Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr1

Orthogroup ID

OG0013689

Physical Location & Seq

Genomic Coordinates Reverse (-)

1957505 .. 1958386

Gene Structure 882 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000000553

Sequence Viewer

CDS Protein Promoter (2k)

Length: 882 bp

ATGAATTGCCACGAATGCCGCTTTCAAACCGATGTGGTGTTCGACCACTCCACCGGCGACGCCGTCTGCAAAAACTGCGGCTTAGTGCTTGAGTCCCACTACATCGACGAGACCAACGAGTGGCGAACCTTCGCCGACGACAATACTCGCGATGATCCTAACCGTGTTGGTGCAGCCACCAACCCATTATTGTCCGGTGGCGGACTGTCCACCGTCATGGCCAAGCCCAACGGAAAGGTCCTCCGTGCTCCGAATAGGGATCCGGACCGGGGCTTGATAATGGCCTTCAAAACCATCGAGACCATGTGTGATAGGTTGGGCCTTGTTTCCACCATCAAGAACCGGGCAAATGAGATGTACAAGACTCTTGAAGATCATAAGTGTAGCAAGGGAAGAAACCAAGATGCATTATTGGCTGCTTGCCTATACATTGCTTGTAAACAAGAAGACAAGCCCAGAACTCTCAAGGAAATCCTCTCCGTCGCGAATGGAGCCTCAAAGAAAGAGATTGGTAGAGCAAAGGAATACATAATCAAGCAACTGGGGTTAATGGAGAAGCCATTTCAAGTAGCAAATGCTGGGGACTATATGAGGCGATTCTGTTCCTCTCTTGGCTTGAACAATCAAGCAATCAAAGCAGCTCAACAAGCTGTGCACAAGTCGCAAGAATTTGATATAAGGAGGAGCCCTGTATCGATAGCCGCAGCAGTGATTTACATCATCACTCAGCTTTCAGATGATAGTAACAAGAGGCCTCTCAAAGATATTGCAAACGTTACAGGAGTAGCTCCAGCAACTATCAAAAATTCATACAGAGACCTTAGTCCTCATGTATCTGAAATAATACCCAACTGGTATCATCTGAATTTGTCGAACACTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044464

KEGG Pathways

Metabolic & Signaling

ko03022 ko05169 ko05203 map03022 map05169 map05203

Pfam Domains

Protein Families

TFIIB TF_Zn_Ribbon

Protein Analysis

294

Amino Acids

32.54

Weight (kDa)

8.65

Isoelectric Point (pI)

40.73

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Zn_Ribbon_TF	PF08271	2 - 44	9.2e-14	TFIIB zinc-binding
TFIIB	PF00382	90 - 172	1.4e-20	Transcription factor TFIIB repeat
TFIIB	PF00382	190 - 275	1.9e-11	Transcription factor TFIIB repeat

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: OG0013689)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_5g39300
rosa_chinensis	RchiOBHm_Chr7g0241511 RchiOBHm_Chr7g0241691
rosa_laevigata	RLG00000000553 RLG00000000574
rosa_multiflora	Rmu_co8351453.1_g000001 Rmu_sc0002268.1_g000006 Rmu_sc0026340.1_g000001
rosa_roxburghii	Rroxscaffold_3G00218810
rosa_rugosa	Rorug03G0267400 Rorug07G0344500 Rorug07G0346400
rosa_samantha	Rh7AG500900 Rh7BG469700 Rh7BG472100 Rh7CG517300 Rh7DG485800
rosa_wichuraiana	Rw7G042320

