Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2D

Orthogroup ID

OG0005882

Physical Location & Seq

Genomic Coordinates Forward (+)

39525005 .. 39526821

Gene Structure 1817 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2DG317900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 648 bp

ATGCTTTATTTATCACCAAGTAAAGATGAATACTATATGATAGCAGCACGAAATTCTTTGGCCTTGAATCGAGGTATTCATGACGAACAGGTTGTTCCAGCTCGATACTGTCAAGAATTCCTGACTGTTGAATGGGAACAGGTGCATCTTCGAACCAGTAAGCAAACAGCGAATCCATGGGTATTTGAACCTAAGTATCCGGGAAAAAGCAGAATATTTGATGGAAGAACGGGGGATCCTTTTGAACACCCTGTTATAATAGGAAAGCCTTATATCTTGAAATTAATTCATCAAGTTGATGATAAAATATATGGACGTTCCAGTGGACATTATGCAATTGTTACACAACAACCCCTTAGAGGAAGGGCCAAGCAAGAGGGACAATGGGTAGGAGAAATGGAAGTTTGGGCTCTAGAGGGATTTGGTGTTGCTCATATTTTACAAGAGATGCTTACTTATAAATCGGATCATATTAGAGCTCGTCAAGAAGTACCTGGTACTACAATCATTGGAGGGACAATACCTCAACCCGCAGAAGCTCCAGAATCTTTTCGATTGCTCGTGCGAGAACTACAATCTTTGGCTCTAGAACTGAACCATTTCCTTGTATCTGAGAAGAACTTCCAGATTAATAGGAAGGAAGCTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0009507 GO:0009536 GO:0030880 GO:0032991 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044444 GO:0044464 GO:0061695 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 map00230 map00240 map01100 map03020

Pfam Domains

Protein Families

RNA_pol_Rpb2_1 RNA_pol_Rpb2_2 RNA_pol_Rpb2_3 RNA_pol_Rpb2_6 RNA_pol_Rpb2_7

Protein Analysis

215

Amino Acids

24.68

Weight (kDa)

6.72

Isoelectric Point (pI)

46.03

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb2_6	PF00562	65 - 124	2.2e-17	RNA polymerase Rpb2, domain 6
RNA_pol_Rpb2_7	PF04560	127 - 201	1.3e-20	RNA polymerase Rpb2, domain 7

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)

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Publication-ready

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Orthologous Genes (Group: OG0005882)

Species	Orthologous Gene IDs
arabidopsis_thaliana	ATCG00190
malus_domestica	MD01G1093300.v1.1 MD16G1169300.v1.1
pyrus_communis	pycom12397g00320 pycom14g07090
rosa_chinensis	RchiOBHm_CPg0502401
rosa_laevigata	RLG00000000047 RLG00000000087 RLG00000000116 RLG00000000175 RLG00000000231 RLG00000000246 RLG00000000284 RLG00000000299 RLG00000000300 RLG00000000314 RLG00000000318 RLG00000000340
rosa_multiflora	Rmu_sc0002986.1_g000010 Rmu_sc0008812.1_g000013 Rmu_sc0011830.1_g000003
rosa_roxburghii	Rroxscaffold_2G00119070
rosa_rugosa	Rorug02G0490800 RorugMtG0001900
rosa_samantha	Rh2AG293900 Rh2AG294000 Rh2DG317800 Rh2DG317900

