Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0001478

Physical Location & Seq

Genomic Coordinates Forward (+)

1685744 .. 1691841

Gene Structure 6098 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG024100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1245 bp

ATGCTTCGATCAGACACGGTTCTGTTTCGACACAAAGAAGAGTACTCCTGTGAACCCCAGATGGTAAATGATGAGATGTTGAGGTTAGGAGGAGAGATTTTGAGGAAGGACAACTGCATCGAATATCTAAAGACCTTGCGGAACTTCAACTACTATGTCTACCACCACTTCGTCAATCTTATGAAAGACTTCAAGCCAAAAGGTGACGACTGTATTGAAACTTTGAAGCAGAAGGTGCAGGACTTATTTGAAGGGTGTCCGGATTTGGTATTAGGGTTCAATGCCTTCTTGCCCATGAGACATAAAATTAACGTCCCAATCTCAATAAAAGTCCAGACCGCCAGAAAACTCCCAATAGTTCTTTCTCGAAAGAGAAAGCGCGACGATGATACTTGTGATGTTGTTGATGATGCTGGATCTAATGACTCTAAGCTTCAAAAGGTGATCGGTTTTGTGAACAAGGTTAGAGATAGATTTCGCAACGATAGTGAGGAAGGTGATGATGTTTTTCAGTCCTTTTTAGATATTTTCTTGAATTATCACTGCAAAAGAAACAAGTCATCACCCAATAGAAACAAATTATCACCCAAAAAGTCCGGCAGTACTGCTGATGAAGATGAGCTTCAGATTTACAAGAAGGTTAAAGCACTTTTCGATGGCCACCCGGACTTGATTGATGAGTTCACCCACTTTTTACCAACAGTGCCTTTACCTTCACTTTCCTCAGTCATTGATTTCGCTAACTGCGAGACTTGCACCCCAAGCTACCGTCTTTTGCCAGAGAGTTTCCCCATTCCTGCTGCCACCAAACGATCGAAGCTTGCTTCTCAAGTATTGAATGATCATTGGATATGCGTTCCGAGTACTAATTCAAGAGGAGGAGGAGGAGGAAACACACAACAAAACATGTTCGGGTGGGAAGATAAAAGGTTCGAACTTGATAGGAAGGTGAACACTGTCAGTTCAGCCTCAAAGAGTATCAAAAAGCTGCTGAAAAAGATTGAAAAGGATAGTCCATCAGAGATCTATATTGAAGATCATCTCACGGAGCTGAATTTGAAGTGCAGTAAGAGATTGTATGATGAGCAAGGGCTTAATGCAATGGATGAGCTGAGGAATAATATTCGAGGGGCTTTGCCTGTGTTGTTGAACCGGTTGAAGCAACAGGAAGAAGAACTGAAACAACGCCGATCATTTCTTAACCAAAAGTGGGCTCATCATATGAAAGTTTTTAATTGCAGGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

ko04139 ko04919 ko05016 ko05202 map04139 map04919 map05016 map05202

Pfam Domains

Protein Families

PAH Sin3_corepress Sin3a_C

Protein Analysis

414

Amino Acids

47.93

Weight (kDa)

8.78

Isoelectric Point (pI)

55.44

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PAH	PF02671	53 - 97	4.7e-11	Paired amphipathic helix repeat
PAH	PF02671	168 - 232	1.2e-07	Paired amphipathic helix repeat
Sin3_corepress	PF08295	251 - 340	3.8e-18	Sin3 family co-repressor

