Basic Information

Type: gene

Biological Identity

Species

rosa_rugosa

Chromosome

GWHBQTZ00000007

Orthogroup ID

OG0002992

Physical Location & Seq

Genomic Coordinates Reverse (-)

3858860 .. 3863159

Gene Structure 4300 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rorug07G0054500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1023 bp

ATGCAGAGGCTTCTTTCTGTGAAATTAGCCTCAAACCTCCCCAAAAACCTATCAACCTCCACCACCCAAAGCTCTTCCCTTTTCCACTTCCAACCTCACAAAACCTTCTCTCTCACCAAACCACCCCAAACCCAGACCCAAAATCACTTCTTTAGCTCCTTCCCCACACACCCACTTCCCCATCAGCACAATCTCACTCACAAAATTCATGGCTTTCTCTCCAACCCATTACTCAGAAAACACTTTTCTTTGGATTCCGCAAATACCCTTTTGAGGGTATCGAGCAAGAGGCTTTCGGATTGCAGGCTTGCCTTTCTCCAAAGCAAGTTTCCCAAACAGAGTTTTAACTTCAACCCAAGTCGTATTTCTAATCAGAGTGCCTGGAGAACATGGTTGCGAAGGTTATCAAGCGGTGACATGGTTTTGGGATTGGTTGTAGCTAATGTTGCTGTTTTTCTTTTATGGAGGATAGCAGACCCTATATTCATGTACAAGAATTTTACTATCTCATTAAACAATTTTACAAGTGGACGTCTTCACACATTGATAACTTCTGCATTTAGTCACGTTGATATTTGGCATATCATTTCTAACATGATTGGACTGTATTTTTTTGGGATCAATATTGGAAGAACTTTTGGGCCTGAGTTTTTGCTGAAGTTGTATCTAGCTGGAGCTATTGGTGGCTCAGTCTTTTACTTGGTGCACCATGCCTTCCTGGCTGCATCATCGAAGAATCGACCATTTGGGATTATGGACGCTTCTAATGCCCCAGGATTGGGGGCAAGCGGTGCTGTTAATGCTATCATGTTGCTTGATATATTCCTTCACCCCACAGCTACCCTCTACCTTGATTTTATCATACCAGTTCCTGCCATGCTGCTGGGAATCTTTCTAATTGGAAAGGATATCTTAAGAATAATGGAGGGAAACAGTCAGATCTCAGGATCTGCACACTTGGGCGGTGCGGCAGTAGCAGCCATAGCCTGGGCAAGACTTCGAAAGGGGCGTGGTTTATTCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000418 GO:0000428 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0006139 GO:0006396 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009892 GO:0009987 GO:0010033 GO:0010467 GO:0010468 GO:0010495 GO:0010605 GO:0010608 GO:0010629 GO:0014070 GO:0016070 GO:0016246 GO:0016441 GO:0016458 GO:0019222 GO:0030422 GO:0030880 GO:0031047 GO:0031050 GO:0031974 GO:0031981 GO:0032991 GO:0034641 GO:0035194 GO:0040029 GO:0042221 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043331 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0046483 GO:0048519 GO:0050789 GO:0050896 GO:0051716 GO:0055029 GO:0060255 GO:0061695 GO:0065007 GO:0070013 GO:0070887 GO:0070918 GO:0071310 GO:0071359 GO:0071407 GO:0071704 GO:0090304 GO:1901360 GO:1901698 GO:1901699 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

DUF3223 RNA_pol_Rpb1_1 RNA_pol_Rpb1_2 RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5

Protein Analysis

340

Amino Acids

37.71

Weight (kDa)

10.88

Isoelectric Point (pI)

35.63

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Rhomboid	PF01694	177 - 330	2.1e-25	Rhomboid domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0002992)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G63020 AT1G63020 AT1G63020 AT1G63020 AT1G63020
fragaria_vesca	FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400 FvH4_5g01400
malus_domestica	MD04G1068800.v1.1 MD06G1069300.v1.1 MD06G1069400.v1.1 MD06G1069500.v1.1 MD06G1069800.v1.1
prunus_persica	Prupe.5G089300_v2.0.a1
pyrus_communis	pycom04g06250
rosa_chinensis	RchiOBHm_Chr7g0199481
rosa_laevigata	RLG00000003790
rosa_multiflora	Rmu_co8411067.1_g000001 Rmu_sc0003890.1_g000001
rosa_roxburghii	Rroxscaffold_3G00256700
rosa_rugosa	Rorug07G0054300 Rorug07G0054400 Rorug07G0054500 Rorug07G0054500
rosa_samantha	Rh7AG179300 Rh7BG182800 Rh7CG188100 Rh7DG182200
rosa_wichuraiana	Rw7G015760

