Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0004353

Physical Location & Seq

Genomic Coordinates Reverse (-)

66949001 .. 66954702

Gene Structure 5702 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG420700.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1215 bp

ATGCAGCAGCAGCAACACCAACATCATCTGGGTTTTGAAGAACCACCAAGTAGCAGTAAGGCGAGTCTATTGATTCGTCACCTTCCAGAAGCCATTCCTGAAGAGACCCTGTTCCGCTTACTGTCCCACTATGGCGCTTCTTCTGTCCGCTCTTGCTCTCCTACCGGCAGGTTGAGAAATTGTGCTTTTGTGGATTTCCAAAACGAAGGCTTGGCTTACCAAGCACAGCGTCAGTTGAATGGGCTGAGGTTTCTTGGGAAGGTGTTAAAAGTGGAGAGGGCTACTAGCAATAGTGATAAGCCATTGCAGGATGGCAACAAGGATTCGGTTTCTGTGCCTCCCACTTCCACGTCATCTTCGGGGTACAATCCTACCGTCAAAAGGGAGACTCGGGAAACTGAAGTTTCTTCAAGATCAGAGCCTATTGCCCCGAGGCTTGGTGTAGATTACTGCTTTCCTCCTCACCTTGAGTATGCTTACCCACCACCAGATGGAAATATTCTGACCAACATTGTAAATGCTCTTATTGCTGTTCCTCGCTTTTATACTCAGGTTTTGCACTTGATGAACAAAATGAATATTCCAGCTCCATTTCGCATGGCTCTTCCCTCTCCCCCTCTACCACCTGCAGCTCCCGTGCCATTTCCCCCACCTCCCCCTCCTCTAGATGCAAAGCCTCCCTCAGCAGATATATCAAGTGATGAGTCTGAAATGGAGTCTTCAGATGAGGAGGCCTCTAGAGGAGCTTCAAGAGGAAAGAAGCGTGTCAAACGGGAATCTATTCTTGGTCCTGCAGTTGATAAAGGTGTAGCACATGAAGATGTTGGATTGAAACAAGCTATTCTAGTCCCAAAAGAGATGCCAATGATAAAGAAGAAGAATCCTCTGCTACAGATAACAATTGCCCAGAAAGTTGCTAACAATGAGCACAAAGATGATAGCACTACCAAAGTAGAAGAGCTTCCGGAGACTGAGAGTTCAGTTATTAACCCTTTTGCAACTCCAGAAGAACTAGAAAGAGGAAAGTTGCCTCCAGAAGAAATATTATCGCTTCCAATGTTTAAGAACTATACTGCTGGGACTCCTGCCCCCGTGTTGTATATAAAGAACTTGGCAAAGGACATTGTTGGTGATGACTTCTACTACATATTTGGTGAGCTCACAAACTTGATAAGTTATATATTTTGTACAATTTGGAATAGTAGTCTTCTGTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000375 GO:0000377 GO:0000398 GO:0003006 GO:0003674 GO:0003676 GO:0003723 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005681 GO:0005689 GO:0006139 GO:0006396 GO:0006397 GO:0006725 GO:0006807 GO:0007275 GO:0008150 GO:0008152 GO:0008380 GO:0009791 GO:0009987 GO:0010229 GO:0010467 GO:0016070 GO:0016071 GO:0017069 GO:0022414 GO:0030626 GO:0032501 GO:0032502 GO:0032991 GO:0034641 GO:0036002 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0048367 GO:0048608 GO:0048731 GO:0048856 GO:0061458 GO:0071704 GO:0090304 GO:0090567 GO:0097157 GO:0097159 GO:1901360 GO:1901363 GO:1990904

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

RRM_1

Protein Analysis

404

Amino Acids

44.64

Weight (kDa)

6.04

Isoelectric Point (pI)

