, 257, 338
AluI AGCT 3 cut(s) 109, 257, 338
Alw26I GTCTC 4 cut(s) 57, 70, 92, 149
AlwI GGATC 1 cut(s) 301
AlwNI CAGNNNCTG 1 cut(s) 236
AoxI GGCC 1 cut(s) 63
AsiGI ACCGGT 1 cut(s) 158
Asp700I GAANNNNTTC 1 cut(s) 201
Asp718I GGTACC 1 cut(s) 5
AsuHPI GGTGA 3 cut(s) 31, 61, 331
AsuNHI GCTAGC 1 cut(s) 109
BanI GGYRCC 1 cut(s) 5
BccI CCATC 1 cut(s) 140
BciT130I CCWGG 1 cut(s) 73
BcoDI GTCTC 4 cut(s) 57, 70, 92, 149
BfaI CTAG 1 cut(s) 110
BfmI CTRYAG 1 cut(s) 288
Bme1390I CCNGG 1 cut(s) 73
BmeRI GACNNNNNGTC 1 cut(s) 49
BmiI GGNNCC 1 cut(s) 7
BmrFI CCNGG 1 cut(s) 73
BmtI GCTAGC 1 cut(s) 113
BsaI GGTCTC 2 cut(s) 92, 149
BsaJI CCNNGG 1 cut(s) 175
BsaWI WCCGGW 2 cut(s) 8, 158
BsaXI ACNNNNNCTCC 2 cut(s) 156, 186
Bsc4I CCNNNNNNNGG 1 cut(s) 72
Bse118I RCCGGY 1 cut(s) 158
Bse1I ACTGG 1 cut(s) 241
Bse3DI GCAATG 1 cut(s) 138
BseBI CCWGG 1 cut(s) 73
BseDI CCNNGG 1 cut(s) 175
BseGI GGATG 1 cut(s) 128
BseLI CCNNNNNNNGG 1 cut(s) 72
BseMI GCAATG 1 cut(s) 138
BseMII CTCAG 1 cut(s) 341
BseNI ACTGG 1 cut(s) 241
BseYI CCCAGC 1 cut(s) 314
BshFI GGCC 1 cut(s) 65
BshNI GGYRCC 1 cut(s) 5
BshTI ACCGGT 1 cut(s) 158
BsiSI CCGG 2 cut(s) 9, 159
BslI CCNNNNNNNGG 1 cut(s) 72
BsmAI GTCTC 4 cut(s) 57, 70, 92, 149
BsmBI CGTCTC 1 cut(s) 70
BsnI GGCC 1 cut(s) 65
Bso31I GGTCTC 2 cut(s) 92, 149
Bsp143I GATC 4 cut(s) 36, 147, 293, 424
Bsp19I CCATGG 1 cut(s) 175
BspACI CCGC 2 cut(s) 282, 401
BspANI GGCC 1 cut(s) 65
BspCNI CTCAG 1 cut(s) 340
BspLI GGNNCC 1 cut(s) 7
BspOI GCTAGC 1 cut(s) 113
BspPI GGATC 1 cut(s) 301
BspQI GCTCTTC 1 cut(s) 247
BspT107I GGYRCC 1 cut(s) 5
BspTNI GGTCTC 2 cut(s) 92, 149
BsrDI GCAATG 1 cut(s) 138
BsrFI RCCGGY 1 cut(s) 158
BsrI ACTGG 1 cut(s) 241
BssAI RCCGGY 1 cut(s) 158
BssECI CCNNGG 1 cut(s) 175
BssMI GATC 4 cut(s) 36, 147, 293, 424
BssT1I CCWWGG 1 cut(s) 175
Bst2UI CCWGG 1 cut(s) 73
Bst4CI ACNGT 1 cut(s) 232
Bst6I CTCTTC 3 cut(s) 95, 226, 247
BstC8I GCNNGC 1 cut(s) 111
BstDEI CTNAG 1 cut(s) 327
BstDSI CCRYGG 1 cut(s) 175
BstENI CCTNNNNNAGG 1 cut(s) 70
BstF5I GGATG 1 cut(s) 128
BstKTI GATC 4 cut(s) 39, 150, 296, 427
BstMAI GTCTC 4 cut(s) 57, 70, 92, 149
BstMBI GATC 4 cut(s) 36, 147, 293, 424
BstMWI GCNNNNNNNGC 1 cut(s) 215
BstNI CCWGG 1 cut(s) 73
BstSCI CCNGG 1 cut(s) 71
BstSFI CTRYAG 1 cut(s) 288
BstX2I RGATCY 1 cut(s) 293
BstYI RGATCY 1 cut(s) 293
BsuRI GGCC 1 cut(s) 65
BtgI CCRYGG 1 cut(s) 175
BtgZI GCGATG 1 cut(s) 118
BtsCI GGATG 1 cut(s) 128
Cac8I GCNNGC 1 cut(s) 111
CaiI CAGNNNCTG 1 cut(s) 236
Cfr10I RCCGGY 1 cut(s) 158
CseI GACGC 1 cut(s) 269
Csp6I GTAC 2 cut(s) 6, 342
CspAI ACCGGT 1 cut(s) 158
CviAII CATG 2 cut(s) 58, 176
CviJI RGCY 9 cut(s) 34, 65, 101, 109, 180, 218, 240, 257, 338
CviKI_1 RGCY 9 cut(s) 34, 65, 101, 109, 180, 218, 240, 257, 338
CviQI GTAC 2 cut(s) 6, 342
DdeI CTNAG 1 cut(s) 327
DpnI GATC 4 cut(s) 38, 149, 295, 426
DpnII GATC 4 cut(s) 36, 147, 293, 424