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AatII	GACGTC	1 cut(s)	535
AccB7I	CCANNNNNTGG	1 cut(s)	987
AciI	CCGC	5 cut(s)	258, 411, 789, 963, 968
AclWI	GGATC	2 cut(s)	626, 955
AcsI	RAATTY	2 cut(s)	204, 496
AcuI	CTGAAG	1 cut(s)	677
AcyI	GRCGYC	1 cut(s)	532
AfaI	GTAC	1 cut(s)	491
AfiI	CCNNNNNNNGG	5 cut(s)	273, 274, 778, 779, 987
AflII	CTTAAG	1 cut(s)	913
AgsI	TTSAA	1 cut(s)	352
AjnI	CCWGG	4 cut(s)	380, 717, 772, 986
AjuI	GAANNNNNNNTTGG	4 cut(s)	312, 344, 349, 381
AluBI	AGCT	6 cut(s)	72, 156, 440, 671, 677, 839
AluI	AGCT	6 cut(s)	72, 156, 440, 671, 677, 839
Alw21I	GWGCWC	1 cut(s)	708
Alw44I	GTGCAC	1 cut(s)	704
AlwI	GGATC	2 cut(s)	626, 955
AlwNI	CAGNNNCTG	2 cut(s)	872, 950
AoxI	GGCC	1 cut(s)	641
ApaLI	GTGCAC	1 cut(s)	704
ApeKI	GCWGC	3 cut(s)	722, 880, 977
ApoI	RAATTY	2 cut(s)	204, 496
AspS9I	GGNCC	1 cut(s)	641
AsuHPI	GGTGA	3 cut(s)	106, 425, 821
AsuII	TTCGAA	1 cut(s)	1000
BaeGI	GKGCMC	1 cut(s)	708
BbsI	GAAGAC	1 cut(s)	527
Bbv12I	GWGCWC	1 cut(s)	708
BbvI	GCAGC	3 cut(s)	709, 867, 989
BccI	CCATC	1 cut(s)	189
BciT130I	CCWGG	4 cut(s)	382, 719, 774, 988
BfaI	CTAG	2 cut(s)	668, 1021
BfrI	CTTAAG	1 cut(s)	913
BglI	GCCNNNNNGGC	1 cut(s)	719
BglII	AGATCT	1 cut(s)	939
BisI	GCNGC	4 cut(s)	723, 881, 969, 978
BlsI	GCNGC	4 cut(s)	724, 882, 970, 979
Bme1390I	CCNGG	4 cut(s)	382, 719, 774, 988
BmgT120I	GGNCC	1 cut(s)	641
BmrFI	CCNGG	4 cut(s)	382, 719, 774, 988
BmsI	GCATC	1 cut(s)	734
BpiI	GAAGAC	1 cut(s)	527
BpmI	CTGGAG	2 cut(s)	403, 693
Bpu14I	TTCGAA	1 cut(s)	1000
BsaHI	GRCGYC	1 cut(s)	532
BsaJI	CCNNGG	2 cut(s)	772, 987
Bsc4I	CCNNNNNNNGG	5 cut(s)	273, 274, 778, 779, 987
Bse1I	ACTGG	1 cut(s)	866
BseBI	CCWGG	4 cut(s)	382, 719, 774, 988
BseDI	CCNNGG	2 cut(s)	772, 987
BseLI	CCNNNNNNNGG	5 cut(s)	273, 274, 778, 779, 987
BseMII	CTCAG	4 cut(s)	247, 636, 702, 957
BseNI	ACTGG	1 cut(s)	866
BseSI	GKGCMC	1 cut(s)	708
BseXI	GCAGC	3 cut(s)	709, 867, 989
BseYI	CCCAGC	1 cut(s)	883
BsgI	GTGCAG	1 cut(s)	936
BshFI	GGCC	1 cut(s)	643
BsiHKAI	GWGCWC	1 cut(s)	708
BslI	CCNNNNNNNGG	5 cut(s)	273, 274, 778, 779, 987
BsnI	GGCC	1 cut(s)	643
Bsp119I	TTCGAA	1 cut(s)	1000
Bsp1286I	GDGCHC	1 cut(s)	708
Bsp1407I	TGTACA	1 cut(s)	489
Bsp143I	GATC	3 cut(s)	618, 939, 947
BspACI	CCGC	5 cut(s)	258, 411, 789, 963, 968
BspANI	GGCC	1 cut(s)	643
BspCNI	CTCAG	4 cut(s)	246, 637, 701, 956
BspPI	GGATC	2 cut(s)	626, 955
BspQI	GCTCTTC	1 cut(s)	79
BspT104I	TTCGAA	1 cut(s)	1000
BspTI	CTTAAG	1 cut(s)	913
BsrGI	TGTACA	1 cut(s)	489
BsrI	ACTGG	1 cut(s)	866