64.97

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RRM_1	PF00076	23 - 90	1.6e-10	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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Orthologous Genes (Group: OG0004353)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G09230 AT1G09230 AT1G09230
fragaria_vesca	FvH4_3g32950 FvH4_3g32950 FvH4_3g32950 FvH4_3g32950 FvH4_3g32950 FvH4_3g32950 FvH4_3g32950 FvH4_3g32950 FvH4_3g32950 FvH4_3g32950 FvH4_3g32950
malus_domestica	MD03G1112900.v1.1
prunus_persica	Prupe.6G097200_v2.0.a1 Prupe.6G097200_v2.0.a1 Prupe.6G097200_v2.0.a1 Prupe.6G097200_v2.0.a1 Prupe.6G097200_v2.0.a1 Prupe.6G097200_v2.0.a1 Prupe.6G097200_v2.0.a1 Prupe.6G097200_v2.0.a1
rosa_chinensis	RchiOBHm_Chr5g0060221
rosa_laevigata	RLG00000035347
rosa_roxburghii	Rroxscaffold_1G00020500
rosa_rugosa	Rorug05G0328400
rosa_samantha	Rh5AG392600 Rh5BG405100 Rh5CG429200 Rh5DG420700
rosa_wichuraiana	Rw5G036990

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	634
Acc36I	ACCTGC	2 cut(s)	159, 634
AccB7I	CCANNNNNTGG	1 cut(s)	491
AccBSI	CCGCTC	1 cut(s)	150
AccIII	TCCGGA	1 cut(s)	964
AciI	CCGC	2 cut(s)	115, 148
AcuI	CTGAAG	3 cut(s)	120, 420, 705
AfaI	GTAC	2 cut(s)	365, 1189
AfiI	CCNNNNNNNGG	3 cut(s)	381, 437, 491
AgsI	TTSAA	5 cut(s)	38, 238, 411, 750, 832
AjiI	CACGTC	1 cut(s)	351
AjuI	GAANNNNNNNTTGG	2 cut(s)	768, 800
AluBI	AGCT	6 cut(s)	587, 632, 746, 839, 961, 1159
AluI	AGCT	6 cut(s)	587, 632, 746, 839, 961, 1159
Alw21I	GWGCWC	2 cut(s)	930, 1161
Alw26I	GTCTC	3 cut(s)	98, 380, 962
Ama87I	CYCGRG	2 cut(s)	390, 430
Aor13HI	TCCGGA	1 cut(s)	964
AoxI	GGCC	1 cut(s)	732
ApeKI	GCWGC	4 cut(s)	4, 7, 10, 629
Asp700I	GAANNNNTTC	3 cut(s)	93, 780, 960
AspLEI	GCGC	1 cut(s)	137
AspS9I	GGNCC	1 cut(s)	788
AsuHPI	GGTGA	4 cut(s)	71, 455, 1142, 1166
AvaI	CYCGRG	2 cut(s)	390, 430
AvaII	GGWCC	1 cut(s)	788
BanII	GRGCYC	1 cut(s)	1161
BarI	GAAGNNNNNNTAC	2 cut(s)	945, 977
BbsI	GAAGAC	2 cut(s)	711, 1199
Bbv12I	GWGCWC	2 cut(s)	930, 1161
BbvCI	CCTCAGC	2 cut(s)	245, 682
BbvI	GCAGC	4 cut(s)	16, 19, 22, 641
BccI	CCATC	2 cut(s)	305, 485
BcoDI	GTCTC	3 cut(s)	98, 380, 962
BfaI	CTAG	5 cut(s)	285, 665, 738, 845, 1013
BfmI	CTRYAG	3 cut(s)	627, 792, 890
BfoI	RGCGCY	1 cut(s)	138