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

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0001478)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G23810 AT1G24210 AT1G24220 AT1G24220 AT1G24230 AT1G24250 AT1G27240 AT1G27260 AT1G27270 AT1G27280
fragaria_vesca	FvH4_3g01921 FvH4_3g01930 FvH4_5g11770 FvH4_5g22630
malus_domestica	MD08G1247800.v1.1
pyrus_communis	pycom08g21470 pycom15g39040
rosa_chinensis	RchiOBHm_Chr5g0002831 RchiOBHm_Chr5g0002841
rosa_laevigata	RLG00000003026 RLG00000003029 RLG00000031063 RLG00000031064
rosa_multiflora	Rmu_co8115592.1_g000001 Rmu_co8158784.1_g000001 Rmu_sc0012670.1_g000008 Rmu_sc0012670.1_g000009 Rmu_sc0013603.1_g000011 Rmu_sc0013603.1_g000012
rosa_roxburghii	Rroxscaffold_1G00073010 Rroxscaffold_1G00073020 Rroxscaffold_3G00248150
rosa_rugosa	Rorug04G0400000 Rorug04G0400100
rosa_samantha	Rh5AG022900 Rh5BG025500 Rh5BG025600 Rh5CG025400 Rh5CG025500 Rh5DG024000 Rh5DG024100 Rh7AG255700 Rh7AG256500 Rh7BG250100 Rh7CG272100 Rh7CG272900 Rh7CG273000 Rh7DG262900
rosa_wichuraiana	Rw5G002120 Rw5G002140 Rw7G021870

