Rh6CG340900

Chloroplast stem-loop binding protein of 41 kDa a

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6C
OG0016578
Physical Location & Seq
Reverse (-)
53217284 .. 53219359
2076 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6CG340900.1

Sequence Viewer

Length: 1209 bp
ATGGCCACTCTTGCTTCATCATCCTCTGTGCTCTTCTCCTCTCCACACTCCAACCTCACTCCACCTTCTCTCTCTCCTTCACGCCTCTCTCTCTCCTCTTCCTCCCACCTCTCCACCACTCTCTCCTCTTCTCTTTCAGTTTCTCATTCTTTTGTCACATACCCTACAACTTCAAGGCGCTTCCGCCCTAGTTCCTTCAGTGTCAAGGCTATTGCTGCAGACAAGAAGAAGGTTCTGATCGTCAACACCAACAGTGGTGGTCATGCAGTCATTGGATTCTACTTTGCAAAAGAGCTTCTGGGCTCTGGCCATGAGGTCACCATTATGACTGTTGGTGAAGAAAGCTCAGACAAGATGAAGAAGACCCCATTCACCAGATTCTCGGAAATTGCAAGTGCTGGAGGGAAGACAGTGTGGGGAGAACCAGCAGAAATAGCCAAGGTTTTGGAGGGATCAGCATTTGATGTTGTGTTGGATAACAACGGCAAGAACTTGGACGCAGTGAAGCCTGTGGCTGATTGGGCAAAGAGTTCTGGTGCAAAGCAATTCCTATTTATCAGCAGTGCTGGGATTTATAAGCCAACCGAGGAGCCTCCTCATGTCGAAGGGGATGTCGTTAAAGCTGATGCTGGTCATGTTGCAGTAGAGAAGTACATTGCAGAAGTGTTTGGTAATTGGGCAAGTTTTCGTCCACAATACATGATAGGATCCGGCAACAACAAAGATTGCGAGGAGTGGTTCTTCGATCGAATTGTGAGGGACAGACCAGTTCCAATCCCTGGCTCTGGAATGCAACTCACAGTCATCTCCCATGTTAGGGACTTGTCGTCTATGCTCACTCTAGCCGTTGAGAAGCCAGATGCTGCATCTGGTAACATTTTCAACTGTGTAAGCGACCGTGCTGTGACTCTCGATGGATTGGCAAAACTCTGTGCTCAAGCCGCAGGACGCCCAGTGAACATAGTGCATTATGATCCAAAAGCTGCTGGGGTTGATGCAAAGAAAACTTTTCCGTTCCGTAACATGCACTTCTATGCAGAACCAAGAGCTGCAAAGGATATCTTGGGATGGAAAAGTACCACAAACCTCACTGAAGACTTGAAAGAGAGATTTGAGGAGTACTTGAAGATTGGGAGAGACAAGAAAGCCATCAAATTTGATTTGGATGATAAGATACTGGAGTCCCTTAAAGTTCCAGTAGCAGTGTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0003674 GO:0003676 GO:0003723 GO:0003727 GO:0005488 GO:0005575 GO:0005576 GO:0005622 GO:0005623 GO:0005737 GO:0005840 GO:0006139 GO:0006355 GO:0006364 GO:0006396 GO:0006412 GO:0006417 GO:0006518 GO:0006725 GO:0006807 GO:0006996 GO:0007623 GO:0008150 GO:0008152 GO:0008187 GO:0008266 GO:0009058 GO:0009059 GO:0009507 GO:0009526 GO:0009532 GO:0009534 GO:0009536 GO:0009570 GO:0009579 GO:0009657 GO:0009658 GO:0009719 GO:0009725 GO:0009735 GO:0009889 GO:0009891 GO:0009893 GO:0009941 GO:0009987 GO:0010033 GO:0010287 GO:0010319 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010608 GO:0010628 GO:0016043 GO:0016070 GO:0016072 GO:0019219 GO:0019222 GO:0019538 GO:0022613 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031967 GO:0031975 GO:0031976 GO:0031984 GO:0032268 GO:0032270 GO:0032544 GO:0032991 GO:0034248 GO:0034250 GO:0034470 GO:0034641 GO:0034645 GO:0034660 GO:0042221 GO:0042254 GO:0043043 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043603 GO:0043604 GO:0044085 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044271 GO:0044422 GO:0044424 GO:0044434 GO:0044435 GO:0044444 GO:0044446 GO:0044464 GO:0045727 GO:0045893 GO:0045935 GO:0046483 GO:0048046 GO:0048511 GO:0048518 GO:0048522 GO:0050789 GO:0050794 GO:0050896 GO:0051171 GO:0051173 GO:0051246 GO:0051247 GO:0051252 GO:0051254 GO:0060255 GO:0065007 GO:0071704 GO:0071840 GO:0080090 GO:0090304 GO:0097159 GO:1901360 GO:1901363 GO:1901564 GO:1901566 GO:1901576 GO:1902680 GO:1903506 GO:1903508 GO:1990904 GO:2000112 GO:2001141
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
Epimerase