BfuAI	ACCTGC	2 cut(s)	159, 634
BisI	GCNGC	4 cut(s)	5, 8, 11, 630
BlsI	GCNGC	4 cut(s)	6, 9, 12, 631
Bme18I	GGWCC	1 cut(s)	788
BmeT110I	CYCGRG	2 cut(s)	390, 430
BmgBI	CACGTC	1 cut(s)	351
BmgT120I	GGNCC	1 cut(s)	788
BmsI	GCATC	2 cut(s)	658, 849
BpiI	GAAGAC	2 cut(s)	711, 1199
BplI	GAGNNNNNCTC	2 cut(s)	719, 751
BpmI	CTGGAG	2 cut(s)	987, 1017
Bpu10I	CCTNAGC	2 cut(s)	245, 682
BpuEI	CTTGAG	1 cut(s)	488
BsaI	GGTCTC	1 cut(s)	98
BsaJI	CCNNGG	1 cut(s)	431
BsaWI	WCCGGW	1 cut(s)	964
Bsc4I	CCNNNNNNNGG	3 cut(s)	381, 437, 491
Bse118I	RCCGGY	1 cut(s)	164
Bse3DI	GCAATG	1 cut(s)	302
BseAI	TCCGGA	1 cut(s)	964
BseDI	CCNNGG	1 cut(s)	431
BseGI	GGATG	1 cut(s)	316
BseLI	CCNNNNNNNGG	3 cut(s)	381, 437, 491
BseMI	GCAATG	1 cut(s)	302
BseMII	CTCAG	4 cut(s)	236, 563, 696, 963
BseRI	GAGGAG	4 cut(s)	450, 651, 743, 756
BseXI	GCAGC	4 cut(s)	16, 19, 22, 641
BseYI	CCCAGC	1 cut(s)	1076
BshFI	GGCC	1 cut(s)	734
BsiHKAI	GWGCWC	2 cut(s)	930, 1161
BsiHKCI	CYCGRG	2 cut(s)	390, 430
BsiSI	CCGG	2 cut(s)	165, 965
BslFI	GGGAC	3 cut(s)	109, 833, 1093
BslI	CCNNNNNNNGG	3 cut(s)	381, 437, 491
BsmAI	GTCTC	3 cut(s)	98, 380, 962
BsmFI	GGGAC	3 cut(s)	109, 833, 1093
BsnI	GGCC	1 cut(s)	734
Bso31I	GGTCTC	1 cut(s)	98
BsoBI	CYCGRG	2 cut(s)	390, 430
Bsp1286I	GDGCHC	2 cut(s)	930, 1161
Bsp13I	TCCGGA	1 cut(s)	964
Bsp1407I	TGTACA	1 cut(s)	1187
Bsp143I	GATC	1 cut(s)	413
BspACI	CCGC	2 cut(s)	115, 148
BspANI	GGCC	1 cut(s)	734
BspCNI	CTCAG	4 cut(s)	237, 562, 695, 964
BspEI	TCCGGA	1 cut(s)	964
BspMAI	CTGCAG	2 cut(s)	631, 796
BspMI	ACCTGC	2 cut(s)	159, 634
BspQI	GCTCTTC	2 cut(s)	609, 951
BspTNI	GGTCTC	1 cut(s)	98
BsrBI	CCGCTC	1 cut(s)	150
BsrDI	GCAATG	1 cut(s)	302
BsrFI	RCCGGY	1 cut(s)	164
BsrGI	TGTACA	1 cut(s)	1187
BssAI	RCCGGY	1 cut(s)	164
BssECI	CCNNGG	1 cut(s)	431
BssMI	GATC	1 cut(s)	413
Bst4CI	ACNGT	2 cut(s)	123, 376
Bst6I	CTCTTC	3 cut(s)	96, 609, 951
BstAUI	TGTACA	1 cut(s)	1187
BstDEI	CTNAG	4 cut(s)	245, 549, 682, 972
BstF5I	GGATG	1 cut(s)	316
BstH2I	RGCGCY	1 cut(s)	138
BstHHI	GCGC	1 cut(s)	137
BstKTI	GATC	1 cut(s)	416
BstMAI	GTCTC	3 cut(s)	98, 380, 962
BstMBI	GATC	1 cut(s)	413
BstMWI	GCNNNNNNNGC	3 cut(s)	10, 221, 527
BstSFI	CTRYAG	3 cut(s)	627, 792, 890
BstV1I	GCAGC	4 cut(s)	16, 19, 22, 641
BstV2I	GAAGAC	2 cut(s)	711, 1199
