Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2C

Orthogroup ID

OG0003670

Physical Location & Seq

Genomic Coordinates Reverse (-)

58003847 .. 58007449

Gene Structure 3603 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2CG426600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1293 bp

ATGGATTCAGACACAGAAGAAACCAAGTCCAAAGCAGAGCCATCAAAGCCATCGCGCAAGCACAAGAAGAGGAAGAAACTCGCAGCAGAAGCCAACCCAGAGAAGCCCAAATCAGTGCAAGCCACCATCAAGGTCATCCCGGGAAACCCAGAGAGAATCCCACCTCTGGTGGGCTATTTCCCATCTGGGTTCGACCCTACCCAGAACCCAGACCAGGATTCGACCAAAGTTGGGGTCTTTAGGCACAAGGAGAGAGGTGGGACTAGGCTTCAGGTTGTGGTGACCCCAAATAAGGAGGCTAAGGTTGATTTTGTTGGGACTAGCTATGCTGGTGAGGCTCAGGCTGGGGAGCTCTGCTCTTATGGACTTGGGATTCTTGATAAGGACACCCAGACTTTGAAGATTGTGCCTATTGCTAGCAACAAGATATTTAGATTGGAGCCAAAAATTCAAGGCCTTCACTTCTCTGGTAAGGAGCCTGCAAGTTCAGCGATGGGAGAACTTTCTGCACATGAGAAGGCAGAAAAACGTATAGACCTTCATAATCGTTATGGAACAAAGAAGTCAATACGGCAGAATAGAAAAATGCAGACCTTGAAGCAAGAAGATGATCCTGATTCTCAAAATGATATGGATGCAATCAAACAAGGTATGACAAACAGGGAGGATACTGAAGCTTCTGAAGGCCATACAGACCGTAATACCCCACCATTTAATGCTTCTGCCACCACTCCCCAGGAGGCTTATCCACTGGATAAAATCATCACCACAGGGGAGTGGAAATTCCTCCAAGATATTAATAAGCTTTTGGAAGGTGGAGCAGAAATCTCACAGAATTCTTTTCCAACATTTGTTTGCAACCGGATCCATAAACTGCAGCTGATTGAGGATGAAGACAAGAAATATAAGCTATCTTGTATTTTCTCATATATTACGCATCTTATAAAGTTCAAAGATCTCCACTCCATGGATGGGTTTTCCTCGGCAAAGGCCCACAGATTCCCAGGCATTATAAGGGATAAATTTTCAAGCATGTTTGATGCAGTGTCGAAGAGGTTATCAACTGAGAAAAGTAATCTTCTCATTAGTTATGTCTTGGTGCTCACTCTTTTTGCGGATGAATTCCAAACAAGTATGACAGACATAGCGAAGGATCTGAGAATGGGGACTGCAACTTTGAGGACGCATTATGAGAAGTTGGGTTGCAAGGTGTCTAAGAAGAATGTCGTATCAACGGTTACCCTTCCTGTCCCCCTCCAATTTCCAACAGTGAGGCGCAAGCGACGCAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005730 GO:0005736 GO:0006139 GO:0006351 GO:0006360 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044452 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:0097747 GO:0140098 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 map00230 map00240 map01100 map03020

Pfam Domains

Protein Families

RNA_pol_I_A49

Protein Analysis

430

Amino Acids

48.29

Weight (kDa)

9.36

Isoelectric Point (pI)

37.13

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_I_A49	PF06870	74 - 422	2.9e-52	A49-like RNA polymerase I associated factor

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

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Orthologous Genes (Group: OG0003670)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G13940
fragaria_vesca	FvH4_2g14600 FvH4_2g14600 FvH4_2g14600 FvH4_6g34180 FvH4_6g47280
malus_domestica	MD09G1187900.v1.1 MD17G1172300.v1.1
prunus_persica	Prupe.3G044800_v2.0.a1
pyrus_communis	pycom09g10420 pycom09g10430 pycom17g16990 pycom17g17000
rosa_chinensis	RchiOBHm_Chr2g0144531 RchiOBHm_Chr2g0166351
rosa_laevigata	RLG00000020086 RLG00000021613
rosa_multiflora	Rmu_sc0005789.1_g000005 Rmu_sc0007974.1_g000004 Rmu_sc0029020.1_g000001 Rmu_sc0029020.1_g000002
rosa_roxburghii	Rroxscaffold_2G00084950 Rroxscaffold_2G00101230
rosa_rugosa	Rorug02G0387600 Rorug02G0522400
rosa_samantha	Rh2AG439600 Rh2AG588500 Rh2BG449700 Rh2BG600500 Rh2CG426600 Rh2CG571300 Rh2DG459600 Rh2DG610700
rosa_wichuraiana	Rw2G035960 Rw2G049040