Protein Analysis

402

Amino Acids

43.59

Weight (kDa)

8.53

Isoelectric Point (pI)

40.76

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Epimerase PF01370 86 - 296 7.2e-09 NAD dependent epimerase/dehydratase family
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0016578)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G63140
fragaria_vesca FvH4_2g23570
malus_domestica MD11G1285100.v1.1
prunus_persica Prupe.8G241000_v2.0.a1
pyrus_communis pycom11g25270
rosa_chinensis RchiOBHm_Chr6g0291041
rosa_laevigata RLG00000012152
rosa_multiflora Rmu_sc0004642.1_g000002
rosa_roxburghii Rroxscaffold_7G00176430
rosa_rugosa Rorug06G0217200
rosa_samantha Rh6AG327200 Rh6BG334700 Rh6CG340900
rosa_wichuraiana Rw6G028460

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 576
AccB7I CCANNNNNTGG 1 cut(s) 779
AciI CCGC 2 cut(s) 184, 942
AclWI GGATC 4 cut(s) 460, 702, 715, 968
AcoI YGGCCR 2 cut(s) 3, 307
AcsI RAATTY 1 cut(s) 1154
AcuI CTGAAG 2 cut(s) 181, 1113
AcyI GRCGYC 1 cut(s) 949
AfaI GTAC 3 cut(s) 653, 1078, 1121
AfiI CCNNNNNNNGG 4 cut(s) 779, 785, 816, 817
AgsI TTSAA 4 cut(s) 174, 883, 1102, 1126
AhdI GACNNNNNGTC 1 cut(s) 826
AjnI CCWGG 1 cut(s) 778
AluBI AGCT 5 cut(s) 295, 345, 623, 983, 1049
AluI AGCT 5 cut(s) 295, 345, 623, 983, 1049
Alw21I GWGCWC 2 cut(s) 33, 937
Alw26I GTCTC 1 cut(s) 1131
AlwI GGATC 4 cut(s) 460, 702, 715, 968
AlwNI CAGNNNCTG 1 cut(s) 863
AoxI GGCC 2 cut(s) 3, 307
ApeKI GCWGC 4 cut(s) 215, 863, 983, 1049
ApoI RAATTY 1 cut(s) 1154
ArsI GACNNNNNNTTYG 2 cut(s) 597, 629
AspLEI GCGC 1 cut(s) 180
AsuHPI GGTGA 3 cut(s) 310, 347, 364
BaeI ACNNNNGTAYC 2 cut(s) 1166, 1199
BalI TGGCCA 2 cut(s) 5, 309
BamHI GGATCC 1 cut(s) 707
BanII GRGCYC 1 cut(s) 305
BbsI GAAGAC 3 cut(s) 368, 413, 1101
Bbv12I GWGCWC 2 cut(s) 33, 937
BbvI GCAGC 4 cut(s) 202, 850, 970, 1036
BccI CCATC 3 cut(s) 908, 1062, 1157
BceAI ACGGC 2 cut(s) 499, 830
BciT130I CCWGG 1 cut(s) 780
BcoDI GTCTC 1 cut(s) 1131
BfaI CTAG 2 cut(s) 189, 842
BfmI CTRYAG 1 cut(s) 216
BfoI RGCGCY 1 cut(s) 181