BsuRI	GGCC	1 cut(s)	734
BtrI	CACGTC	1 cut(s)	351
BtsCI	GGATG	1 cut(s)	316
BveI	ACCTGC	2 cut(s)	159, 634
CfoI	GCGC	1 cut(s)	137
Cfr10I	RCCGGY	1 cut(s)	164
Cfr13I	GGNCC	1 cut(s)	788
CseI	GACGC	1 cut(s)	218
Csp6I	GTAC	2 cut(s)	364, 1188
CviAII	CATG	2 cut(s)	598, 815
CviQI	GTAC	2 cut(s)	364, 1188
DdeI	CTNAG	4 cut(s)	245, 549, 682, 972
DpnI	GATC	1 cut(s)	415
DpnII	GATC	1 cut(s)	413
Eam1104I	CTCTTC	3 cut(s)	96, 609, 951
EarI	CTCTTC	3 cut(s)	96, 609, 951
Ecl136II	GAGCTC	1 cut(s)	1159
Eco147I	AGGCCT	1 cut(s)	734
Eco24I	GRGCYC	1 cut(s)	1161
Eco31I	GGTCTC	1 cut(s)	98
Eco47I	GGWCC	1 cut(s)	788
Eco53kI	GAGCTC	1 cut(s)	1159
Eco57I	CTGAAG	3 cut(s)	120, 420, 705
Eco88I	CYCGRG	2 cut(s)	390, 430
EcoICRI	GAGCTC	1 cut(s)	1159
EcoT38I	GRGCYC	1 cut(s)	1161
FaeI	CATG	2 cut(s)	601, 818
FaqI	GGGAC	3 cut(s)	109, 833, 1093
FatI	CATG	2 cut(s)	597, 814
Fnu4HI	GCNGC	4 cut(s)	5, 8, 11, 630
FokI	GGATG	1 cut(s)	323
FriOI	GRGCYC	1 cut(s)	1161
Fsp4HI	GCNGC	4 cut(s)	5, 8, 11, 630
FspBI	CTAG	5 cut(s)	285, 665, 738, 845, 1013
GlaI	GCGC	1 cut(s)	136
GluI	GCNGC	4 cut(s)	5, 8, 11, 630
GsaI	CCCAGC	1 cut(s)	1080
GsuI	CTGGAG	2 cut(s)	987, 1017
HaeII	RGCGCY	1 cut(s)	138
HaeIII	GGCC	1 cut(s)	734
HapII	CCGG	2 cut(s)	165, 965
HgaI	GACGC	1 cut(s)	218
HhaI	GCGC	1 cut(s)	137
Hin1II	CATG	2 cut(s)	601, 818
Hin6I	GCGC	1 cut(s)	135
HinP1I	GCGC	1 cut(s)	135
HinfI	GANTC	9 cut(s)	64, 73, 323, 388, 704, 716, 776, 880, 1081
HpaII	CCGG	2 cut(s)	165, 965
HphI	GGTGA	4 cut(s)	71, 455, 1142, 1166
Hpy188I	TCNGA	4 cut(s)	418, 504, 709, 724
HpyAV	CCTTC	3 cut(s)	92, 200, 253
HpyCH4III	ACNGT	2 cut(s)	123, 376
HpyCH4IV	ACGT	1 cut(s)	350
HpyCH4V	TGCA	7 cut(s)	4, 307, 559, 629, 671, 794, 998
HpyF10VI	GCNNNNNNNGC	3 cut(s)	10, 221, 527
HpyF3I	CTNAG	4 cut(s)	245, 549, 682, 972
HpySE526I	ACGT	1 cut(s)	350
Hsp92II	CATG	2 cut(s)	601, 818
HspAI	GCGC	1 cut(s)	135
Kpn2I	TCCGGA	1 cut(s)	964
Kzo9I	GATC	1 cut(s)	413
LguI	GCTCTTC	2 cut(s)	609, 951
LmnI	GCTCC	3 cut(s)	592, 637, 743
Lsp1109I	GCAGC	4 cut(s)	16, 19, 22, 641
LweI	GCATC	2 cut(s)	658, 849
MaeI	CTAG	5 cut(s)	285, 665, 738, 845, 1013
MaeII	ACGT	1 cut(s)	350
MaeIII	GTNAC	1 cut(s)	77
MalI	GATC	1 cut(s)	415
MbiI	CCGCTC	1 cut(s)	150
MboI	GATC	1 cut(s)	413