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	1230
AccI	GTMKAC	1 cut(s)	159
AccII	CGCG	1 cut(s)	381
AccIII	TCCGGA	1 cut(s)	259
AciI	CCGC	2 cut(s)	139, 339
AclWI	GGATC	1 cut(s)	424
AcoI	YGGCCR	1 cut(s)	658
AcsI	RAATTY	1 cut(s)	1054
AcuI	CTGAAG	1 cut(s)	608
AfaI	GTAC	3 cut(s)	44, 604, 865
AfiI	CCNNNNNNNGG	1 cut(s)	1210
AflIII	ACRYGT	1 cut(s)	906
AgeI	ACCGGT	1 cut(s)	1152
AjuI	GAANNNNNNNTTGG	2 cut(s)	346, 378
AluBI	AGCT	7 cut(s)	433, 622, 765, 820, 988, 1051, 1111
AluI	AGCT	7 cut(s)	433, 622, 765, 820, 988, 1051, 1111
Alw26I	GTCTC	2 cut(s)	292, 743
AlwI	GGATC	1 cut(s)	424
Aor13HI	TCCGGA	1 cut(s)	259
AoxI	GGCC	1 cut(s)	658
ApeKI	GCWGC	2 cut(s)	800, 988
ApoI	RAATTY	1 cut(s)	1054
AsiGI	ACCGGT	1 cut(s)	1152
Asp700I	GAANNNNTTC	1 cut(s)	188
AspLEI	GCGC	1 cut(s)	381
AsuC2I	CCSGG	1 cut(s)	665
AsuHPI	GGTGA	7 cut(s)	215, 454, 509, 555, 576, 676, 961
AsuII	TTCGAA	1 cut(s)	933
BalI	TGGCCA	1 cut(s)	660
BanII	GRGCYC	1 cut(s)	1216
BbvCI	CCTCAGC	1 cut(s)	1112
BbvI	GCAGC	2 cut(s)	787, 975
BccI	CCATC	3 cut(s)	55, 650, 1024
BclI	TGATCA	1 cut(s)	841
BcnI	CCSGG	1 cut(s)	665
BcoDI	GTCTC	2 cut(s)	292, 743
BfuAI	ACCTGC	1 cut(s)	1230
BglII	AGATCT	1 cut(s)	1023
BisI	GCNGC	2 cut(s)	801, 989
BlsI	GCNGC	2 cut(s)	802, 990
BmcAI	AGTACT	3 cut(s)	44, 604, 865
Bme1390I	CCNGG	1 cut(s)	665
BmrFI	CCNGG	1 cut(s)	665
BmsI	GCATC	2 cut(s)	126, 400
Bpu10I	CCTNAGC	1 cut(s)	1112
Bpu14I	TTCGAA	1 cut(s)	933
BpuEI	CTTGAG	1 cut(s)	813
BpuMI	CCSGG	1 cut(s)	665
BsaWI	WCCGGW	2 cut(s)	259, 1152
Bsc4I	CCNNNNNNNGG	1 cut(s)	1210
Bse118I	RCCGGY	1 cut(s)	1152
Bse3DI	GCAATG	1 cut(s)	1107
BseAI	TCCGGA	1 cut(s)	259
BseGI	GGATG	1 cut(s)	1111
BseLI	CCNNNNNNNGG	1 cut(s)	1210
BseMI	GCAATG	1 cut(s)	1107
BseMII	CTCAG	2 cut(s)	738, 1103
BseRI	GAGGAG	5 cut(s)	105, 891, 894, 897, 900
BseXI	GCAGC	2 cut(s)	787, 975
BsgI	GTGCAG	2 cut(s)	257, 1084
Bsh1236I	CGCG	1 cut(s)	381
Bsh1285I	CGRYCG	1 cut(s)	815
BshFI	GGCC	1 cut(s)	660
BshTI	ACCGGT	1 cut(s)	1152
BsiEI	CGRYCG	1 cut(s)	815
BsiSI	CCGG	4 cut(s)	260, 597, 665, 1153
BslFI	GGGAC	1 cut(s)	299
BslI	CCNNNNNNNGG	1 cut(s)	1210
BsmAI	GTCTC	2 cut(s)	292, 743
BsmFI	GGGAC	1 cut(s)	299
BsnI	GGCC	1 cut(s)	660
Bsp119I	TTCGAA	1 cut(s)	933
Bsp1286I	GDGCHC	1 cut(s)	1216
Bsp13I	TCCGGA	1 cut(s)	259
Bsp143I	GATC	8 cut(s)	8, 416, 444, 812, 841, 1023, 1036, 1190
BspACI	CCGC	2 cut(s)	139, 339
BspANI	GGCC	1 cut(s)	660
BspCNI	CTCAG	2 cut(s)	737, 1104
BspEI	TCCGGA	1 cut(s)	259
BspFNI	CGCG	1 cut(s)	381
BspMI	ACCTGC	1 cut(s)	1230
BspPI	GGATC	1 cut(s)	424
BspT104I	TTCGAA	1 cut(s)	933
BsrDI	GCAATG	1 cut(s)	1107
BsrFI	RCCGGY	1 cut(s)	1152
BssAI	RCCGGY	1 cut(s)	1152
BssMI	GATC	8 cut(s)	8, 416, 444, 812, 841, 1023, 1036, 1190