BisI GCNGC 5 cut(s) 216, 864, 942, 984, 1050
BlsI GCNGC 5 cut(s) 217, 865, 943, 985, 1051
BmcAI AGTACT 1 cut(s) 1121
Bme1390I CCNGG 1 cut(s) 780
BmeRI GACNNNNNGTC 1 cut(s) 826
BmiI GGNNCC 2 cut(s) 591, 709
BmrFI CCNGG 1 cut(s) 780
BmrI ACTGGG 1 cut(s) 947
BmsI GCATC 4 cut(s) 616, 850, 875, 985
BmuI ACTGGG 1 cut(s) 947
BpiI GAAGAC 3 cut(s) 368, 413, 1101
BpmI CTGGAG 2 cut(s) 420, 1199
BpuEI CTTGAG 1 cut(s) 921
BsaHI GRCGYC 1 cut(s) 949
BsaJI CCNNGG 3 cut(s) 438, 585, 778
Bsc4I CCNNNNNNNGG 4 cut(s) 779, 785, 816, 817
Bse1I ACTGG 4 cut(s) 767, 953, 1182, 1196
Bse3DI GCAATG 1 cut(s) 654
BseBI CCWGG 1 cut(s) 780
BseDI CCNNGG 3 cut(s) 438, 585, 778
BseGI GGATG 4 cut(s) 20, 616, 1073, 1171
BseLI CCNNNNNNNGG 4 cut(s) 779, 785, 816, 817
BseMI GCAATG 1 cut(s) 654
BseMII CTCAG 1 cut(s) 360
BseNI ACTGG 4 cut(s) 767, 953, 1182, 1196
BseRI GAGGAG 7 cut(s) 28, 85, 115, 585, 602, 746, 1130
BseXI GCAGC 4 cut(s) 202, 850, 970, 1036
BseYI CCCAGC 2 cut(s) 566, 986
Bsh1285I CGRYCG 2 cut(s) 748, 898
BshFI GGCC 2 cut(s) 5, 309
BsiEI CGRYCG 2 cut(s) 748, 898
BsiHKAI GWGCWC 2 cut(s) 33, 937
BsiSI CCGG 1 cut(s) 711
BslFI GGGAC 3 cut(s) 773, 833, 1168
BslI CCNNNNNNNGG 4 cut(s) 779, 785, 816, 817
BsmAI GTCTC 1 cut(s) 1131
BsmFI GGGAC 3 cut(s) 773, 833, 1168
BsmI GAATGC 1 cut(s) 795
BsnI GGCC 2 cut(s) 5, 309
Bsp1286I GDGCHC 3 cut(s) 33, 305, 937
Bsp143I GATC 5 cut(s) 237, 452, 707, 745, 973
BspACI CCGC 2 cut(s) 184, 942
BspANI GGCC 2 cut(s) 5, 309
BspCNI CTCAG 1 cut(s) 359
BspLI GGNNCC 2 cut(s) 591, 709
BspMAI CTGCAG 1 cut(s) 220
BspPI GGATC 4 cut(s) 460, 702, 715, 968
BspQI GCTCTTC 1 cut(s) 38
BsrDI GCAATG 1 cut(s) 654
BsrI ACTGG 4 cut(s) 767, 953, 1182, 1196
BssECI CCNNGG 3 cut(s) 438, 585, 778
BssMI GATC 5 cut(s) 237, 452, 707, 745, 973
BssNI GRCGYC 1 cut(s) 949
BssT1I CCWWGG 1 cut(s) 438
Bst2UI CCWGG 1 cut(s) 780
Bst4CI ACNGT 6 cut(s) 254, 331, 412, 802, 887, 899
Bst6I CTCTTC 3 cut(s) 38, 103, 133
BstACI GRCGYC 1 cut(s) 949
BstDEI CTNAG 1 cut(s) 346
BstEII GGTNACC 1 cut(s) 316