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	944, 1013
AccB7I	CCANNNNNTGG	1 cut(s)	967
AccII	CGCG	1 cut(s)	55
AciI	CCGC	1 cut(s)	1115
AclWI	GGATC	4 cut(s)	605, 859, 872, 1161
AcsI	RAATTY	5 cut(s)	447, 782, 835, 1022, 1121
AcuI	CTGAAG	3 cut(s)	254, 693, 702
AfiI	CCNNNNNNNGG	7 cut(s)	166, 170, 214, 231, 292, 967, 972
AgsI	TTSAA	5 cut(s)	400, 452, 598, 952, 1029
AjnI	CCWGG	3 cut(s)	213, 735, 1003
AluBI	AGCT	6 cut(s)	324, 352, 677, 805, 880, 910
AluI	AGCT	6 cut(s)	324, 352, 677, 805, 880, 910
Alw21I	GWGCWC	2 cut(s)	354, 1104
AlwI	GGATC	4 cut(s)	605, 859, 872, 1161
Ama87I	CYCGRG	1 cut(s)	139
AoxI	GGCC	3 cut(s)	454, 685, 990
ApeKI	GCWGC	2 cut(s)	83, 877
ApoI	RAATTY	5 cut(s)	447, 782, 835, 1022, 1121
ArsI	GACNNNNNNTTYG	4 cut(s)	219, 251, 1159, 1191
AseI	ATTAAT	1 cut(s)	798
AspLEI	GCGC	2 cut(s)	57, 1278
AspS9I	GGNCC	1 cut(s)	991
AsuC2I	CCSGG	2 cut(s)	140, 141
AsuHPI	GGTGA	3 cut(s)	292, 344, 757
AsuNHI	GCTAGC	1 cut(s)	416
AvaI	CYCGRG	1 cut(s)	139
BamHI	GGATCC	1 cut(s)	864
BanII	GRGCYC	1 cut(s)	354
BbsI	GAAGAC	1 cut(s)	900
Bbv12I	GWGCWC	2 cut(s)	354, 1104
BbvI	GCAGC	2 cut(s)	95, 889
BccI	CCATC	6 cut(s)	49, 58, 134, 190, 487, 965
BceAI	ACGGC	1 cut(s)	587
BciT130I	CCWGG	3 cut(s)	215, 737, 1005
BciVI	GTATCC	1 cut(s)	661
BcnI	CCSGG	2 cut(s)	140, 141
BfaI	CTAG	3 cut(s)	264, 321, 417
BfmI	CTRYAG	1 cut(s)	875
BfuI	GTATCC	1 cut(s)	661
BglII	AGATCT	1 cut(s)	955
BisI	GCNGC	2 cut(s)	84, 878
BlsI	GCNGC	2 cut(s)	85, 879
Bme1390I	CCNGG	5 cut(s)	140, 141, 215, 737, 1005
BmeT110I	CYCGRG	1 cut(s)	139
BmgT120I	GGNCC	1 cut(s)	991
BmiI	GGNNCC	3 cut(s)	441, 477, 866
BmrFI	CCNGG	5 cut(s)	140, 141, 215, 737, 1005
BmsI	GCATC	3 cut(s)	625, 946, 1030
BmtI	GCTAGC	1 cut(s)	420
BpiI	GAAGAC	1 cut(s)	900
BplI	GAGNNNNNCTC	2 cut(s)	341, 373
Bpu10I	CCTNAGC	2 cut(s)	300, 339
BpuMI	CCSGG	2 cut(s)	140, 141
BsaJI	CCNNGG	5 cut(s)	139, 735, 966, 981, 1003
BsaWI	WCCGGW	1 cut(s)	861
Bsc4I	CCNNNNNNNGG	7 cut(s)	166, 170, 214, 231, 292, 967, 972
Bse1I	ACTGG	1 cut(s)	756
BseBI	CCWGG	3 cut(s)	215, 737, 1005
BseDI	CCNNGG	5 cut(s)	139, 735, 966, 981, 1003
BseGI	GGATG	5 cut(s)	135, 640, 895, 976, 1123
BseLI	CCNNNNNNNGG	7 cut(s)	166, 170, 214, 231, 292, 967, 972
BseMII	CTCAG	3 cut(s)	353, 1056, 1148
BseNI	ACTGG	1 cut(s)	756
BseXI	GCAGC	2 cut(s)	95, 889
BseYI	CCCAGC	1 cut(s)	344
