Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0006476

Physical Location & Seq

Genomic Coordinates Reverse (-)

60081020 .. 60206624

Gene Structure 125605 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG387700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 537 bp

ATGGCGGAGCACTTGGCTTCAATCTTTGGGACGGAGAAGGACAGAGTGAACTGCCCCTTCTACTTCAAAATAGGGGCGTGCAGGCACGGCGATCGGTGCTCCAGGCTTCACACGAAGCCCAGCGTCAGCCCGACTCTGTTGCTCTCCAATATGTACCAGAGGCCCGATATGATCACCCCCGGCGTCGACGCCCAGGGCCAGCCTATCGACCCCCGCCAGATGCAAACCCATTTCGAGGAATTTTATGAGGATCTCTTTCAAGAGCTGAGTAAGTATGGAGAAATTGAAAGCCTGAATGTCTGCGACAACCTAGCTGACCACATGGTGGGCAATGTGTATGTTCAGTTTAGGGAGGAAGAGCATGCTGCAAATGCACTCAAGAATCTGACTGGAAGATTTTATGCTGGGCGTCCTATCATTGTGGACTTCTCTCCGGTGACAGACTTCCGTGAAGCCACCTGCAGGCAATATGAGGAAAATACGTGCAATCGTGGTGGATGCTGCAATTTTATGCATCTGAAAAGGATTGGGAGGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

ko03040 ko05131 map03040 map05131

Pfam Domains

Protein Families

RRM_1 zf-CCCH

Protein Analysis

178

Amino Acids

20.46

Weight (kDa)

5.97

Isoelectric Point (pI)

41.55

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
zf-CCCH	PF00642	14 - 38	1.1e-07	Zinc finger C-x8-C-x5-C-x3-H type (and similar)
RRM_1	PF00076	83 - 139	2.9e-07	RNA recognition motif

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

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

Orthologous Genes (Group: OG0006476)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G27650 AT1G27650
fragaria_vesca	FvH4_3g29970 FvH4_3g29970 FvH4_3g29970 FvH4_3g29970
malus_domestica	MD03G1134200.v1.1 MD11G1156400.v1.1
prunus_persica	Prupe.6G118600_v2.0.a1 Prupe.6G118600_v2.0.a1
pyrus_communis	pycom03g09020 pycom11g12700
rosa_chinensis	RchiOBHm_Chr5g0055381 RchiOBHm_Chr5g0055431
rosa_laevigata	RLG00000034985
rosa_multiflora	Rmu_sc0001673.1_g000027 Rmu_sc0014407.1_g000001
rosa_roxburghii	Rroxscaffold_1G00024920 Rroxscaffold_1G00024960
rosa_samantha	Rh5AG362400 Rh5BG374600 Rh5CG396200 Rh5CG396400 Rh5DG387700
rosa_wichuraiana	Rw5G034090 Rw5G034120