BstF5I GGATG 4 cut(s) 20, 616, 1073, 1171
BstH2I RGCGCY 1 cut(s) 181
BstHHI GCGC 1 cut(s) 180
BstKTI GATC 5 cut(s) 240, 455, 710, 748, 976
BstMAI GTCTC 1 cut(s) 1131
BstMBI GATC 5 cut(s) 237, 452, 707, 745, 973
BstMCI CGRYCG 2 cut(s) 748, 898
BstMWI GCNNNNNNNGC 5 cut(s) 11, 215, 434, 521, 941
BstNI CCWGG 1 cut(s) 780
BstNSI RCATGY 1 cut(s) 1027
BstPI GGTNACC 1 cut(s) 316
BstSCI CCNGG 1 cut(s) 778
BstSFI CTRYAG 1 cut(s) 216
BstV1I GCAGC 4 cut(s) 202, 850, 970, 1036
BstV2I GAAGAC 3 cut(s) 368, 413, 1101
BstX2I RGATCY 1 cut(s) 707
BstXI CCANNNNNNTGG 1 cut(s) 445
BstYI RGATCY 1 cut(s) 707
BsuRI GGCC 2 cut(s) 5, 309
BtsCI GGATG 4 cut(s) 20, 616, 1073, 1171
BtsI GCAGTG 3 cut(s) 507, 568, 1209
BtsIMutI CAGTG 8 cut(s) 205, 259, 417, 507, 568, 960, 1089, 1209
CaiI CAGNNNCTG 1 cut(s) 863
CfoI GCGC 1 cut(s) 180
CseI GACGC 2 cut(s) 506, 957
Csp6I GTAC 3 cut(s) 652, 1077, 1120
CspCI CAANNNNNGTGG 2 cut(s) 238, 273
CviAII CATG 7 cut(s) 263, 311, 599, 635, 700, 812, 1024
CviQI GTAC 3 cut(s) 652, 1077, 1120
DdeI CTNAG 1 cut(s) 346
DpnI GATC 5 cut(s) 239, 454, 709, 747, 975
DpnII GATC 5 cut(s) 237, 452, 707, 745, 973
DriI GACNNNNNGTC 1 cut(s) 826
EaeI YGGCCR 2 cut(s) 3, 307
Eam1104I CTCTTC 3 cut(s) 38, 103, 133
Eam1105I GACNNNNNGTC 1 cut(s) 826
EarI CTCTTC 3 cut(s) 38, 103, 133
EciI GGCGGA 1 cut(s) 173
Eco130I CCWWGG 1 cut(s) 438
Eco24I GRGCYC 1 cut(s) 305
Eco32I GATATC 1 cut(s) 1060
Eco57I CTGAAG 2 cut(s) 181, 1113
Eco91I GGTNACC 1 cut(s) 316
EcoO65I GGTNACC 1 cut(s) 316
EcoRII CCWGG 1 cut(s) 778
EcoRV GATATC 1 cut(s) 1060
EcoT14I CCWWGG 1 cut(s) 438
EcoT38I GRGCYC 1 cut(s) 305
ErhI CCWWGG 1 cut(s) 438
FaeI CATG 7 cut(s) 266, 314, 602, 638, 703, 815, 1027
FalI AAGNNNNNCTT 2 cut(s) 1046, 1078
FaqI GGGAC 3 cut(s) 773, 833, 1168
FatI CATG 7 cut(s) 262, 310, 598, 634, 699, 811, 1023
Fnu4HI GCNGC 5 cut(s) 216, 864, 942, 984, 1050
FokI GGATG 4 cut(s) 7, 623, 1080, 1178
FriOI GRGCYC 1 cut(s) 305
Fsp4HI GCNGC 5 cut(s) 216, 864, 942, 984, 1050
FspBI CTAG 2 cut(s) 189, 842