MfeI	CAATTG	1 cut(s)	900
MhlI	GDGCHC	2 cut(s)	930, 1161
MluCI	AATT	3 cut(s)	178, 900, 1191
MlyI	GAGTC	5 cut(s)	73, 382, 713, 725, 1075
MmeI	TCCRAC	1 cut(s)	805
MroI	TCCGGA	1 cut(s)	964
MroXI	GAANNNNTTC	3 cut(s)	93, 780, 960
MseI	TTAA	3 cut(s)	266, 987, 1062
MslI	CAYNNNNRTG	2 cut(s)	819, 933
MspI	CCGG	2 cut(s)	165, 965
MunI	CAATTG	1 cut(s)	900
MwoI	GCNNNNNNNGC	3 cut(s)	10, 221, 527
NdeII	GATC	1 cut(s)	413
NlaIII	CATG	2 cut(s)	601, 818
NmuCI	GTSAC	1 cut(s)	77
PaqCI	CACCTGC	1 cut(s)	634
PceI	AGGCCT	1 cut(s)	734
PciSI	GCTCTTC	2 cut(s)	609, 951
PdmI	GAANNNNTTC	3 cut(s)	93, 780, 960
PfeI	GAWTC	4 cut(s)	73, 323, 776, 880
PflMI	CCANNNNNTGG	1 cut(s)	491
PkrI	GCNGC	4 cut(s)	6, 9, 12, 631
PleI	GAGTC	5 cut(s)	72, 382, 712, 724, 1075
PpsI	GAGTC	5 cut(s)	72, 382, 712, 724, 1075
Psp124BI	GAGCTC	1 cut(s)	1161
PspFI	CCCAGC	1 cut(s)	1076
PspPI	GGNCC	1 cut(s)	788
PstI	CTGCAG	2 cut(s)	631, 796
RsaI	GTAC	2 cut(s)	365, 1189
RsaNI	GTAC	2 cut(s)	364, 1188
RseI	CAYNNNNRTG	2 cut(s)	819, 933
SacI	GAGCTC	1 cut(s)	1161
SapI	GCTCTTC	2 cut(s)	609, 951
SaqAI	TTAA	3 cut(s)	266, 987, 1062
SatI	GCNGC	4 cut(s)	5, 8, 11, 630
Sau3AI	GATC	1 cut(s)	413
Sau96I	GGNCC	1 cut(s)	788
SchI	GAGTC	5 cut(s)	73, 382, 713, 725, 1075
SduI	GDGCHC	2 cut(s)	930, 1161
SfaNI	GCATC	2 cut(s)	658, 849
SfcI	CTRYAG	3 cut(s)	627, 792, 890
SinI	GGWCC	1 cut(s)	788
SmiMI	CAYNNNNRTG	2 cut(s)	819, 933
SmlI	CTYRAG	1 cut(s)	467
SmoI	CTYRAG	1 cut(s)	467
Sse9I	AATT	3 cut(s)	178, 900, 1191
SseBI	AGGCCT	1 cut(s)	734
SsiI	CCGC	2 cut(s)	115, 148
SspI	AATATT	3 cut(s)	499, 580, 1044
SspMI	CTAG	5 cut(s)	285, 665, 738, 845, 1013
SstI	GAGCTC	1 cut(s)	1161
StuI	AGGCCT	1 cut(s)	734
TaaI	ACNGT	2 cut(s)	123, 376
TaiI	ACGT	1 cut(s)	353
TasI	AATT	3 cut(s)	178, 900, 1191
TatI	WGTACW	1 cut(s)	1187
TfiI	GAWTC	4 cut(s)	73, 323, 776, 880
Tru1I	TTAA	3 cut(s)	266, 987, 1062
Tru9I	TTAA	3 cut(s)	266, 987, 1062
TseFI	GTSAC	1 cut(s)	77
TseI	GCWGC	4 cut(s)	4, 7, 10, 629
Tsp45I	GTSAC	1 cut(s)	77
TspDTI	ATGAA	3 cut(s)	581, 590, 831
Van91I	CCANNNNNTGG	1 cut(s)	491
VpaK11BI	GGWCC	1 cut(s)	788
XbaI	TCTAGA	2 cut(s)	664, 737
XmnI	GAANNNNTTC	3 cut(s)	93, 780, 960
XspI	CTAG	5 cut(s)	285, 665, 738, 845, 1013

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