BsgI	GTGCAG	1 cut(s)	492
Bsh1236I	CGCG	1 cut(s)	55
BshFI	GGCC	3 cut(s)	456, 687, 992
BsiHKAI	GWGCWC	2 cut(s)	354, 1104
BsiHKCI	CYCGRG	1 cut(s)	139
BsiSI	CCGG	2 cut(s)	140, 862
BslFI	GGGAC	4 cut(s)	274, 331, 1180, 1235
BslI	CCNNNNNNNGG	7 cut(s)	166, 170, 214, 231, 292, 967, 972
BsmFI	GGGAC	4 cut(s)	274, 331, 1180, 1235
BsnI	GGCC	3 cut(s)	456, 687, 992
BsoBI	CYCGRG	1 cut(s)	139
Bsp1286I	GDGCHC	2 cut(s)	354, 1104
Bsp143I	GATC	4 cut(s)	610, 864, 955, 1153
Bsp19I	CCATGG	1 cut(s)	966
BspACI	CCGC	1 cut(s)	1115
BspANI	GGCC	3 cut(s)	456, 687, 992
BspCNI	CTCAG	3 cut(s)	352, 1057, 1149
BspFNI	CGCG	1 cut(s)	55
BspLI	GGNNCC	3 cut(s)	441, 477, 866
BspMAI	CTGCAG	1 cut(s)	879
BspOI	GCTAGC	1 cut(s)	420
BspPI	GGATC	4 cut(s)	605, 859, 872, 1161
BsrI	ACTGG	1 cut(s)	756
BssECI	CCNNGG	5 cut(s)	139, 735, 966, 981, 1003
BssMI	GATC	4 cut(s)	610, 864, 955, 1153
BssT1I	CCWWGG	1 cut(s)	966
Bst2UI	CCWGG	3 cut(s)	215, 737, 1005
Bst4CI	ACNGT	3 cut(s)	698, 1237, 1270
Bst6I	CTCTTC	2 cut(s)	62, 1046
BstC8I	GCNNGC	5 cut(s)	59, 120, 418, 480, 1280
BstDEI	CTNAG	5 cut(s)	300, 339, 1065, 1157, 1215
BstDSI	CCRYGG	1 cut(s)	966
BstEII	GGTNACC	2 cut(s)	280, 1237
BstF5I	GGATG	5 cut(s)	135, 640, 895, 976, 1123
BstFNI	CGCG	1 cut(s)	55
BstHHI	GCGC	2 cut(s)	57, 1278
BstKTI	GATC	4 cut(s)	613, 867, 958, 1156
BstMBI	GATC	4 cut(s)	610, 864, 955, 1153
BstMWI	GCNNNNNNNGC	5 cut(s)	46, 89, 335, 488, 1284
BstNI	CCWGG	3 cut(s)	215, 737, 1005
BstNSI	RCATGY	1 cut(s)	1036
BstPI	GGTNACC	2 cut(s)	280, 1237
BstSCI	CCNGG	5 cut(s)	138, 139, 213, 735, 1003
BstSFI	CTRYAG	1 cut(s)	875
BstUI	CGCG	1 cut(s)	55
BstV1I	GCAGC	2 cut(s)	95, 889
BstV2I	GAAGAC	1 cut(s)	900
BstX2I	RGATCY	3 cut(s)	864, 955, 1153
BstYI	RGATCY	3 cut(s)	864, 955, 1153
BsuI	GTATCC	1 cut(s)	661
BsuRI	GGCC	3 cut(s)	456, 687, 992
BtgI	CCRYGG	1 cut(s)	966
BtgZI	GCGATG	2 cut(s)	36, 506
BtsCI	GGATG	5 cut(s)	135, 640, 895, 976, 1123
BtsI	GCAGTG	1 cut(s)	1050
BtsIMutI	CAGTG	4 cut(s)	120, 749, 1050, 1275
Cac8I	GCNNGC	5 cut(s)	59, 120, 418, 480, 1280
CfoI	GCGC	2 cut(s)	57, 1278
Cfr13I	GGNCC	1 cut(s)	991
Cfr9I	CCCGGG	1 cut(s)	139
CseI	GACGC	1 cut(s)	1192
CviAII	CATG	3 cut(s)	512, 967, 1033
DdeI	CTNAG	5 cut(s)	300, 339, 1065, 1157, 1215
DpnI	GATC	4 cut(s)	612, 866, 957, 1155
DpnII	GATC	4 cut(s)	610, 864, 955, 1153
Eam1104I	CTCTTC	2 cut(s)	62, 1046