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	467
Acc36I	ACCTGC	1 cut(s)	467
AccB7I	CCANNNNNTGG	1 cut(s)	325
AccI	GTMKAC	1 cut(s)	186
AciI	CCGC	2 cut(s)	5, 214
AclWI	GGATC	1 cut(s)	258
AcsI	RAATTY	1 cut(s)	239
AcyI	GRCGYC	3 cut(s)	183, 189, 409
AdeI	CACNNNGTG	1 cut(s)	325
AfaI	GTAC	1 cut(s)	155
AfiI	CCNNNNNNNGG	3 cut(s)	235, 325, 462
AgsI	TTSAA	4 cut(s)	21, 67, 260, 287
AjnI	CCWGG	2 cut(s)	101, 192
AluBI	AGCT	2 cut(s)	265, 314
AluI	AGCT	2 cut(s)	265, 314
Alw21I	GWGCWC	2 cut(s)	12, 101
AlwI	GGATC	1 cut(s)	258
AoxI	GGCC	2 cut(s)	161, 196
ApeKI	GCWGC	2 cut(s)	365, 501
ApoI	RAATTY	1 cut(s)	239
AspS9I	GGNCC	2 cut(s)	162, 196
AsuC2I	CCSGG	1 cut(s)	180
AsuHPI	GGTGA	2 cut(s)	166, 448
Bbv12I	GWGCWC	2 cut(s)	12, 101
BbvI	GCAGC	2 cut(s)	352, 488
BceAI	ACGGC	1 cut(s)	103
BcgI	CGANNNNNNTGC	4 cut(s)	74, 108, 121, 155
BciT130I	CCWGG	2 cut(s)	103, 194
BclI	TGATCA	1 cut(s)	171
BcnI	CCSGG	1 cut(s)	180
BfaI	CTAG	1 cut(s)	311
BfmI	CTRYAG	1 cut(s)	460
BfuAI	ACCTGC	1 cut(s)	467
BisI	GCNGC	2 cut(s)	366, 502
BlsI	GCNGC	2 cut(s)	367, 503
Bme1390I	CCNGG	3 cut(s)	103, 180, 194
BmgT120I	GGNCC	2 cut(s)	162, 196
BmrFI	CCNGG	3 cut(s)	103, 180, 194
BmsI	GCATC	3 cut(s)	210, 488, 523
BpmI	CTGGAG	1 cut(s)	85
BpuEI	CTTGAG	1 cut(s)	362
BpuMI	CCSGG	1 cut(s)	180
BsaAI	YACGTR	1 cut(s)	483
BsaHI	GRCGYC	3 cut(s)	183, 189, 409
BsaJI	CCNNGG	3 cut(s)	178, 192, 193
BsaWI	WCCGGW	1 cut(s)	433
Bsc4I	CCNNNNNNNGG	3 cut(s)	235, 325, 462
Bse1I	ACTGG	1 cut(s)	394
Bse3DI	GCAATG	1 cut(s)	337
BseBI	CCWGG	2 cut(s)	103, 194
BseDI	CCNNGG	3 cut(s)	178, 192, 193
BseGI	GGATG	1 cut(s)	503
BseLI	CCNNNNNNNGG	3 cut(s)	235, 325, 462
BseMI	GCAATG	1 cut(s)	337
BseMII	CTCAG	1 cut(s)	257
BseNI	ACTGG	1 cut(s)	394
BseXI	GCAGC	2 cut(s)	352, 488
BseYI	CCCAGC	2 cut(s)	119, 404
BsgI	GTGCAG	1 cut(s)	100
Bsh1285I	CGRYCG	1 cut(s)	94
BshFI	GGCC	2 cut(s)	163, 198
BsiEI	CGRYCG	1 cut(s)	94
BsiHKAI	GWGCWC	2 cut(s)	12, 101
BsiSI	CCGG	2 cut(s)	180, 434
BslFI	GGGAC	1 cut(s)	43
BslI	CCNNNNNNNGG	3 cut(s)	235, 325, 462
BsmFI	GGGAC	1 cut(s)	43
BsnI	GGCC	2 cut(s)	163, 198
Bsp1286I	GDGCHC	2 cut(s)	12, 101
Bsp143I	GATC	3 cut(s)	91, 171, 250
BspACI	CCGC	2 cut(s)	5, 214
BspANI	GGCC	2 cut(s)	163, 198
BspCNI	CTCAG	1 cut(s)	258
BspMAI	CTGCAG	1 cut(s)	464
BspMI	ACCTGC	1 cut(s)	467
BspPI	GGATC	1 cut(s)	258
BspQI	GCTCTTC	1 cut(s)	351
BsrDI	GCAATG	1 cut(s)	337
BsrI	ACTGG	1 cut(s)	394
BssECI	CCNNGG	3 cut(s)	178, 192, 193