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	120
AccII	CGCG	2 cut(s)	150, 485
AccIII	TCCGGA	1 cut(s)	262
AciI	CCGC	4 cut(s)	19, 78, 201, 702
AclI	AACGTT	1 cut(s)	774
AclWI	GGATC	3 cut(s)	149, 254, 267
AcoI	YGGCCR	1 cut(s)	219
AcsI	RAATTY	3 cut(s)	668, 805, 865
AcyI	GRCGYC	1 cut(s)	60
AfaI	GTAC	1 cut(s)	359
AfiI	CCNNNNNNNGG	2 cut(s)	120, 269
AgsI	TTSAA	5 cut(s)	26, 289, 371, 566, 619
AluBI	AGCT	4 cut(s)	641, 650, 730, 788
AluI	AGCT	4 cut(s)	641, 650, 730, 788
Alw21I	GWGCWC	2 cut(s)	250, 657
Alw26I	GTCTC	3 cut(s)	104, 293, 810
Alw44I	GTGCAC	1 cut(s)	653
AlwI	GGATC	3 cut(s)	149, 254, 267
Aor13HI	TCCGGA	1 cut(s)	262
AoxI	GGCC	4 cut(s)	219, 282, 319, 752
ApaLI	GTGCAC	1 cut(s)	653
ApeKI	GCWGC	4 cut(s)	173, 416, 638, 704
ApoI	RAATTY	3 cut(s)	668, 805, 865
AspS9I	GGNCC	3 cut(s)	238, 265, 319
AsuC2I	CCSGG	2 cut(s)	269, 344
AvaII	GGWCC	2 cut(s)	238, 265
BaeGI	GKGCMC	1 cut(s)	657
BalI	TGGCCA	1 cut(s)	221
BamHI	GGATCC	1 cut(s)	259
BanII	GRGCYC	1 cut(s)	689
BbsI	GAAGAC	1 cut(s)	453
Bbv12I	GWGCWC	2 cut(s)	250, 657
BbvI	GCAGC	4 cut(s)	185, 403, 650, 716
BccI	CCATC	2 cut(s)	302, 341
BceAI	ACGGC	1 cut(s)	47
BcnI	CCSGG	2 cut(s)	269, 344
BcoDI	GTCTC	3 cut(s)	104, 293, 810
BisI	GCNGC	7 cut(s)	19, 79, 174, 417, 639, 702, 705
BlsI	GCNGC	7 cut(s)	20, 80, 175, 418, 640, 703, 706
Bme1390I	CCNGG	2 cut(s)	269, 344
Bme18I	GGWCC	2 cut(s)	238, 265
BmgT120I	GGNCC	3 cut(s)	238, 265, 319
BmiI	GGNNCC	3 cut(s)	261, 493, 686
BmrFI	CCNGG	2 cut(s)	269, 344
BmrI	ACTGGG	1 cut(s)	551
BmsI	GCATC	1 cut(s)	394
BmuI	ACTGGG	1 cut(s)	551
BoxI	GACNNNNGTC	1 cut(s)	822
BpiI	GAAGAC	1 cut(s)	453
BpmI	CTGGAG	1 cut(s)	774
BpuEI	CTTGAG	2 cut(s)	110, 449
BpuMI	CCSGG	2 cut(s)	269, 344
Bsa29I	ATCGAT	1 cut(s)	695
BsaBI	GATNNNNATC	1 cut(s)	716
BsaHI	GRCGYC	1 cut(s)	60
BsaI	GGTCTC	3 cut(s)	104, 293, 810
BsaJI	CCNNGG	1 cut(s)	268
BsaWI	WCCGGW	2 cut(s)	194, 262
Bsc4I	CCNNNNNNNGG	2 cut(s)	120, 269
Bse118I	RCCGGY	1 cut(s)	53
Bse1I	ACTGG	2 cut(s)	546, 857
Bse3DI	GCAATG	1 cut(s)	429
Bse8I	GATNNNNATC	1 cut(s)	716
BseAI	TCCGGA	1 cut(s)	262
BseCI	ATCGAT	1 cut(s)	695
BseDI	CCNNGG	1 cut(s)	268
BseJI	GATNNNNATC	1 cut(s)	716
BseLI	CCNNNNNNNGG	2 cut(s)	120, 269
BseMI	GCAATG	1 cut(s)	429
BseMII	CTCAG	1 cut(s)	740
BseNI	ACTGG	2 cut(s)	546, 857
BseRI	GAGGAG	1 cut(s)	697
BseSI	GKGCMC	1 cut(s)	657
BseXI	GCAGC	4 cut(s)	185, 403, 650, 716