GlaI GCGC 1 cut(s) 179
GluI GCNGC 5 cut(s) 216, 864, 942, 984, 1050
GsaI CCCAGC 2 cut(s) 570, 990
GsuI CTGGAG 2 cut(s) 420, 1199
HaeII RGCGCY 1 cut(s) 181
HaeIII GGCC 2 cut(s) 5, 309
HapII CCGG 1 cut(s) 711
HgaI GACGC 2 cut(s) 506, 957
HhaI GCGC 1 cut(s) 180
Hin1I GRCGYC 1 cut(s) 949
Hin1II CATG 7 cut(s) 266, 314, 602, 638, 703, 815, 1027
Hin6I GCGC 1 cut(s) 178
HinP1I GCGC 1 cut(s) 178
HincII GTYRAC 1 cut(s) 244
HindII GTYRAC 1 cut(s) 244
HinfI GANTC 4 cut(s) 276, 378, 907, 1181
HpaII CCGG 1 cut(s) 711
HphI GGTGA 3 cut(s) 310, 347, 364
Hpy166II GTNNAC 3 cut(s) 244, 692, 958
Hpy188I TCNGA 3 cut(s) 237, 349, 385
Hpy188III TCNNGA 2 cut(s) 786, 911
Hpy8I GTNNAC 3 cut(s) 244, 692, 958
HpyAV CCTTC 5 cut(s) 75, 87, 205, 223, 599
HpyCH4III ACNGT 6 cut(s) 254, 331, 412, 802, 887, 899
HpyF10VI GCNNNNNNNGC 5 cut(s) 11, 215, 434, 521, 941
HpyF3I CTNAG 1 cut(s) 346
Hsp92I GRCGYC 1 cut(s) 949
Hsp92II CATG 7 cut(s) 266, 314, 602, 638, 703, 815, 1027
HspAI GCGC 1 cut(s) 178
Kzo9I GATC 5 cut(s) 237, 452, 707, 745, 973
LguI GCTCTTC 1 cut(s) 38
LmnI GCTCC 1 cut(s) 589
Lsp1109I GCAGC 4 cut(s) 202, 850, 970, 1036
LweI GCATC 4 cut(s) 616, 850, 875, 985
MaeI CTAG 2 cut(s) 189, 842
MaeIII GTNAC 5 cut(s) 154, 316, 872, 904, 1019
MalI GATC 5 cut(s) 239, 454, 709, 747, 975
MboI GATC 5 cut(s) 237, 452, 707, 745, 973
MflI RGATCY 1 cut(s) 707
MhlI GDGCHC 3 cut(s) 33, 305, 937
MlsI TGGCCA 2 cut(s) 5, 309
MluCI AATT 5 cut(s) 387, 545, 673, 750, 1154
MluNI TGGCCA 2 cut(s) 5, 309
MlyI GAGTC 2 cut(s) 901, 1190
MmeI TCCRAC 2 cut(s) 75, 453
Mox20I TGGCCA 2 cut(s) 5, 309
MscI TGGCCA 2 cut(s) 5, 309
MseI TTAA 2 cut(s) 618, 1188
MslI CAYNNNNRTG 2 cut(s) 323, 1032
Msp20I TGGCCA 2 cut(s) 5, 309
MspI CCGG 1 cut(s) 711
MspR9I CCNGG 1 cut(s) 780
Mva1269I GAATGC 1 cut(s) 795
MvaI CCWGG 1 cut(s) 780
MwoI GCNNNNNNNGC 5 cut(s) 11, 215, 434, 521, 941
NdeII GATC 5 cut(s) 237, 452, 707, 745, 973
NlaIII CATG 7 cut(s) 266, 314, 602, 638, 703, 815, 1027
NlaIV GGNNCC 2 cut(s) 591, 709
NmuCI GTSAC 3 cut(s) 154, 316, 904