Bst4CI	ACNGT	5 cut(s)	19, 212, 703, 770, 958
Bst6I	CTCTTC	1 cut(s)	33
BstAPI	GCANNNNNTGC	1 cut(s)	235
BstBI	TTCGAA	1 cut(s)	933
BstC8I	GCNNGC	1 cut(s)	822
BstDEI	CTNAG	3 cut(s)	429, 724, 1112
BstF5I	GGATG	1 cut(s)	1111
BstFNI	CGCG	1 cut(s)	381
BstHHI	GCGC	1 cut(s)	381
BstKTI	GATC	8 cut(s)	11, 419, 447, 815, 844, 1026, 1039, 1193
BstMAI	GTCTC	2 cut(s)	292, 743
BstMBI	GATC	8 cut(s)	8, 416, 444, 812, 841, 1023, 1036, 1190
BstMCI	CGRYCG	1 cut(s)	815
BstMWI	GCNNNNNNNGC	3 cut(s)	235, 753, 762
BstNSI	RCATGY	1 cut(s)	910
BstSCI	CCNGG	1 cut(s)	663
BstUI	CGCG	1 cut(s)	381
BstV1I	GCAGC	2 cut(s)	787, 975
BstX2I	RGATCY	2 cut(s)	416, 1023
BstYI	RGATCY	2 cut(s)	416, 1023
BsuRI	GGCC	1 cut(s)	660
BtsCI	GGATG	1 cut(s)	1111
BtsI	GCAGTG	1 cut(s)	541
BtsIMutI	CAGTG	3 cut(s)	541, 708, 954
BveI	ACCTGC	1 cut(s)	1230
Cac8I	GCNNGC	1 cut(s)	822
CfoI	GCGC	1 cut(s)	381
Cfr10I	RCCGGY	1 cut(s)	1152
Csp6I	GTAC	3 cut(s)	43, 603, 864
CspAI	ACCGGT	1 cut(s)	1152
CviAII	CATG	2 cut(s)	295, 907
CviQI	GTAC	3 cut(s)	43, 603, 864
DdeI	CTNAG	3 cut(s)	429, 724, 1112
DpnI	GATC	8 cut(s)	10, 418, 446, 814, 843, 1025, 1038, 1192
DpnII	GATC	8 cut(s)	8, 416, 444, 812, 841, 1023, 1036, 1190
EaeI	YGGCCR	1 cut(s)	658
Eam1104I	CTCTTC	1 cut(s)	33
EarI	CTCTTC	1 cut(s)	33
Eco24I	GRGCYC	1 cut(s)	1216
Eco57I	CTGAAG	1 cut(s)	608
EcoT38I	GRGCYC	1 cut(s)	1216
FaeI	CATG	2 cut(s)	298, 910
FalI	AAGNNNNNCTT	2 cut(s)	606, 638
FaqI	GGGAC	1 cut(s)	299
FatI	CATG	2 cut(s)	294, 906
FauNDI	CATATG	1 cut(s)	1221
FbaI	TGATCA	1 cut(s)	841
FblI	GTMKAC	1 cut(s)	159
Fnu4HI	GCNGC	2 cut(s)	801, 989
FokI	GGATG	1 cut(s)	1118
FriOI	GRGCYC	1 cut(s)	1216
Fsp4HI	GCNGC	2 cut(s)	801, 989
GlaI	GCGC	1 cut(s)	380
GluI	GCNGC	2 cut(s)	801, 989
HaeIII	GGCC	1 cut(s)	660
HapII	CCGG	4 cut(s)	260, 597, 665, 1153
HhaI	GCGC	1 cut(s)	381
Hin1II	CATG	2 cut(s)	298, 910
Hin6I	GCGC	1 cut(s)	379
HinP1I	GCGC	1 cut(s)	379
HindIII	AAGCTT	2 cut(s)	431, 818
HinfI	GANTC	1 cut(s)	425
HpaII	CCGG	4 cut(s)	260, 597, 665, 1153
HphI	GGTGA	7 cut(s)	215, 454, 509, 555, 576, 676, 961
Hpy166II	GTNNAC	5 cut(s)	53, 160, 457, 684, 952
Hpy188I	TCNGA	4 cut(s)	13, 627, 861, 1021
Hpy188III	TCNNGA	5 cut(s)	260, 334, 366, 532, 873
Hpy8I	GTNNAC	5 cut(s)	53, 160, 457, 684, 952
Hpy99I	CGWCG	1 cut(s)	386
HpyAV	CCTTC	8 cut(s)	100, 226, 245, 295, 488, 631, 723, 940
HpyCH4III	ACNGT	5 cut(s)	19, 212, 703, 770, 958
HpyCH4IV	ACGT	1 cut(s)	312
HpyCH4V	TGCA	7 cut(s)	117, 238, 546, 756, 1065, 1100, 1239
HpyF10VI	GCNNNNNNNGC	3 cut(s)	235, 753, 762
HpyF3I	CTNAG	3 cut(s)	429, 724, 1112
HpySE526I	ACGT	1 cut(s)	312
Hsp92II	CATG	2 cut(s)	298, 910
HspAI	GCGC	1 cut(s)	379
Kpn2I	TCCGGA	1 cut(s)	259
Ksp22I	TGATCA	1 cut(s)	841