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	2 cut(s)	257, 459
AciI	CCGC	1 cut(s)	531
AclWI	GGATC	3 cut(s)	230, 243, 474
AcsI	RAATTY	2 cut(s)	52, 116
AfaI	GTAC	2 cut(s)	492, 499
AfiI	CCNNNNNNNGG	1 cut(s)	359
AgsI	TTSAA	5 cut(s)	67, 131, 188, 245, 280
AjnI	CCWGG	1 cut(s)	493
AloI	GAACNNNNNNTCC	2 cut(s)	220, 252
AluBI	AGCT	4 cut(s)	101, 479, 539, 644
AluI	AGCT	4 cut(s)	101, 479, 539, 644
Alw21I	GWGCWC	1 cut(s)	481
AlwI	GGATC	3 cut(s)	230, 243, 474
AoxI	GGCC	2 cut(s)	60, 366
ApeKI	GCWGC	1 cut(s)	44
ApoI	RAATTY	2 cut(s)	52, 116
AseI	ATTAAT	2 cut(s)	284, 630
Asp700I	GAANNNNTTC	3 cut(s)	549, 599, 620
AspS9I	GGNCC	1 cut(s)	366
AsuC2I	CCSGG	1 cut(s)	201
AsuHPI	GGTGA	1 cut(s)	6
AsuII	TTCGAA	1 cut(s)	151
BaeI	ACNNNNGTAYC	2 cut(s)	179, 212
BamHI	GGATCC	1 cut(s)	235
BanII	GRGCYC	2 cut(s)	412, 481
BauI	CACGAG	1 cut(s)	560
Bbv12I	GWGCWC	1 cut(s)	481
BbvI	GCAGC	1 cut(s)	56
BccI	CCATC	1 cut(s)	215
BciT130I	CCWGG	1 cut(s)	495
BciVI	GTATCC	1 cut(s)	207
BcnI	CCSGG	1 cut(s)	201
BfaI	CTAG	2 cut(s)	413, 587
BfuI	GTATCC	1 cut(s)	207
BisI	GCNGC	1 cut(s)	45
BlsI	GCNGC	1 cut(s)	46
Bme1390I	CCNGG	2 cut(s)	201, 495
BmgT120I	GGNCC	1 cut(s)	366
BmiI	GGNNCC	1 cut(s)	237
BmrFI	CCNGG	2 cut(s)	201, 495
BmsI	GCATC	2 cut(s)	154, 438
BpmI	CTGGAG	1 cut(s)	525
Bpu14I	TTCGAA	1 cut(s)	151
BpuMI	CCSGG	1 cut(s)	201
BsaJI	CCNNGG	1 cut(s)	176
Bsc4I	CCNNNNNNNGG	1 cut(s)	359
Bse1I	ACTGG	2 cut(s)	156, 321
BseBI	CCWGG	1 cut(s)	495
BseDI	CCNNGG	1 cut(s)	176
BseLI	CCNNNNNNNGG	1 cut(s)	359
BseMII	CTCAG	1 cut(s)	603
BseNI	ACTGG	2 cut(s)	156, 321
BseXI	GCAGC	1 cut(s)	56
BshFI	GGCC	2 cut(s)	62, 368
BsiHKAI	GWGCWC	1 cut(s)	481
BsiSI	CCGG	1 cut(s)	200
BslFI	GGGAC	2 cut(s)	393, 529
BslI	CCNNNNNNNGG	1 cut(s)	359
BsmFI	GGGAC	2 cut(s)	393, 529
BsnI	GGCC	2 cut(s)	62, 368
Bsp119I	TTCGAA	1 cut(s)	151
Bsp1286I	GDGCHC	2 cut(s)	412, 481
Bsp143I	GATC	2 cut(s)	235, 466
Bsp19I	CCATGG	1 cut(s)	176
BspACI	CCGC	1 cut(s)	531
BspANI	GGCC	2 cut(s)	62, 368
BspCNI	CTCAG	1 cut(s)	604
BspHI	TCATGA	1 cut(s)	79
BspLI	GGNNCC	1 cut(s)	237
BspPI	GGATC	3 cut(s)	230, 243, 474
BspT104I	TTCGAA	1 cut(s)	151
BsrI	ACTGG	2 cut(s)	156, 321
BssECI	CCNNGG	1 cut(s)	176
BssMI	GATC	2 cut(s)	235, 466