BssECI	CCNNGG	2 cut(s)	772, 987
BssMI	GATC	3 cut(s)	618, 939, 947
BssNI	GRCGYC	1 cut(s)	532
Bst2UI	CCWGG	4 cut(s)	382, 719, 774, 988
Bst4CI	ACNGT	2 cut(s)	606, 935
Bst6I	CTCTTC	1 cut(s)	79
BstACI	GRCGYC	1 cut(s)	532
BstAFI	CTTAAG	1 cut(s)	913
BstAPI	GCANNNNNTGC	1 cut(s)	791
BstAUI	TGTACA	1 cut(s)	489
BstBI	TTCGAA	1 cut(s)	1000
BstC8I	GCNNGC	3 cut(s)	305, 309, 787
BstDEI	CTNAG	4 cut(s)	233, 645, 688, 943
BstKTI	GATC	3 cut(s)	621, 942, 950
BstMBI	GATC	3 cut(s)	618, 939, 947
BstMWI	GCNNNNNNNGC	8 cut(s)	446, 719, 767, 791, 800, 974, 977, 983
BstNI	CCWGG	4 cut(s)	382, 719, 774, 988
BstSCI	CCNGG	4 cut(s)	380, 717, 772, 986
BstSLI	GKGCMC	1 cut(s)	708
BstV1I	GCAGC	3 cut(s)	709, 867, 989
BstV2I	GAAGAC	1 cut(s)	527
BstX2I	RGATCY	2 cut(s)	939, 947
BstXI	CCANNNNNNTGG	1 cut(s)	883
BstYI	RGATCY	2 cut(s)	939, 947
BsuRI	GGCC	1 cut(s)	643
Cac8I	GCNNGC	3 cut(s)	305, 309, 787
CaiI	CAGNNNCTG	2 cut(s)	872, 950
Cfr13I	GGNCC	1 cut(s)	641
CseI	GACGC	1 cut(s)	767
Csp6I	GTAC	1 cut(s)	490
CviAII	CATG	8 cut(s)	209, 390, 418, 487, 595, 710, 808, 877
CviQI	GTAC	1 cut(s)	490
DdeI	CTNAG	4 cut(s)	233, 645, 688, 943
DpnI	GATC	3 cut(s)	620, 941, 949
DpnII	GATC	3 cut(s)	618, 939, 947
Eam1104I	CTCTTC	1 cut(s)	79
EarI	CTCTTC	1 cut(s)	79
Eco32I	GATATC	1 cut(s)	910
Eco57I	CTGAAG	1 cut(s)	677
EcoRII	CCWGG	4 cut(s)	380, 717, 772, 986
EcoRV	GATATC	1 cut(s)	910
FaeI	CATG	8 cut(s)	212, 393, 421, 490, 598, 713, 811, 880
FalI	AAGNNNNNCTT	2 cut(s)	896, 928
FatI	CATG	8 cut(s)	208, 389, 417, 486, 594, 709, 807, 876
Fnu4HI	GCNGC	4 cut(s)	723, 881, 969, 978
Fsp4HI	GCNGC	4 cut(s)	723, 881, 969, 978
FspBI	CTAG	2 cut(s)	668, 1021
GluI	GCNGC	4 cut(s)	723, 881, 969, 978
GsaI	CCCAGC	1 cut(s)	887
GsuI	CTGGAG	2 cut(s)	403, 693
HaeIII	GGCC	1 cut(s)	643
HgaI	GACGC	1 cut(s)	767
Hin1I	GRCGYC	1 cut(s)	532
Hin1II	CATG	8 cut(s)	212, 393, 421, 490, 598, 713, 811, 880
HinfI	GANTC	3 cut(s)	254, 736, 888
HphI	GGTGA	3 cut(s)	106, 425, 821
Hpy166II	GTNNAC	2 cut(s)	530, 706
Hpy188I	TCNGA	4 cut(s)	236, 298, 375, 939
Hpy188III	TCNNGA	1 cut(s)	945
Hpy8I	GTNNAC	2 cut(s)	530, 706
HpyAV	CCTTC	5 cut(s)	115, 169, 393, 724, 836
HpyCH4III	ACNGT	2 cut(s)	606, 935
HpyCH4IV	ACGT	2 cut(s)	532, 567
HpyCH4V	TGCA	6 cut(s)	4, 303, 557, 706, 725, 953
HpyF10VI	GCNNNNNNNGC	8 cut(s)	446, 719, 767, 791, 800, 974, 977, 983
HpyF3I	CTNAG	4 cut(s)	233, 645, 688, 943
HpySE526I	ACGT	2 cut(s)	532, 567
Hsp92I	GRCGYC	1 cut(s)	532
Hsp92II	CATG	8 cut(s)	212, 393, 421, 490, 598, 713, 811, 880
Kzo9I	GATC	3 cut(s)	618, 939, 947