BseYI	CCCAGC	1 cut(s)	578
BsgI	GTGCAG	1 cut(s)	192
Bsh1236I	CGCG	2 cut(s)	150, 485
BshFI	GGCC	4 cut(s)	221, 284, 321, 754
BshVI	ATCGAT	1 cut(s)	695
BsiHKAI	GWGCWC	2 cut(s)	250, 657
BsiSI	CCGG	5 cut(s)	54, 195, 263, 268, 343
BslFI	GGGAC	2 cut(s)	79, 596
BslI	CCNNNNNNNGG	2 cut(s)	120, 269
BsmAI	GTCTC	3 cut(s)	104, 293, 810
BsmFI	GGGAC	2 cut(s)	79, 596
BsmI	GAATGC	1 cut(s)	20
BsnI	GGCC	4 cut(s)	221, 284, 321, 754
Bso31I	GGTCTC	3 cut(s)	104, 293, 810
Bsp1286I	GDGCHC	3 cut(s)	250, 657, 689
Bsp13I	TCCGGA	1 cut(s)	262
Bsp1407I	TGTACA	1 cut(s)	357
Bsp143I	GATC	3 cut(s)	154, 259, 373
Bsp68I	TCGCGA	2 cut(s)	150, 485
BspACI	CCGC	4 cut(s)	19, 78, 201, 702
BspANI	GGCC	4 cut(s)	221, 284, 321, 754
BspCNI	CTCAG	1 cut(s)	739
BspDI	ATCGAT	1 cut(s)	695
BspEI	TCCGGA	1 cut(s)	262
BspFNI	CGCG	2 cut(s)	150, 485
BspLI	GGNNCC	3 cut(s)	261, 493, 686
BspPI	GGATC	3 cut(s)	149, 254, 267
BspTNI	GGTCTC	3 cut(s)	104, 293, 810
BsrDI	GCAATG	1 cut(s)	429
BsrFI	RCCGGY	1 cut(s)	53
BsrGI	TGTACA	1 cut(s)	357
BsrI	ACTGG	2 cut(s)	546, 857
BssAI	RCCGGY	1 cut(s)	53
BssECI	CCNNGG	1 cut(s)	268
BssMI	GATC	3 cut(s)	154, 259, 373
BssNI	GRCGYC	1 cut(s)	60
Bst4CI	ACNGT	3 cut(s)	164, 207, 214
BstACI	GRCGYC	1 cut(s)	60
BstAPI	GCANNNNNTGC	1 cut(s)	75
BstAUI	TGTACA	1 cut(s)	357
BstC8I	GCNNGC	1 cut(s)	421
BstDEI	CTNAG	3 cut(s)	82, 726, 821
BstFNI	CGCG	2 cut(s)	150, 485
BstKTI	GATC	3 cut(s)	157, 262, 376
BstMAI	GTCTC	3 cut(s)	104, 293, 810
BstMBI	GATC	3 cut(s)	154, 259, 373
BstMWI	GCNNNNNNNGC	7 cut(s)	15, 75, 413, 491, 635, 647, 661
BstPAI	GACNNNNGTC	1 cut(s)	822
BstSCI	CCNGG	2 cut(s)	267, 342
BstSLI	GKGCMC	1 cut(s)	657
BstUI	CGCG	2 cut(s)	150, 485
BstV1I	GCAGC	4 cut(s)	185, 403, 650, 716
BstV2I	GAAGAC	1 cut(s)	453
BstX2I	RGATCY	1 cut(s)	259
BstXI	CCANNNNNNTGG	1 cut(s)	217
BstYI	RGATCY	1 cut(s)	259
Bsu15I	ATCGAT	1 cut(s)	695
BsuRI	GGCC	4 cut(s)	221, 284, 321, 754
BsuTUI	ATCGAT	1 cut(s)	695
BtgZI	GCGATG	1 cut(s)	165
BtsI	GCAGTG	1 cut(s)	714
BtsIMutI	CAGTG	1 cut(s)	714
BtuMI	TCGCGA	2 cut(s)	150, 485
Cac8I	GCNNGC	1 cut(s)	421
Cfr10I	RCCGGY	1 cut(s)	53
Cfr13I	GGNCC	3 cut(s)	238, 265, 319
ClaI	ATCGAT	1 cut(s)	695
CpoI	CGGWCCG	1 cut(s)	265
CseI	GACGC	1 cut(s)	68
Csp6I	GTAC	1 cut(s)	358
CspI	CGGWCCG	1 cut(s)	265
CviAII	CATG	3 cut(s)	217, 304, 830
CviQI	GTAC	1 cut(s)	358
DdeI	CTNAG	3 cut(s)	82, 726, 821