EarI	CTCTTC	2 cut(s)	62, 1046
Ecl136II	GAGCTC	1 cut(s)	352
Eco130I	CCWWGG	1 cut(s)	966
Eco147I	AGGCCT	1 cut(s)	456
Eco24I	GRGCYC	1 cut(s)	354
Eco53kI	GAGCTC	1 cut(s)	352
Eco57I	CTGAAG	3 cut(s)	254, 693, 702
Eco88I	CYCGRG	1 cut(s)	139
Eco91I	GGTNACC	2 cut(s)	280, 1237
EcoICRI	GAGCTC	1 cut(s)	352
EcoO65I	GGTNACC	2 cut(s)	280, 1237
EcoRI	GAATTC	2 cut(s)	835, 1121
EcoRII	CCWGG	3 cut(s)	213, 735, 1003
EcoT14I	CCWWGG	1 cut(s)	966
EcoT38I	GRGCYC	1 cut(s)	354
ErhI	CCWWGG	1 cut(s)	966
FaeI	CATG	3 cut(s)	515, 970, 1036
FaqI	GGGAC	4 cut(s)	274, 331, 1180, 1235
FatI	CATG	3 cut(s)	511, 966, 1032
Fnu4HI	GCNGC	2 cut(s)	84, 878
FokI	GGATG	5 cut(s)	122, 647, 902, 983, 1130
FriOI	GRGCYC	1 cut(s)	354
Fsp4HI	GCNGC	2 cut(s)	84, 878
FspBI	CTAG	3 cut(s)	264, 321, 417
GlaI	GCGC	2 cut(s)	56, 1277
GluI	GCNGC	2 cut(s)	84, 878
GsaI	CCCAGC	1 cut(s)	348
HaeIII	GGCC	3 cut(s)	456, 687, 992
HapII	CCGG	2 cut(s)	140, 862
HgaI	GACGC	1 cut(s)	1192
HhaI	GCGC	2 cut(s)	57, 1278
Hin1II	CATG	3 cut(s)	515, 970, 1036
Hin6I	GCGC	2 cut(s)	55, 1276
HinP1I	GCGC	2 cut(s)	55, 1276
HindIII	AAGCTT	2 cut(s)	675, 803
HinfI	GANTC	6 cut(s)	5, 156, 218, 373, 617, 999
HpaII	CCGG	2 cut(s)	140, 862
HphI	GGTGA	3 cut(s)	292, 344, 757
Hpy188I	TCNGA	3 cut(s)	10, 682, 1158
Hpy188III	TCNNGA	2 cut(s)	377, 614
Hpy99I	CGWCG	1 cut(s)	1287
HpyAV	CCTTC	7 cut(s)	467, 511, 548, 677, 806, 1144, 1253
HpyCH4III	ACNGT	3 cut(s)	698, 1237, 1270
HpyCH4IV	ACGT	1 cut(s)	529
HpyF10VI	GCNNNNNNNGC	5 cut(s)	46, 89, 335, 488, 1284
HpyF3I	CTNAG	5 cut(s)	300, 339, 1065, 1157, 1215
HpySE526I	ACGT	1 cut(s)	529
Hsp92II	CATG	3 cut(s)	515, 970, 1036
HspAI	GCGC	2 cut(s)	55, 1276
Kzo9I	GATC	4 cut(s)	610, 864, 955, 1153
LmnI	GCTCC	4 cut(s)	349, 439, 475, 818
Lsp1109I	GCAGC	2 cut(s)	95, 889
LweI	GCATC	3 cut(s)	625, 946, 1030
MaeI	CTAG	3 cut(s)	264, 321, 417
MaeII	ACGT	1 cut(s)	529
MaeIII	GTNAC	2 cut(s)	280, 1237
MalI	GATC	4 cut(s)	612, 866, 957, 1155
MboI	GATC	4 cut(s)	610, 864, 955, 1153
MboII	GAAGA	9 cut(s)	29, 79, 85, 412, 617, 905, 1063, 1070, 1231
MfeI	CAATTG	1 cut(s)	1288
MflI	RGATCY	3 cut(s)	864, 955, 1153
MhlI	GDGCHC	2 cut(s)	354, 1104
MluCI	AATT	7 cut(s)	447, 782, 835, 1022, 1121, 1259, 1288
MmeI	TCCRAC	2 cut(s)	869, 1289
MseI	TTAA	2 cut(s)	714, 798
MspA1I	CMGCKG	1 cut(s)	880
MspI	CCGG	2 cut(s)	140, 862