DrdI GACNNNNNNGTC 1 cut(s) 84
DriI GACNNNNNGTC 1 cut(s) 49
DseDI GACNNNNNNGTC 1 cut(s) 84
Eam1104I CTCTTC 3 cut(s) 95, 226, 247
Eam1105I GACNNNNNGTC 1 cut(s) 49
EarI CTCTTC 3 cut(s) 95, 226, 247
EciI GGCGGA 1 cut(s) 416
Eco130I CCWWGG 1 cut(s) 175
Eco31I GGTCTC 2 cut(s) 92, 149
EcoNI CCTNNNNNAGG 1 cut(s) 70
EcoRII CCWGG 1 cut(s) 71
EcoT14I CCWWGG 1 cut(s) 175
ErhI CCWWGG 1 cut(s) 175
Esp3I CGTCTC 1 cut(s) 70
FaeI CATG 2 cut(s) 61, 179
FaiI YATR 3 cut(s) 29, 59, 177
FatI CATG 2 cut(s) 57, 175
FokI GGATG 1 cut(s) 115
FspBI CTAG 1 cut(s) 110
GsaI CCCAGC 1 cut(s) 318
HaeIII GGCC 1 cut(s) 65
HapII CCGG 2 cut(s) 9, 159
HgaI GACGC 1 cut(s) 269
Hin1II CATG 2 cut(s) 61, 179
HincII GTYRAC 1 cut(s) 164
HindII GTYRAC 1 cut(s) 164
HindIII AAGCTT 1 cut(s) 336
HpaII CCGG 2 cut(s) 9, 159
HphI GGTGA 3 cut(s) 31, 61, 331
Hpy166II GTNNAC 2 cut(s) 164, 322
Hpy188I TCNGA 2 cut(s) 154, 330
Hpy188III TCNNGA 2 cut(s) 350, 417
Hpy8I GTNNAC 2 cut(s) 164, 322
HpyAV CCTTC 2 cut(s) 76, 195
HpyCH4III ACNGT 1 cut(s) 232
HpyF10VI GCNNNNNNNGC 1 cut(s) 215
HpyF3I CTNAG 1 cut(s) 327
Hsp92II CATG 2 cut(s) 61, 179
KpnI GGTACC 1 cut(s) 9
Kzo9I GATC 4 cut(s) 36, 147, 293, 424
LguI GCTCTTC 1 cut(s) 247
MaeI CTAG 1 cut(s) 110
MaeIII GTNAC 1 cut(s) 232
MalI GATC 4 cut(s) 38, 149, 295, 426
MboI GATC 4 cut(s) 36, 147, 293, 424
MboII GAAGA 7 cut(s) 28, 82, 213, 234, 261, 365, 419
MflI RGATCY 1 cut(s) 293
MluCI AATT 4 cut(s) 21, 377, 431, 442
MmeI TCCRAC 1 cut(s) 363
MnlI CCTC 5 cut(s) 182, 220, 229, 235, 390
MroXI GAANNNNTTC 1 cut(s) 201
MseI TTAA 2 cut(s) 309, 441
MslI CAYNNNNRTG 1 cut(s) 143
MspI CCGG 2 cut(s) 9, 159
MspR9I CCNGG 1 cut(s) 73
MvaI CCWGG 1 cut(s) 73
MwoI GCNNNNNNNGC 1 cut(s) 215
NcoI CCATGG 1 cut(s) 175
NdeII GATC 4 cut(s) 36, 147, 293, 424
NheI GCTAGC 1 cut(s) 109
NlaIII CATG 2 cut(s) 61, 179
NlaIV GGNNCC 1 cut(s) 7
PciSI GCTCTTC 1 cut(s) 247
PdmI GAANNNNTTC 1 cut(s) 201
PinAI ACCGGT 1 cut(s) 158
Psp6I CCWGG 1 cut(s) 71
PspFI CCCAGC 1 cut(s) 314
PspGI CCWGG 1 cut(s) 71
PspN4I GGNNCC 1 cut(s) 7
PstNI CAGNNNCTG 1 cut(s) 236
PsuI RGATCY 1 cut(s) 293
RsaI GTAC 2 cut(s) 7, 343
RsaNI GTAC 2 cut(s) 6, 342
RseI CAYNNNNRTG 1 cut(s) 143
SapI GCTCTTC 1 cut(s) 247
SaqAI TTAA 2 cut(s) 309, 441
Sau3AI GATC 4 cut(s) 36, 147, 293, 424
ScrFI CCNGG 1 cut(s) 73
SetI ASST 6 cut(s) 88, 111, 169, 174, 259, 340
SfcI CTRYAG 1 cut(s) 288
SmiMI CAYNNNNRTG 1 cut(s) 143
Sse9I AATT 4 cut(s) 21, 377, 431, 442
SsiI CCGC 2 cut(s) 282, 401
SspMI CTAG 1 cut(s) 110
StyD4I CCNGG 1 cut(s) 71
StyI CCWWGG 1 cut(s) 175
TaaI ACNGT 1 cut(s) 232
TasI AATT 4 cut(s) 21, 377, 431, 442
Tru1I TTAA 2 cut(s) 309, 441
Tru9I TTAA 2 cut(s) 309, 441
TspDTI ATGAA 1 cut(s) 117
XagI CCTNNNNNAGG 1 cut(s) 70
XmnI GAANNNNTTC 1 cut(s) 201
XspI CTAG 1 cut(s) 110
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.