NspI RCATGY 1 cut(s) 1027
PciSI GCTCTTC 1 cut(s) 38
PctI GAATGC 1 cut(s) 795
PfeI GAWTC 2 cut(s) 276, 378
PflMI CCANNNNNTGG 1 cut(s) 779
PkrI GCNGC 5 cut(s) 217, 865, 943, 985, 1051
Ple19I CGATCG 1 cut(s) 748
PleI GAGTC 2 cut(s) 901, 1189
PpsI GAGTC 2 cut(s) 901, 1189
PsiI TTATAA 1 cut(s) 576
Psp6I CCWGG 1 cut(s) 778
PspEI GGTNACC 1 cut(s) 316
PspFI CCCAGC 2 cut(s) 566, 986
PspGI CCWGG 1 cut(s) 778
PspN4I GGNNCC 2 cut(s) 591, 709
PstI CTGCAG 1 cut(s) 220
PstNI CAGNNNCTG 1 cut(s) 863
PsuI RGATCY 1 cut(s) 707
PvuI CGATCG 1 cut(s) 748
RsaI GTAC 3 cut(s) 653, 1078, 1121
RsaNI GTAC 3 cut(s) 652, 1077, 1120
RseI CAYNNNNRTG 2 cut(s) 323, 1032
SapI GCTCTTC 1 cut(s) 38
SaqAI TTAA 2 cut(s) 618, 1188
SatI GCNGC 5 cut(s) 216, 864, 942, 984, 1050
Sau3AI GATC 5 cut(s) 237, 452, 707, 745, 973
ScaI AGTACT 1 cut(s) 1121
SchI GAGTC 2 cut(s) 901, 1190
ScrFI CCNGG 1 cut(s) 780
SduI GDGCHC 3 cut(s) 33, 305, 937
SfaNI GCATC 4 cut(s) 616, 850, 875, 985
SfcI CTRYAG 1 cut(s) 216
SmiMI CAYNNNNRTG 2 cut(s) 323, 1032
SmlI CTYRAG 1 cut(s) 936
SmoI CTYRAG 1 cut(s) 936
Sse9I AATT 5 cut(s) 387, 545, 673, 750, 1154
SsiI CCGC 2 cut(s) 184, 942
SspMI CTAG 2 cut(s) 189, 842
StyD4I CCNGG 1 cut(s) 778
StyI CCWWGG 1 cut(s) 438
TaaI ACNGT 6 cut(s) 254, 331, 412, 802, 887, 899
TaqI TCGA 4 cut(s) 603, 744, 748, 912
TasI AATT 5 cut(s) 387, 545, 673, 750, 1154
TatI WGTACW 2 cut(s) 651, 1119
TauI GCSGC 1 cut(s) 944
TfiI GAWTC 2 cut(s) 276, 378
Tru1I TTAA 2 cut(s) 618, 1188
Tru9I TTAA 2 cut(s) 618, 1188
TscAI CASTG 8 cut(s) 205, 259, 417, 507, 568, 960, 1096, 1209
TseFI GTSAC 3 cut(s) 154, 316, 904
TseI GCWGC 4 cut(s) 215, 863, 983, 1049
Tsp45I GTSAC 3 cut(s) 154, 316, 904
TspDTI ATGAA 2 cut(s) 6, 371
TspGWI ACGGA 2 cut(s) 1002, 1007
TspRI CASTG 8 cut(s) 205, 259, 417, 507, 568, 960, 1096, 1209
Van91I CCANNNNNTGG 1 cut(s) 779
XapI RAATTY 1 cut(s) 1154
XceI RCATGY 1 cut(s) 1027
XspI CTAG 2 cut(s) 189, 842
ZrmI AGTACT 1 cut(s) 1121
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.