MspR9I	CCNGG	5 cut(s)	140, 141, 215, 737, 1005
MunI	CAATTG	1 cut(s)	1288
MvaI	CCWGG	3 cut(s)	215, 737, 1005
MvnI	CGCG	1 cut(s)	55
MwoI	GCNNNNNNNGC	5 cut(s)	46, 89, 335, 488, 1284
NciI	CCSGG	2 cut(s)	140, 141
NcoI	CCATGG	1 cut(s)	966
NdeII	GATC	4 cut(s)	610, 864, 955, 1153
NheI	GCTAGC	1 cut(s)	416
NlaIII	CATG	3 cut(s)	515, 970, 1036
NlaIV	GGNNCC	3 cut(s)	441, 477, 866
NmeAIII	GCCGAG	1 cut(s)	962
NmuCI	GTSAC	1 cut(s)	280
NspI	RCATGY	1 cut(s)	1036
PceI	AGGCCT	1 cut(s)	456
PfeI	GAWTC	6 cut(s)	5, 156, 218, 373, 617, 999
PflMI	CCANNNNNTGG	1 cut(s)	967
PkrI	GCNGC	2 cut(s)	85, 879
PshBI	ATTAAT	1 cut(s)	798
PsiI	TTATAA	2 cut(s)	944, 1013
Psp124BI	GAGCTC	1 cut(s)	354
Psp6I	CCWGG	3 cut(s)	213, 735, 1003
PspEI	GGTNACC	2 cut(s)	280, 1237
PspFI	CCCAGC	1 cut(s)	344
PspGI	CCWGG	3 cut(s)	213, 735, 1003
PspN4I	GGNNCC	3 cut(s)	441, 477, 866
PspPI	GGNCC	1 cut(s)	991
PstI	CTGCAG	1 cut(s)	879
PsuI	RGATCY	3 cut(s)	864, 955, 1153
PvuII	CAGCTG	1 cut(s)	880
SacI	GAGCTC	1 cut(s)	354
SaqAI	TTAA	2 cut(s)	714, 798
SatI	GCNGC	2 cut(s)	84, 878
Sau3AI	GATC	4 cut(s)	610, 864, 955, 1153
Sau96I	GGNCC	1 cut(s)	991
ScrFI	CCNGG	5 cut(s)	140, 141, 215, 737, 1005
SduI	GDGCHC	2 cut(s)	354, 1104
SfaNI	GCATC	3 cut(s)	625, 946, 1030
SfcI	CTRYAG	1 cut(s)	875
SmaI	CCCGGG	1 cut(s)	141
Sse9I	AATT	7 cut(s)	447, 782, 835, 1022, 1121, 1259, 1288
SseBI	AGGCCT	1 cut(s)	456
SsiI	CCGC	1 cut(s)	1115
SspMI	CTAG	3 cut(s)	264, 321, 417
SstI	GAGCTC	1 cut(s)	354
StuI	AGGCCT	1 cut(s)	456
StyD4I	CCNGG	5 cut(s)	138, 139, 213, 735, 1003
StyI	CCWWGG	1 cut(s)	966
TaaI	ACNGT	3 cut(s)	698, 1237, 1270
TaiI	ACGT	1 cut(s)	532
TaqI	TCGA	3 cut(s)	192, 221, 1049
TasI	AATT	7 cut(s)	447, 782, 835, 1022, 1121, 1259, 1288
TfiI	GAWTC	6 cut(s)	5, 156, 218, 373, 617, 999
Tru1I	TTAA	2 cut(s)	714, 798
Tru9I	TTAA	2 cut(s)	714, 798
TscAI	CASTG	4 cut(s)	120, 756, 1050, 1275
TseFI	GTSAC	1 cut(s)	280
TseI	GCWGC	2 cut(s)	83, 877
Tsp45I	GTSAC	1 cut(s)	280
TspDTI	ATGAA	3 cut(s)	530, 906, 1134
TspMI	CCCGGG	1 cut(s)	139
TspRI	CASTG	4 cut(s)	120, 756, 1050, 1275
Van91I	CCANNNNNTGG	1 cut(s)	967
VspI	ATTAAT	1 cut(s)	798
XapI	RAATTY	5 cut(s)	447, 782, 835, 1022, 1121
XceI	RCATGY	1 cut(s)	1036
XcmI	CCANNNNNNNNNTGG	1 cut(s)	968
XmaI	CCCGGG	1 cut(s)	139
XspI	CTAG	3 cut(s)	264, 321, 417

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