BssSI	CACGAG	1 cut(s)	560
BssT1I	CCWWGG	1 cut(s)	176
Bst2BI	CACGAG	1 cut(s)	560
Bst2UI	CCWGG	1 cut(s)	495
Bst4CI	ACNGT	2 cut(s)	110, 127
BstBI	TTCGAA	1 cut(s)	151
BstDEI	CTNAG	3 cut(s)	192, 356, 612
BstDSI	CCRYGG	1 cut(s)	176
BstKTI	GATC	2 cut(s)	238, 469
BstMBI	GATC	2 cut(s)	235, 466
BstNI	CCWGG	1 cut(s)	495
BstSCI	CCNGG	2 cut(s)	199, 493
BstV1I	GCAGC	1 cut(s)	56
BstX2I	RGATCY	1 cut(s)	235
BstYI	RGATCY	1 cut(s)	235
BsuI	GTATCC	1 cut(s)	207
BsuRI	GGCC	2 cut(s)	62, 368
BtgI	CCRYGG	1 cut(s)	176
BtsIMutI	CAGTG	1 cut(s)	328
CciI	TCATGA	1 cut(s)	79
Cfr13I	GGNCC	1 cut(s)	366
CsiI	ACCWGGT	1 cut(s)	493
Csp6I	GTAC	2 cut(s)	491, 498
CviAII	CATG	2 cut(s)	80, 177
CviJI	RGCY	9 cut(s)	62, 101, 268, 368, 410, 479, 539, 584, 644
CviKI_1	RGCY	9 cut(s)	62, 101, 268, 368, 410, 479, 539, 584, 644
CviQI	GTAC	2 cut(s)	491, 498
DdeI	CTNAG	3 cut(s)	192, 356, 612
DpnI	GATC	2 cut(s)	237, 468
DpnII	GATC	2 cut(s)	235, 466
Ecl136II	GAGCTC	1 cut(s)	479
Eco130I	CCWWGG	1 cut(s)	176
Eco24I	GRGCYC	2 cut(s)	412, 481
Eco53kI	GAGCTC	1 cut(s)	479
EcoICRI	GAGCTC	1 cut(s)	479
EcoRI	GAATTC	1 cut(s)	116
EcoRII	CCWGG	1 cut(s)	493
EcoT14I	CCWWGG	1 cut(s)	176
EcoT38I	GRGCYC	2 cut(s)	412, 481
ErhI	CCWWGG	1 cut(s)	176
FaeI	CATG	2 cut(s)	83, 180
FalI	AAGNNNNNCTT	2 cut(s)	435, 467
FaqI	GGGAC	2 cut(s)	393, 529
FatI	CATG	2 cut(s)	79, 176
FauI	CCCGC	1 cut(s)	538
Fnu4HI	GCNGC	1 cut(s)	45
FriOI	GRGCYC	2 cut(s)	412, 481
Fsp4HI	GCNGC	1 cut(s)	45
FspBI	CTAG	2 cut(s)	413, 587
GluI	GCNGC	1 cut(s)	45
GsuI	CTGGAG	1 cut(s)	525
HaeIII	GGCC	2 cut(s)	62, 368
HapII	CCGG	1 cut(s)	200
Hin1II	CATG	2 cut(s)	83, 180
HindIII	AAGCTT	1 cut(s)	642
HinfI	GANTC	3 cut(s)	67, 172, 545
HpaII	CCGG	1 cut(s)	200
HphI	GGTGA	1 cut(s)	6
Hpy166II	GTNNAC	1 cut(s)	326
Hpy188I	TCNGA	2 cut(s)	466, 613
Hpy188III	TCNNGA	9 cut(s)	80, 113, 121, 277, 413, 485, 542, 587, 625
Hpy8I	GTNNAC	1 cut(s)	326
HpyAV	CCTTC	2 cut(s)	357, 631
HpyCH4III	ACNGT	2 cut(s)	110, 127
HpyCH4IV	ACGT	1 cut(s)	316
HpyCH4V	TGCA	2 cut(s)	145, 335
HpyF3I	CTNAG	3 cut(s)	192, 356, 612
HpySE526I	ACGT	1 cut(s)	316
Hsp92II	CATG	2 cut(s)	83, 180
Kzo9I	GATC	2 cut(s)	235, 466
LmnI	GCTCC	1 cut(s)	544
Lsp1109I	GCAGC	1 cut(s)	56
LweI	GCATC	2 cut(s)	154, 438