LguI	GCTCTTC	1 cut(s)	79
LmnI	GCTCC	2 cut(s)	161, 674
Lsp1109I	GCAGC	3 cut(s)	709, 867, 989
LweI	GCATC	1 cut(s)	734
MaeI	CTAG	2 cut(s)	668, 1021
MaeII	ACGT	2 cut(s)	532, 567
MaeIII	GTNAC	2 cut(s)	413, 563
MalI	GATC	3 cut(s)	620, 941, 949
MboI	GATC	3 cut(s)	618, 939, 947
MboII	GAAGA	4 cut(s)	66, 527, 642, 745
MflI	RGATCY	2 cut(s)	939, 947
MhlI	GDGCHC	1 cut(s)	708
MluCI	AATT	5 cut(s)	23, 204, 496, 517, 897
MmeI	TCCRAC	2 cut(s)	115, 246
MnlI	CCTC	9 cut(s)	40, 47, 67, 105, 267, 282, 459, 854, 919
MseI	TTAA	4 cut(s)	345, 512, 798, 914
MspCI	CTTAAG	1 cut(s)	913
MspR9I	CCNGG	4 cut(s)	382, 719, 774, 988
MvaI	CCWGG	4 cut(s)	382, 719, 774, 988
MwoI	GCNNNNNNNGC	8 cut(s)	446, 719, 767, 791, 800, 974, 977, 983
NdeII	GATC	3 cut(s)	618, 939, 947
NlaIII	CATG	8 cut(s)	212, 393, 421, 490, 598, 713, 811, 880
NmuCI	GTSAC	2 cut(s)	413, 563
NspV	TTCGAA	1 cut(s)	1000
PciSI	GCTCTTC	1 cut(s)	79
PcsI	WCGNNNNNNNCGW	1 cut(s)	1006
PfeI	GAWTC	3 cut(s)	254, 736, 888
PflMI	CCANNNNNTGG	1 cut(s)	987
PkrI	GCNGC	4 cut(s)	724, 882, 970, 979
Psp6I	CCWGG	4 cut(s)	380, 717, 772, 986
PspFI	CCCAGC	1 cut(s)	883
PspGI	CCWGG	4 cut(s)	380, 717, 772, 986
PspPI	GGNCC	1 cut(s)	641
PstNI	CAGNNNCTG	2 cut(s)	872, 950
PsuI	RGATCY	2 cut(s)	939, 947
RsaI	GTAC	1 cut(s)	491
RsaNI	GTAC	1 cut(s)	490
SapI	GCTCTTC	1 cut(s)	79
SaqAI	TTAA	4 cut(s)	345, 512, 798, 914
SatI	GCNGC	4 cut(s)	723, 881, 969, 978
Sau3AI	GATC	3 cut(s)	618, 939, 947
Sau96I	GGNCC	1 cut(s)	641
ScrFI	CCNGG	4 cut(s)	382, 719, 774, 988
SduI	GDGCHC	1 cut(s)	708
SfaNI	GCATC	1 cut(s)	734
SfuI	TTCGAA	1 cut(s)	1000
SmlI	CTYRAG	1 cut(s)	913
SmoI	CTYRAG	1 cut(s)	913
Sse9I	AATT	5 cut(s)	23, 204, 496, 517, 897
SsiI	CCGC	5 cut(s)	258, 411, 789, 963, 968
SspI	AATATT	1 cut(s)	625
SspMI	CTAG	2 cut(s)	668, 1021
StyD4I	CCNGG	4 cut(s)	380, 717, 772, 986
TaaI	ACNGT	2 cut(s)	606, 935
TaiI	ACGT	2 cut(s)	535, 570
TaqI	TCGA	4 cut(s)	281, 731, 739, 1000
TasI	AATT	5 cut(s)	23, 204, 496, 517, 897
TatI	WGTACW	1 cut(s)	489
TauI	GCSGC	1 cut(s)	971
TfiI	GAWTC	3 cut(s)	254, 736, 888
Tru1I	TTAA	4 cut(s)	345, 512, 798, 914
Tru9I	TTAA	4 cut(s)	345, 512, 798, 914
TseFI	GTSAC	2 cut(s)	413, 563
TseI	GCWGC	3 cut(s)	722, 880, 977
Tsp45I	GTSAC	2 cut(s)	413, 563
TspDTI	ATGAA	2 cut(s)	197, 475
Van91I	CCANNNNNTGG	1 cut(s)	987
Vha464I	CTTAAG	1 cut(s)	913
VneI	GTGCAC	1 cut(s)	704
XapI	RAATTY	2 cut(s)	204, 496
XspI	CTAG	2 cut(s)	668, 1021
ZraI	GACGTC	1 cut(s)	533

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