DpnI	GATC	3 cut(s)	156, 261, 375
DpnII	GATC	3 cut(s)	154, 259, 373
EaeI	YGGCCR	1 cut(s)	219
EciI	GGCGGA	1 cut(s)	216
Eco147I	AGGCCT	1 cut(s)	754
Eco24I	GRGCYC	1 cut(s)	689
Eco31I	GGTCTC	3 cut(s)	104, 293, 810
Eco47I	GGWCC	2 cut(s)	238, 265
EcoO109I	RGGNCCY	1 cut(s)	238
EcoT22I	ATGCAT	1 cut(s)	409
EcoT38I	GRGCYC	1 cut(s)	689
FaeI	CATG	3 cut(s)	220, 307, 833
FaqI	GGGAC	2 cut(s)	79, 596
FatI	CATG	3 cut(s)	216, 303, 829
Fnu4HI	GCNGC	7 cut(s)	19, 79, 174, 417, 639, 702, 705
FriOI	GRGCYC	1 cut(s)	689
Fsp4HI	GCNGC	7 cut(s)	19, 79, 174, 417, 639, 702, 705
GluI	GCNGC	7 cut(s)	19, 79, 174, 417, 639, 702, 705
GsaI	CCCAGC	1 cut(s)	582
GsuI	CTGGAG	1 cut(s)	774
HaeIII	GGCC	4 cut(s)	221, 284, 321, 754
HapII	CCGG	5 cut(s)	54, 195, 263, 268, 343
HgaI	GACGC	1 cut(s)	68
Hin1I	GRCGYC	1 cut(s)	60
Hin1II	CATG	3 cut(s)	220, 307, 833
HinfI	GANTC	3 cut(s)	92, 364, 597
HpaII	CCGG	5 cut(s)	54, 195, 263, 268, 343
Hpy166II	GTNNAC	3 cut(s)	210, 440, 655
Hpy188I	TCNGA	4 cut(s)	252, 736, 838, 864
Hpy188III	TCNNGA	6 cut(s)	149, 263, 298, 337, 368, 484
Hpy8I	GTNNAC	3 cut(s)	210, 440, 655
Hpy99I	CGWCG	4 cut(s)	62, 110, 140, 485
HpyAV	CCTTC	2 cut(s)	139, 295
HpyCH4III	ACNGT	3 cut(s)	164, 207, 214
HpyCH4IV	ACGT	1 cut(s)	774
HpyCH4V	TGCA	5 cut(s)	69, 173, 407, 655, 770
HpyF10VI	GCNNNNNNNGC	7 cut(s)	15, 75, 413, 491, 635, 647, 661
HpyF3I	CTNAG	3 cut(s)	82, 726, 821
HpySE526I	ACGT	1 cut(s)	774
Hsp92I	GRCGYC	1 cut(s)	60
Hsp92II	CATG	3 cut(s)	220, 307, 833
Kpn2I	TCCGGA	1 cut(s)	262
Kzo9I	GATC	3 cut(s)	154, 259, 373
LmnI	GCTCC	4 cut(s)	253, 491, 684, 793
Lsp1109I	GCAGC	4 cut(s)	185, 403, 650, 716
LweI	GCATC	1 cut(s)	394
MaeII	ACGT	1 cut(s)	774
MaeIII	GTNAC	2 cut(s)	743, 775
MalI	GATC	3 cut(s)	156, 261, 375
MboI	GATC	3 cut(s)	154, 259, 373
MboII	GAAGA	3 cut(s)	383, 405, 458
MflI	RGATCY	1 cut(s)	259
MhlI	GDGCHC	3 cut(s)	250, 657, 689
MlsI	TGGCCA	1 cut(s)	221
MluCI	AATT	4 cut(s)	4, 668, 805, 865
MluNI	TGGCCA	1 cut(s)	221
MlyI	GAGTC	2 cut(s)	101, 358
MnlI	CCTC	9 cut(s)	251, 485, 505, 585, 616, 675, 744, 765, 837
Mox20I	TGGCCA	1 cut(s)	221
Mph1103I	ATGCAT	1 cut(s)	409
MroI	TCCGGA	1 cut(s)	262
MscI	TGGCCA	1 cut(s)	221
MseI	TTAA	1 cut(s)	548
MslI	CAYNNNNRTG	1 cut(s)	215
Msp20I	TGGCCA	1 cut(s)	221
MspI	CCGG	5 cut(s)	54, 195, 263, 268, 343
MspR9I	CCNGG	2 cut(s)	269, 344
Mva1269I	GAATGC	1 cut(s)	20