Kzo9I	GATC	8 cut(s)	8, 416, 444, 812, 841, 1023, 1036, 1190
LmnI	GCTCC	1 cut(s)	1048
Lsp1109I	GCAGC	2 cut(s)	787, 975
LweI	GCATC	2 cut(s)	126, 400
MaeII	ACGT	1 cut(s)	312
MaeIII	GTNAC	1 cut(s)	203
MalI	GATC	8 cut(s)	10, 418, 446, 814, 843, 1025, 1038, 1192
MboI	GATC	8 cut(s)	8, 416, 444, 812, 841, 1023, 1036, 1190
MboII	GAAGA	6 cut(s)	50, 626, 932, 1046, 1181, 1184
MflI	RGATCY	2 cut(s)	416, 1023
MhlI	GDGCHC	1 cut(s)	1216
MlsI	TGGCCA	1 cut(s)	660
MluCI	AATT	6 cut(s)	306, 535, 578, 868, 1054, 1234
MluNI	TGGCCA	1 cut(s)	660
MlyI	GAGTC	1 cut(s)	419
Mox20I	TGGCCA	1 cut(s)	660
MroI	TCCGGA	1 cut(s)	259
MroXI	GAANNNNTTC	1 cut(s)	188
MscI	TGGCCA	1 cut(s)	660
MseI	TTAA	5 cut(s)	309, 642, 1095, 1200, 1233
Msp20I	TGGCCA	1 cut(s)	660
MspI	CCGG	4 cut(s)	260, 597, 665, 1153
MspR9I	CCNGG	1 cut(s)	665
MvnI	CGCG	1 cut(s)	381
MwoI	GCNNNNNNNGC	3 cut(s)	235, 753, 762
NciI	CCSGG	1 cut(s)	665
NdeI	CATATG	1 cut(s)	1221
NdeII	GATC	8 cut(s)	8, 416, 444, 812, 841, 1023, 1036, 1190
NlaIII	CATG	2 cut(s)	298, 910
NmuCI	GTSAC	1 cut(s)	203
NspI	RCATGY	1 cut(s)	910
NspV	TTCGAA	1 cut(s)	933
PciI	ACATGT	1 cut(s)	906
PcsI	WCGNNNNNNNCGW	1 cut(s)	744
PdmI	GAANNNNTTC	1 cut(s)	188
PinAI	ACCGGT	1 cut(s)	1152
PkrI	GCNGC	2 cut(s)	802, 990
Ple19I	CGATCG	1 cut(s)	815
PleI	GAGTC	1 cut(s)	419
PpsI	GAGTC	1 cut(s)	419
PscI	ACATGT	1 cut(s)	906
PsrI	GAACNNNNNNTAC	2 cut(s)	134, 166
PsuI	RGATCY	2 cut(s)	416, 1023
PvuI	CGATCG	1 cut(s)	815
RsaI	GTAC	3 cut(s)	44, 604, 865
RsaNI	GTAC	3 cut(s)	43, 603, 864
SaqAI	TTAA	5 cut(s)	309, 642, 1095, 1200, 1233
SatI	GCNGC	2 cut(s)	801, 989
Sau3AI	GATC	8 cut(s)	8, 416, 444, 812, 841, 1023, 1036, 1190
ScaI	AGTACT	3 cut(s)	44, 604, 865
SchI	GAGTC	1 cut(s)	419
ScrFI	CCNGG	1 cut(s)	665
SduI	GDGCHC	1 cut(s)	1216
SfaNI	GCATC	2 cut(s)	126, 400
SfuI	TTCGAA	1 cut(s)	933
SmlI	CTYRAG	1 cut(s)	828
SmoI	CTYRAG	1 cut(s)	828
Sse9I	AATT	6 cut(s)	306, 535, 578, 868, 1054, 1234
SsiI	CCGC	2 cut(s)	139, 339
SspI	AATATT	1 cut(s)	1123
StyD4I	CCNGG	1 cut(s)	663
TaaI	ACNGT	5 cut(s)	19, 212, 703, 770, 958
TaiI	ACGT	1 cut(s)	315
TaqI	TCGA	8 cut(s)	7, 28, 120, 367, 654, 815, 933, 1126
TasI	AATT	6 cut(s)	306, 535, 578, 868, 1054, 1234
TatI	WGTACW	3 cut(s)	42, 602, 863
Tru1I	TTAA	5 cut(s)	309, 642, 1095, 1200, 1233
Tru9I	TTAA	5 cut(s)	309, 642, 1095, 1200, 1233
TscAI	CASTG	3 cut(s)	548, 708, 961
TseFI	GTSAC	1 cut(s)	203
TseI	GCWGC	2 cut(s)	800, 988
Tsp45I	GTSAC	1 cut(s)	203
TspDTI	ATGAA	3 cut(s)	197, 627, 1238
TspGWI	ACGGA	1 cut(s)	1061
TspRI	CASTG	3 cut(s)	548, 708, 961
XapI	RAATTY	1 cut(s)	1054
XceI	RCATGY	1 cut(s)	910
XmiI	GTMKAC	1 cut(s)	159
XmnI	GAANNNNTTC	1 cut(s)	188
ZrmI	AGTACT	3 cut(s)	44, 604, 865

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