Rroxscaffold_6G00427820

Rubisco accumulation factor

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000006
OG0014193
Physical Location & Seq
Forward (+)
48387216 .. 48388564
1349 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_6G00427820.1

Sequence Viewer

Length: 1248 bp
ATGCTTTCCTTAACATCAAACACCCTCAAACCCTTCTTCTCTCCCTTCACCTCCACCTCCACCACCACCCTAAACCCTCACCCACCTCATCTCCTCTACCCAAAACCTTGCCTTAAACCCATCTCAGCCTCCATCCAACACCTCCCCTCTTCCACCCCAAAACCAAAACCACCCCATCCAAACCAACAAGTCTACCAACCTTTCCGGCCACCCCCTTCTCCTATCCCCGAGCAATACAGCTCCTTGGACGCCAATGGCCGTCTCGAAATCCTCGCCAACCGTCTCGGCTTATGGTACGAGCTCGCCCTGTTGATCCCTTCTCTACTTCAACAGGGCTTCACCCCTCCCACCATTGAAGAAATCACAGGGATGTCCTCGGTTGAGCAGAACCGACTAGTCGTGGCAGCTAAAGTGAGGGACTCTCTGATCCATTCCAAGACGGACCCAGAAATCTTGGCGGAGTTTGACACCGGAGGGTCGGAGTTGTTGTACGAAATAAGGCTGCTCAGTGTTCAGCAGCGGGCGGCGGCGGCGAGGTTCATTGTGGAGAAGAAGCTTGATGCAAAAGGAGCTGAGGACCTCGCACGTGCCACTAAGGACTTCGCAAGGAGGCGCGGGGATAAGGGTTGGGAGAGCTTTGATTATACACACCCTGGAGATTGTTTGGCGTTTATGTACTATAGGCAAGCTAGGGAGCATAAGAATCCTTCTGAGCCTAGGACTTCGGCTTTGGAGGAGGCATTGAAGGTTGTGGAGAGTGAGACGGCGAGGAATGTGATTCTTAAGGAGTTGGGAGGGGAGAGTGGGGAGAGTGAGGAGGAAGGGGATGTTGTGGCGGGGGTGAAGGTTCCGGTGGTGAGGTTAAAGTTTGGGGAGGTGGCAGAGTCGAGTAGGGTGGTGATATTGCCGGTTTGTAAGGCGCAGGAGAAGGATAAGGAGGTAATGGAGGCGCCGTGGGAGTGTGAGAGTGAGGGGGAGTTTGGTGTTGTGGTGGCGGAGAAGGGGTGGAAGAGGTGGTATAAGGAGGAGCCTATATTGGTGGTGGCTGATAGGAGTAAGAAGGAGGTGGCAGCTGATGATGGGTTTTATTTGGCAGCAATGGATGGGGGTGATTTGGGGTTTAAGGTTGAGAGGGGATCGGCATTGAAGGAAGCTGGTGTGACGGAGAGTTTGGGGACTGTGGTGTTGATAGTGAGGCCACCAAAGGATGAGACAGAAAATGAATTGGCTGAGGAAGATTGGGAGTGA

Protein Analysis

415

Amino Acids

46.04

Weight (kDa)

5.13

Isoelectric Point (pI)

51.38

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Raf1_HTH PF18579 83 - 142 9.2e-22 Rubisco accumulation factor 1 helix turn helix domain
Raf1_N PF18578 155 - 264 7e-38 Rubisco accumulation factor 1 alpha helical domain
RuBisCo_chap_C PF18087 283 - 339 8.2e-08 Rubisco Assembly chaperone C-terminal domain
RuBisCo_chap_C PF18087 342 - 402 3.5e-09 Rubisco Assembly chaperone C-terminal domain
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: OG0014193)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G04550 AT5G28500 AT5G28500
fragaria_vesca FvH4_6g02280
malus_domestica MD04G1228600.v1.1 MD12G1245900.v1.1
prunus_persica Prupe.6G348600_v2.0.a1
pyrus_communis pycom12g22550
rosa_chinensis RchiOBHm_Chr3g0450031
rosa_laevigata RLG00000025764
rosa_multiflora Rmu_sc0002646.1_g000021
rosa_roxburghii Rroxscaffold_6G00427820
rosa_samantha Rh3AG024000 Rh3BG024600 Rh3CG023600 Rh3DG024600
rosa_wichuraiana Rw3G001910