BssMI	GATC	3 cut(s)	91, 171, 250
BssNI	GRCGYC	3 cut(s)	183, 189, 409
Bst2UI	CCWGG	2 cut(s)	103, 194
Bst6I	CTCTTC	1 cut(s)	351
BstACI	GRCGYC	3 cut(s)	183, 189, 409
BstBAI	YACGTR	1 cut(s)	483
BstC8I	GCNNGC	5 cut(s)	79, 83, 200, 363, 464
BstDEI	CTNAG	1 cut(s)	266
BstF5I	GGATG	1 cut(s)	503
BstKTI	GATC	3 cut(s)	94, 174, 253
BstMBI	GATC	3 cut(s)	91, 171, 250
BstMCI	CGRYCG	1 cut(s)	94
BstMWI	GCNNNNNNNGC	3 cut(s)	87, 96, 371
BstNI	CCWGG	2 cut(s)	103, 194
BstNSI	RCATGY	1 cut(s)	365
BstSCI	CCNGG	3 cut(s)	101, 178, 192
BstSFI	CTRYAG	1 cut(s)	460
BstV1I	GCAGC	2 cut(s)	352, 488
BstX2I	RGATCY	1 cut(s)	250
BstYI	RGATCY	1 cut(s)	250
BsuRI	GGCC	2 cut(s)	163, 198
BtsCI	GGATG	1 cut(s)	503
BveI	ACCTGC	1 cut(s)	467
Cac8I	GCNNGC	5 cut(s)	79, 83, 200, 363, 464
Cfr13I	GGNCC	2 cut(s)	162, 196
CseI	GACGC	4 cut(s)	112, 172, 197, 398
Csp6I	GTAC	1 cut(s)	154
CspCI	CAANNNNNGTGG	2 cut(s)	475, 510
CviAII	CATG	2 cut(s)	322, 362
CviQI	GTAC	1 cut(s)	154
DdeI	CTNAG	1 cut(s)	266
DpnI	GATC	3 cut(s)	93, 173, 252
DpnII	GATC	3 cut(s)	91, 171, 250
DraIII	CACNNNGTG	1 cut(s)	325
Eam1104I	CTCTTC	1 cut(s)	351
EarI	CTCTTC	1 cut(s)	351
EciI	GGCGGA	1 cut(s)	20
EcoRII	CCWGG	2 cut(s)	101, 192
EcoT22I	ATGCAT	1 cut(s)	516
FaeI	CATG	2 cut(s)	325, 365
FaqI	GGGAC	1 cut(s)	43
FatI	CATG	2 cut(s)	321, 361
FauI	CCCGC	1 cut(s)	221
FbaI	TGATCA	1 cut(s)	171
FblI	GTMKAC	1 cut(s)	186
Fnu4HI	GCNGC	2 cut(s)	366, 502
FokI	GGATG	1 cut(s)	510
Fsp4HI	GCNGC	2 cut(s)	366, 502
FspBI	CTAG	1 cut(s)	311
GluI	GCNGC	2 cut(s)	366, 502
GsaI	CCCAGC	2 cut(s)	123, 408
GsuI	CTGGAG	1 cut(s)	85
HaeIII	GGCC	2 cut(s)	163, 198
HapII	CCGG	2 cut(s)	180, 434
HgaI	GACGC	4 cut(s)	112, 172, 197, 398
Hin1I	GRCGYC	3 cut(s)	183, 189, 409
Hin1II	CATG	2 cut(s)	325, 365
HincII	GTYRAC	1 cut(s)	187
HindII	GTYRAC	1 cut(s)	187
HinfI	GANTC	2 cut(s)	133, 382
HpaII	CCGG	2 cut(s)	180, 434
HphI	GGTGA	2 cut(s)	166, 448
Hpy166II	GTNNAC	3 cut(s)	49, 187, 424
Hpy188I	TCNGA	2 cut(s)	387, 519
Hpy188III	TCNNGA	2 cut(s)	260, 379
Hpy8I	GTNNAC	3 cut(s)	49, 187, 424
Hpy99I	CGWCG	2 cut(s)	188, 191
HpyAV	CCTTC	2 cut(s)	31, 67
HpyCH4IV	ACGT	1 cut(s)	482
HpyCH4V	TGCA	8 cut(s)	81, 223, 368, 374, 462, 486, 504, 514
HpyF10VI	GCNNNNNNNGC	3 cut(s)	87, 96, 371
HpyF3I	CTNAG	1 cut(s)	266
HpySE526I	ACGT	1 cut(s)	482
Hsp92I	GRCGYC	3 cut(s)	183, 189, 409
Hsp92II	CATG	2 cut(s)	325, 365
Ksp22I	TGATCA	1 cut(s)	171
Kzo9I	GATC	3 cut(s)	91, 171, 250
LguI	GCTCTTC	1 cut(s)	351