MvnI	CGCG	2 cut(s)	150, 485
MwoI	GCNNNNNNNGC	7 cut(s)	15, 75, 413, 491, 635, 647, 661
NciI	CCSGG	2 cut(s)	269, 344
NdeII	GATC	3 cut(s)	154, 259, 373
NlaIII	CATG	3 cut(s)	220, 307, 833
NlaIV	GGNNCC	3 cut(s)	261, 493, 686
NruI	TCGCGA	2 cut(s)	150, 485
NsiI	ATGCAT	1 cut(s)	409
PceI	AGGCCT	1 cut(s)	754
PcsI	WCGNNNNNNNCGW	1 cut(s)	114
PctI	GAATGC	1 cut(s)	20
PfeI	GAWTC	1 cut(s)	597
PflFI	GACNNNGTC	1 cut(s)	62
PflMI	CCANNNNNTGG	1 cut(s)	120
PkrI	GCNGC	7 cut(s)	20, 80, 175, 418, 640, 703, 706
PleI	GAGTC	2 cut(s)	100, 358
PpsI	GAGTC	2 cut(s)	100, 358
PpuMI	RGGWCCY	1 cut(s)	238
PshAI	GACNNNNGTC	1 cut(s)	822
Psp1406I	AACGTT	1 cut(s)	774
Psp5II	RGGWCCY	1 cut(s)	238
PspFI	CCCAGC	1 cut(s)	578
PspN4I	GGNNCC	3 cut(s)	261, 493, 686
PspPI	GGNCC	3 cut(s)	238, 265, 319
PspPPI	RGGWCCY	1 cut(s)	238
PsuI	RGATCY	1 cut(s)	259
PsyI	GACNNNGTC	1 cut(s)	62
RruI	TCGCGA	2 cut(s)	150, 485
RsaI	GTAC	1 cut(s)	359
RsaNI	GTAC	1 cut(s)	358
RseI	CAYNNNNRTG	1 cut(s)	215
Rsr2I	CGGWCCG	1 cut(s)	265
RsrII	CGGWCCG	1 cut(s)	265
SaqAI	TTAA	1 cut(s)	548
SatI	GCNGC	7 cut(s)	19, 79, 174, 417, 639, 702, 705
Sau3AI	GATC	3 cut(s)	154, 259, 373
Sau96I	GGNCC	3 cut(s)	238, 265, 319
SchI	GAGTC	2 cut(s)	101, 358
ScrFI	CCNGG	2 cut(s)	269, 344
SduI	GDGCHC	3 cut(s)	250, 657, 689
SetI	ASST	9 cut(s)	131, 240, 317, 643, 652, 732, 777, 790, 822
SfaNI	GCATC	1 cut(s)	394
SgrAI	CRCCGGYG	1 cut(s)	53
SinI	GGWCC	2 cut(s)	238, 265
SmiMI	CAYNNNNRTG	1 cut(s)	215
SmlI	CTYRAG	2 cut(s)	89, 464
SmoI	CTYRAG	2 cut(s)	89, 464
Sse9I	AATT	4 cut(s)	4, 668, 805, 865
SseBI	AGGCCT	1 cut(s)	754
SsiI	CCGC	4 cut(s)	19, 78, 201, 702
StuI	AGGCCT	1 cut(s)	754
StyD4I	CCNGG	2 cut(s)	267, 342
TaaI	ACNGT	3 cut(s)	164, 207, 214
TaiI	ACGT	1 cut(s)	777
TaqI	TCGA	5 cut(s)	42, 105, 297, 695, 872
TasI	AATT	4 cut(s)	4, 668, 805, 865
TatI	WGTACW	1 cut(s)	357
TauI	GCSGC	3 cut(s)	21, 81, 704
TfiI	GAWTC	1 cut(s)	597
Tru1I	TTAA	1 cut(s)	548
Tru9I	TTAA	1 cut(s)	548
TscAI	CASTG	1 cut(s)	714
TseI	GCWGC	4 cut(s)	173, 416, 638, 704
TspDTI	ATGAA	2 cut(s)	17, 798
TspGWI	ACGGA	3 cut(s)	233, 246, 469
TspRI	CASTG	1 cut(s)	714
Tth111I	GACNNNGTC	1 cut(s)	62
Van91I	CCANNNNNTGG	1 cut(s)	120
VneI	GTGCAC	1 cut(s)	653
VpaK11BI	GGWCC	2 cut(s)	238, 265
XapI	RAATTY	3 cut(s)	668, 805, 865
Zsp2I	ATGCAT	1 cut(s)	409

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