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 949
AccI GTMKAC 1 cut(s) 192
AccII CGCG 1 cut(s) 615
AciI CCGC 8 cut(s) 458, 520, 524, 527, 530, 615, 836, 995
AclWI GGATC 3 cut(s) 307, 421, 1144
AcoI YGGCCR 2 cut(s) 206, 256
AcvI CACGTG 1 cut(s) 587
AcyI GRCGYC 2 cut(s) 249, 950
AfaI GTAC 3 cut(s) 296, 491, 677
AflII CTTAAG 1 cut(s) 782
AgsI TTSAA 4 cut(s) 329, 356, 745, 1147
AhlI ACTAGT 1 cut(s) 394
AjnI CCWGG 1 cut(s) 652
AluBI AGCT 9 cut(s) 240, 301, 407, 556, 572, 636, 689, 1073, 1154
AluI AGCT 9 cut(s) 240, 301, 407, 556, 572, 636, 689, 1073, 1154
Alw21I GWGCWC 1 cut(s) 303
Alw26I GTCTC 4 cut(s) 266, 287, 755, 1205
AlwI GGATC 3 cut(s) 307, 421, 1144
Ama87I CYCGRG 1 cut(s) 227
AoxI GGCC 3 cut(s) 206, 256, 1196
ApeKI GCWGC 5 cut(s) 404, 502, 517, 1070, 1094
ArsI GACNNNNNNTTYG 4 cut(s) 712, 744, 1153, 1185
AspA2I CCTAGG 1 cut(s) 716
AspLEI GCGC 3 cut(s) 615, 922, 952
AspS9I GGNCC 2 cut(s) 442, 577
AsuHPI GGTGA 7 cut(s) 40, 71, 331, 853, 868, 910, 1121
AvaI CYCGRG 1 cut(s) 227
AvaII GGWCC 2 cut(s) 442, 577
AvrII CCTAGG 1 cut(s) 716
BanI GGYRCC 1 cut(s) 949
BanII GRGCYC 1 cut(s) 303
BbrPI CACGTG 1 cut(s) 587
Bbv12I GWGCWC 1 cut(s) 303
BbvCI CCTCAGC 2 cut(s) 573, 1230
BbvI GCAGC 5 cut(s) 416, 489, 529, 1082, 1106
BccI CCATC 5 cut(s) 128, 140, 183, 1073, 1097
BceAI ACGGC 3 cut(s) 243, 780, 937
BciT130I CCWGG 1 cut(s) 654
BcoDI GTCTC 4 cut(s) 266, 287, 755, 1205
BcuI ACTAGT 1 cut(s) 394
BfaI CTAG 3 cut(s) 395, 690, 717
BfmI CTRYAG 1 cut(s) 679
BfoI RGCGCY 1 cut(s) 953
BfrI CTTAAG 1 cut(s) 782
BisI GCNGC 8 cut(s) 405, 503, 518, 525, 528, 531, 1071, 1095
BlnI CCTAGG 1 cut(s) 716
BlsI GCNGC 8 cut(s) 406, 504, 519, 526, 529, 532, 1072, 1096
Bme1390I CCNGG 1 cut(s) 654
Bme18I GGWCC 2 cut(s) 442, 577
BmeT110I CYCGRG 1 cut(s) 227
BmgT120I GGNCC 2 cut(s) 442, 577
BmiI GGNNCC 4 cut(s) 444, 849, 951, 1029
BmrFI CCNGG 1 cut(s) 654
BmsI GCATC 1 cut(s) 550
BplI GAGNNNNNCTC 2 cut(s) 406, 438
BpmI CTGGAG 1 cut(s) 675
Bpu10I CCTNAGC 2 cut(s) 573, 1230
BsaAI YACGTR 1 cut(s) 587
BsaHI GRCGYC 2 cut(s) 249, 950
BsaJI CCNNGG 5 cut(s) 243, 375, 652, 716, 953
BsaWI WCCGGW 2 cut(s) 470, 850
BsaXI ACNNNNNCTCC 8 cut(s) 75, 105, 473, 503, 938, 968, 989, 1019
Bse118I RCCGGY 1 cut(s) 907
Bse3DI GCAATG 1 cut(s) 1104
BseBI CCWGG 1 cut(s) 654
BseDI CCNNGG 5 cut(s) 243, 375, 652, 716, 953
BseGI GGATG 6 cut(s) 132, 175, 375, 832, 1108, 1213
BseMI GCAATG 1 cut(s) 1104
BseMII CTCAG 5 cut(s) 138, 520, 564, 702, 1221