MabI	ACCWGGT	1 cut(s)	493
MaeI	CTAG	2 cut(s)	413, 587
MaeII	ACGT	1 cut(s)	316
MaeIII	GTNAC	1 cut(s)	340
MalI	GATC	2 cut(s)	237, 468
MboI	GATC	2 cut(s)	235, 466
MboII	GAAGA	3 cut(s)	140, 237, 628
MfeI	CAATTG	1 cut(s)	336
MflI	RGATCY	1 cut(s)	235
MhlI	GDGCHC	2 cut(s)	412, 481
MluCI	AATT	5 cut(s)	52, 116, 281, 285, 336
MnlI	CCTC	6 cut(s)	65, 353, 370, 409, 506, 534
MroXI	GAANNNNTTC	3 cut(s)	549, 599, 620
MseI	TTAA	3 cut(s)	284, 630, 646
MspI	CCGG	1 cut(s)	200
MspR9I	CCNGG	2 cut(s)	201, 495
MunI	CAATTG	1 cut(s)	336
MvaI	CCWGG	1 cut(s)	495
NciI	CCSGG	1 cut(s)	201
NcoI	CCATGG	1 cut(s)	176
NdeII	GATC	2 cut(s)	235, 466
NlaIII	CATG	2 cut(s)	83, 180
NlaIV	GGNNCC	1 cut(s)	237
NspV	TTCGAA	1 cut(s)	151
PagI	TCATGA	1 cut(s)	79
PdmI	GAANNNNTTC	3 cut(s)	549, 599, 620
PfeI	GAWTC	3 cut(s)	67, 172, 545
PfoI	TCCNGGA	1 cut(s)	199
PkrI	GCNGC	1 cut(s)	46
PshBI	ATTAAT	2 cut(s)	284, 630
PsiI	TTATAA	2 cut(s)	257, 459
Psp124BI	GAGCTC	1 cut(s)	481
Psp6I	CCWGG	1 cut(s)	493
PspGI	CCWGG	1 cut(s)	493
PspN4I	GGNNCC	1 cut(s)	237
PspPI	GGNCC	1 cut(s)	366
PsuI	RGATCY	1 cut(s)	235
RsaI	GTAC	2 cut(s)	492, 499
RsaNI	GTAC	2 cut(s)	491, 498
SacI	GAGCTC	1 cut(s)	481
SaqAI	TTAA	3 cut(s)	284, 630, 646
SatI	GCNGC	1 cut(s)	45
Sau3AI	GATC	2 cut(s)	235, 466
Sau96I	GGNCC	1 cut(s)	366
ScrFI	CCNGG	2 cut(s)	201, 495
SduI	GDGCHC	2 cut(s)	412, 481
SexAI	ACCWGGT	1 cut(s)	493
SfaNI	GCATC	2 cut(s)	154, 438
SfuI	TTCGAA	1 cut(s)	151
Sse9I	AATT	5 cut(s)	52, 116, 281, 285, 336
SsiI	CCGC	1 cut(s)	531
SspI	AATATT	1 cut(s)	216
SspMI	CTAG	2 cut(s)	413, 587
SstI	GAGCTC	1 cut(s)	481
StyD4I	CCNGG	2 cut(s)	199, 493
StyI	CCWWGG	1 cut(s)	176
TaaI	ACNGT	2 cut(s)	110, 127
TaiI	ACGT	1 cut(s)	319
TaqI	TCGA	4 cut(s)	70, 103, 151, 553
TasI	AATT	5 cut(s)	52, 116, 281, 285, 336
TfiI	GAWTC	3 cut(s)	67, 172, 545
Tru1I	TTAA	3 cut(s)	284, 630, 646
Tru9I	TTAA	3 cut(s)	284, 630, 646
TscAI	CASTG	1 cut(s)	328
TseI	GCWGC	1 cut(s)	44
TspDTI	ATGAA	3 cut(s)	42, 68, 278
TspRI	CASTG	1 cut(s)	328
VspI	ATTAAT	2 cut(s)	284, 630
XapI	RAATTY	2 cut(s)	52, 116
XbaI	TCTAGA	2 cut(s)	412, 586
XmnI	GAANNNNTTC	3 cut(s)	549, 599, 620
XspI	CTAG	2 cut(s)	413, 587

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