LmnI	GCTCC	2 cut(s)	7, 104
Lsp1109I	GCAGC	2 cut(s)	352, 488
LweI	GCATC	3 cut(s)	210, 488, 523
MaeI	CTAG	1 cut(s)	311
MaeII	ACGT	1 cut(s)	482
MaeIII	GTNAC	1 cut(s)	436
MalI	GATC	3 cut(s)	93, 173, 252
MboI	GATC	3 cut(s)	91, 171, 250
MboII	GAAGA	2 cut(s)	368, 405
MflI	RGATCY	1 cut(s)	250
MhlI	GDGCHC	2 cut(s)	12, 101
MluCI	AATT	3 cut(s)	239, 282, 505
MlyI	GAGTC	1 cut(s)	127
MnlI	CCTC	6 cut(s)	153, 229, 241, 346, 466, 525
Mph1103I	ATGCAT	1 cut(s)	516
MspI	CCGG	2 cut(s)	180, 434
MspR9I	CCNGG	3 cut(s)	103, 180, 194
MvaI	CCWGG	2 cut(s)	103, 194
MwoI	GCNNNNNNNGC	3 cut(s)	87, 96, 371
NciI	CCSGG	1 cut(s)	180
NdeII	GATC	3 cut(s)	91, 171, 250
NlaIII	CATG	2 cut(s)	325, 365
NmuCI	GTSAC	1 cut(s)	436
NsiI	ATGCAT	1 cut(s)	516
NspI	RCATGY	1 cut(s)	365
PaeI	GCATGC	1 cut(s)	365
PaqCI	CACCTGC	1 cut(s)	467
PasI	CCCWGGG	1 cut(s)	193
PciSI	GCTCTTC	1 cut(s)	351
PfeI	GAWTC	1 cut(s)	382
PflMI	CCANNNNNTGG	1 cut(s)	325
PkrI	GCNGC	2 cut(s)	367, 503
Ple19I	CGATCG	1 cut(s)	94
PleI	GAGTC	1 cut(s)	127
PpsI	GAGTC	1 cut(s)	127
Ppu21I	YACGTR	1 cut(s)	483
Psp6I	CCWGG	2 cut(s)	101, 192
PspFI	CCCAGC	2 cut(s)	119, 404
PspGI	CCWGG	2 cut(s)	101, 192
PspPI	GGNCC	2 cut(s)	162, 196
PstI	CTGCAG	1 cut(s)	464
PsuI	RGATCY	1 cut(s)	250
PvuI	CGATCG	1 cut(s)	94
RsaI	GTAC	1 cut(s)	155
RsaNI	GTAC	1 cut(s)	154
SalI	GTCGAC	1 cut(s)	185
SapI	GCTCTTC	1 cut(s)	351
SatI	GCNGC	2 cut(s)	366, 502
Sau3AI	GATC	3 cut(s)	91, 171, 250
Sau96I	GGNCC	2 cut(s)	162, 196
SbfI	CCTGCAGG	1 cut(s)	464
SchI	GAGTC	1 cut(s)	127
ScrFI	CCNGG	3 cut(s)	103, 180, 194
SdaI	CCTGCAGG	1 cut(s)	464
SduI	GDGCHC	2 cut(s)	12, 101
SetI	ASST	6 cut(s)	267, 312, 316, 461, 485, 536
SfaNI	GCATC	3 cut(s)	210, 488, 523
SfcI	CTRYAG	1 cut(s)	460
SgrDI	CGTCGACG	1 cut(s)	185
SmlI	CTYRAG	1 cut(s)	377
SmoI	CTYRAG	1 cut(s)	377
SphI	GCATGC	1 cut(s)	365
Sse8387I	CCTGCAGG	1 cut(s)	464
Sse9I	AATT	3 cut(s)	239, 282, 505
SsiI	CCGC	2 cut(s)	5, 214
SspMI	CTAG	1 cut(s)	311
StyD4I	CCNGG	3 cut(s)	101, 178, 192
TaiI	ACGT	1 cut(s)	485
TaqI	TCGA	3 cut(s)	186, 207, 234
TasI	AATT	3 cut(s)	239, 282, 505
TfiI	GAWTC	1 cut(s)	382
TseFI	GTSAC	1 cut(s)	436
TseI	GCWGC	2 cut(s)	365, 501
Tsp45I	GTSAC	1 cut(s)	436
TspGWI	ACGGA	2 cut(s)	47, 437
Van91I	CCANNNNNTGG	1 cut(s)	325
XapI	RAATTY	1 cut(s)	239
XceI	RCATGY	1 cut(s)	365
XmiI	GTMKAC	1 cut(s)	186
XspI	CTAG	1 cut(s)	311
Zsp2I	ATGCAT	1 cut(s)	516

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