BseRI GAGGAG 4 cut(s) 83, 749, 830, 1040
BseXI GCAGC 5 cut(s) 416, 489, 529, 1082, 1106
Bsh1236I CGCG 1 cut(s) 615
BshFI GGCC 3 cut(s) 208, 258, 1198
BshNI GGYRCC 1 cut(s) 949
BsiHKAI GWGCWC 1 cut(s) 303
BsiHKCI CYCGRG 1 cut(s) 227
BsiSI CCGG 4 cut(s) 205, 471, 851, 908
BslFI GGGAC 2 cut(s) 431, 1189
BsmAI GTCTC 4 cut(s) 266, 287, 755, 1205
BsmBI CGTCTC 3 cut(s) 266, 287, 755
BsmFI GGGAC 2 cut(s) 431, 1189
BsnI GGCC 3 cut(s) 208, 258, 1198
BsoBI CYCGRG 1 cut(s) 227
Bsp1286I GDGCHC 1 cut(s) 303
Bsp143I GATC 3 cut(s) 312, 426, 1136
BspACI CCGC 8 cut(s) 458, 520, 524, 527, 530, 615, 836, 995
BspANI GGCC 3 cut(s) 208, 258, 1198
BspCNI CTCAG 5 cut(s) 137, 519, 565, 703, 1222
BspFNI CGCG 1 cut(s) 615
BspLI GGNNCC 4 cut(s) 444, 849, 951, 1029
BspPI GGATC 3 cut(s) 307, 421, 1144
BspT107I GGYRCC 1 cut(s) 949
BspTI CTTAAG 1 cut(s) 782
BsrDI GCAATG 1 cut(s) 1104
BsrFI RCCGGY 1 cut(s) 907
BssAI RCCGGY 1 cut(s) 907
BssECI CCNNGG 5 cut(s) 243, 375, 652, 716, 953
BssMI GATC 3 cut(s) 312, 426, 1136
BssNI GRCGYC 2 cut(s) 249, 950
BssT1I CCWWGG 2 cut(s) 243, 716
Bst2UI CCWGG 1 cut(s) 654
Bst4CI ACNGT 2 cut(s) 281, 1180
Bst6I CTCTTC 2 cut(s) 154, 1004
BstACI GRCGYC 2 cut(s) 249, 950
BstAFI CTTAAG 1 cut(s) 782
BstBAI YACGTR 1 cut(s) 587
BstC8I GCNNGC 3 cut(s) 303, 522, 687
BstDEI CTNAG 6 cut(s) 124, 506, 573, 594, 711, 1230
BstDSI CCRYGG 1 cut(s) 953
BstF5I GGATG 6 cut(s) 132, 175, 375, 832, 1108, 1213
BstFNI CGCG 1 cut(s) 615
BstH2I RGCGCY 1 cut(s) 953
BstHHI GCGC 3 cut(s) 615, 922, 952
BstKTI GATC 3 cut(s) 315, 429, 1139
BstMAI GTCTC 4 cut(s) 266, 287, 755, 1205
BstMBI GATC 3 cut(s) 312, 426, 1136
BstMWI GCNNNNNNNGC 2 cut(s) 530, 569
BstNI CCWGG 1 cut(s) 654
BstSCI CCNGG 1 cut(s) 652
BstSFI CTRYAG 1 cut(s) 679
BstUI CGCG 1 cut(s) 615
BstV1I GCAGC 5 cut(s) 416, 489, 529, 1082, 1106
BsuRI GGCC 3 cut(s) 208, 258, 1198
BtgI CCRYGG 1 cut(s) 953
BtsCI GGATG 6 cut(s) 132, 175, 375, 832, 1108, 1213
BtsIMutI CAGTG 1 cut(s) 514
Cac8I GCNNGC 3 cut(s) 303, 522, 687
CfoI GCGC 3 cut(s) 615, 922, 952
Cfr10I RCCGGY 1 cut(s) 907
Cfr13I GGNCC 2 cut(s) 442, 577
CseI GACGC 1 cut(s) 257
Csp6I GTAC 3 cut(s) 295, 490, 676
CviQI GTAC 3 cut(s) 295, 490, 676
DdeI CTNAG 6 cut(s) 124, 506, 573, 594, 711, 1230
DinI GGCGCC 1 cut(s) 951
DpnI GATC 3 cut(s) 314, 428, 1138
DpnII GATC 3 cut(s) 312, 426, 1136
EaeI YGGCCR 2 cut(s) 206, 256
Eam1104I CTCTTC 2 cut(s) 154, 1004
EarI CTCTTC 2 cut(s) 154, 1004
EciI GGCGGA 2 cut(s) 473, 1010
Ecl136II GAGCTC 1 cut(s) 301
Eco130I CCWWGG 2 cut(s) 243, 716
Eco24I GRGCYC 1 cut(s) 303
Eco47I GGWCC 2 cut(s) 442, 577
Eco53kI GAGCTC 1 cut(s) 301
Eco72I CACGTG 1 cut(s) 587
Eco88I CYCGRG 1 cut(s) 227
EcoICRI GAGCTC 1 cut(s) 301
EcoO109I RGGNCCY 1 cut(s) 577
EcoRII CCWGG 1 cut(s) 652
EcoT14I CCWWGG 2 cut(s) 243, 716
EcoT38I GRGCYC 1 cut(s) 303
EgeI GGCGCC 1 cut(s) 951
EheI GGCGCC 1 cut(s) 951
ErhI CCWWGG 2 cut(s) 243, 716
Esp3I CGTCTC 3 cut(s) 266, 287, 755
FaiI YATR 7 cut(s) 292, 645, 674, 681, 699, 1020, 1034
FaqI GGGAC 2 cut(s) 431, 1189
FauI CCCGC 3 cut(s) 513, 608, 829
FblI GTMKAC 1 cut(s) 192
Fnu4HI GCNGC 8 cut(s) 405, 503, 518, 525, 528, 531, 1071, 1095
FokI GGATG 6 cut(s) 119, 162, 382, 839, 1115, 1220
FriOI GRGCYC 1 cut(s) 303
Fsp4HI GCNGC 8 cut(s) 405, 503, 518, 525, 528, 531, 1071, 1095
FspBI CTAG 3 cut(s) 395, 690, 717
GlaI GCGC 3 cut(s) 614, 921, 951
GluI GCNGC 8 cut(s) 405, 503, 518, 525, 528, 531, 1071, 1095
GsuI CTGGAG 1 cut(s) 675
HaeII RGCGCY 1 cut(s) 953
HaeIII GGCC 3 cut(s) 208, 258, 1198
HapII CCGG 4 cut(s) 205, 471, 851, 908
HgaI GACGC 1 cut(s) 257
HhaI GCGC 3 cut(s) 615, 922, 952
Hin1I GRCGYC 2 cut(s) 249, 950
Hin6I GCGC 3 cut(s) 613, 920, 950
HinP1I GCGC 3 cut(s) 613, 920, 950
HindIII AAGCTT 1 cut(s) 554
HinfI GANTC 4 cut(s) 419, 703, 778, 884
HpaII CCGG 4 cut(s) 205, 471, 851, 908
HphI GGTGA 7 cut(s) 40, 71, 331, 853, 868, 910, 1121
Hpy166II GTNNAC 1 cut(s) 193
Hpy188I TCNGA 3 cut(s) 426, 481, 712
Hpy188III TCNNGA 1 cut(s) 263
Hpy8I GTNNAC 1 cut(s) 193
HpyCH4III ACNGT 2 cut(s) 281, 1180
HpyCH4IV ACGT 1 cut(s) 586
HpyCH4V TGCA 1 cut(s) 563
HpyF10VI GCNNNNNNNGC 2 cut(s) 530, 569
HpyF3I CTNAG 6 cut(s) 124, 506, 573, 594, 711, 1230
HpySE526I ACGT 1 cut(s) 586
Hsp92I GRCGYC 2 cut(s) 249, 950
HspAI GCGC 3 cut(s) 613, 920, 950
KasI GGCGCC 1 cut(s) 949
Kzo9I GATC 3 cut(s) 312, 426, 1136
LmnI GCTCC 4 cut(s) 245, 569, 694, 1027
Lsp1109I GCAGC 5 cut(s) 416, 489, 529, 1082, 1106
LweI GCATC 1 cut(s) 550
MaeI CTAG 3 cut(s) 395, 690, 717
MaeII ACGT 1 cut(s) 586
MaeIII GTNAC 1 cut(s) 1159
MalI GATC 3 cut(s) 314, 428, 1138
MboI GATC 3 cut(s) 312, 426, 1136
MboII GAAGA 6 cut(s) 28, 141, 368, 562, 1021, 1247
MhlI GDGCHC 1 cut(s) 303
MluCI AATT 1 cut(s) 1223
Mly113I GGCGCC 1 cut(s) 950
MlyI GAGTC 2 cut(s) 413, 893
MmeI TCCRAC 2 cut(s) 160, 459
MseI TTAA 5 cut(s) 11, 114, 783, 863, 1122
MslI CAYNNNNRTG 1 cut(s) 368
MspA1I CMGCKG 2 cut(s) 520, 1073
MspCI CTTAAG 1 cut(s) 782
MspI CCGG 4 cut(s) 205, 471, 851, 908
MspR9I CCNGG 1 cut(s) 654
MvaI CCWGG 1 cut(s) 654
MvnI CGCG 1 cut(s) 615
MwoI GCNNNNNNNGC 2 cut(s) 530, 569
NarI GGCGCC 1 cut(s) 950
NdeII GATC 3 cut(s) 312, 426, 1136
NlaIV GGNNCC 4 cut(s) 444, 849, 951, 1029
NmeAIII GCCGAG 1 cut(s) 264
NmuCI GTSAC 1 cut(s) 1159
PfeI GAWTC 2 cut(s) 703, 778
PkrI GCNGC 8 cut(s) 406, 504, 519, 526, 529, 532, 1072, 1096
PleI GAGTC 2 cut(s) 413, 892
PluTI GGCGCC 1 cut(s) 953
PmaCI CACGTG 1 cut(s) 587
PmlI CACGTG 1 cut(s) 587
PpsI GAGTC 2 cut(s) 413, 892
Ppu21I YACGTR 1 cut(s) 587
PpuMI RGGWCCY 1 cut(s) 577
Psp124BI GAGCTC 1 cut(s) 303
Psp5II RGGWCCY 1 cut(s) 577
Psp6I CCWGG 1 cut(s) 652
PspCI CACGTG 1 cut(s) 587
PspGI CCWGG 1 cut(s) 652
PspN4I GGNNCC 4 cut(s) 444, 849, 951, 1029
PspPI GGNCC 2 cut(s) 442, 577
PspPPI RGGWCCY 1 cut(s) 577
PvuII CAGCTG 1 cut(s) 1073
RsaI GTAC 3 cut(s) 296, 491, 677
RsaNI GTAC 3 cut(s) 295, 490, 676
RseI CAYNNNNRTG 1 cut(s) 368
SacI GAGCTC 1 cut(s) 303
SaqAI TTAA 5 cut(s) 11, 114, 783, 863, 1122
SatI GCNGC 8 cut(s) 405, 503, 518, 525, 528, 531, 1071, 1095
Sau3AI GATC 3 cut(s) 312, 426, 1136
Sau96I GGNCC 2 cut(s) 442, 577
SchI GAGTC 2 cut(s) 413, 893
ScrFI CCNGG 1 cut(s) 654
SduI GDGCHC 1 cut(s) 303
SfaNI GCATC 1 cut(s) 550
SfcI CTRYAG 1 cut(s) 679
SfoI GGCGCC 1 cut(s) 951
SinI GGWCC 2 cut(s) 442, 577
SmiMI CAYNNNNRTG 1 cut(s) 368
SmlI CTYRAG 1 cut(s) 782
SmoI CTYRAG 1 cut(s) 782
SpeI ACTAGT 1 cut(s) 394
Sse9I AATT 1 cut(s) 1223
SsiI CCGC 8 cut(s) 458, 520, 524, 527, 530, 615, 836, 995
SspDI GGCGCC 1 cut(s) 949
SspMI CTAG 3 cut(s) 395, 690, 717
SstI GAGCTC 1 cut(s) 303
StyD4I CCNGG 1 cut(s) 652
StyI CCWWGG 2 cut(s) 243, 716
TaaI ACNGT 2 cut(s) 281, 1180
TaiI ACGT 1 cut(s) 589
TaqI TCGA 2 cut(s) 264, 887
TasI AATT 1 cut(s) 1223
TatI WGTACW 1 cut(s) 675
TauI GCSGC 3 cut(s) 527, 530, 533
TfiI GAWTC 2 cut(s) 703, 778
Tru1I TTAA 5 cut(s) 11, 114, 783, 863, 1122
Tru9I TTAA 5 cut(s) 11, 114, 783, 863, 1122
TscAI CASTG 1 cut(s) 514
TseFI GTSAC 1 cut(s) 1159
TseI GCWGC 5 cut(s) 404, 502, 517, 1070, 1094
Tsp45I GTSAC 1 cut(s) 1159
TspDTI ATGAA 2 cut(s) 529, 1236
TspGWI ACGGA 2 cut(s) 455, 1178
TspRI CASTG 1 cut(s) 514
Vha464I CTTAAG 1 cut(s) 782
VpaK11BI GGWCC 2 cut(s) 442, 577
XmaJI CCTAGG 1 cut(s) 716
XmiI GTMKAC 1 cut(s) 192
XspI CTAG 3 cut(s) 395, 690, 717
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.