Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0010170

Physical Location & Seq

Genomic Coordinates Forward (+)

71842789 .. 71852030

Gene Structure 9242 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG416500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 948 bp

ATGTTCTACCGTAGCCGAATTGAGCACTCATTGCGTCTGCCTCCTTCTCTGCTTAGCCTTCGTCTACAAGATGCAGTTAAGGGAGAGCTTGAGAAGCTATTCTTAGATAAGGTTATCTCGAATTTGGGACTTTGCATTTCTGTCTATGATATCCAATCCATTAAAGATCACTTCATCTTGCCAAATGATGGTCATCCAACTCTAACGGTGGTGTTCACACTGATTATGTTTCGTCCATTTGTGGGAGAGATAATTACTGCAAAAGTCACAGAGTCTACTGCCAATGGTTTACGTTTGTCACTGGGATTTTTTGATGATATTTATATACCTACTCATCGTTTTCCTACACCATGCCACAAGAAGGATGACTCAAAAAAGAATGTTGTCTTATGGTATTGGAAGCCTTCTGATGATGAATTTTCAATTGATTTGAAGGACCAGATACGATTCCAGGTTGAAAGTGTAAACTATCCTAAAATTCCAATTGAGCAGCCAGAAAACTCAAAACCATTTGCCCCTATGGAGGTTAAAGCCAATGCGGCGTCGGGATTTGCTGTGGATGATGATTGCAAACTAAAGTTCTTGGACTTGAAGGCCAAAAGAACTTACCGCTTCATAGTATTCAAGATTGAGGAGAAGCAGAAGCAGGTGATCGTGGAGAAATTAGGTGAGCCAGCTCAAAGCTATGAAGATTTCACTGCAAGCCTTCCAGCTGATGAATGCAGATATGCTGTCTATGATTTTGATTTTGTGACTGCTGAAAACTGTCAGAAAAGCAGGATTTTCTTCATTGCATGGTCCCCTGATACATCAAAGGTGAGAAACAAGATGATTTATGCAAGCTCCAAGGACAGGTTCAAGAGAGAATTGGATGGTATCCAAATAGAGCTGCAGGCCACTGACCCAACTGAGATGGATCTTGATGTTATCAGAAGTCGTGCCAGCTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000228 GO:0000428 GO:0000785 GO:0000790 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005694 GO:0006139 GO:0006351 GO:0006352 GO:0006383 GO:0006384 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009987 GO:0010467 GO:0016070 GO:0018130 GO:0019438 GO:0030880 GO:0031974 GO:0031981 GO:0032774 GO:0032991 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:0044427 GO:0044428 GO:0044446 GO:0044451 GO:0044454 GO:0044464 GO:0046483 GO:0055029 GO:0061695 GO:0070013 GO:0071704 GO:0090304 GO:0097659 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990234

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_Rbc25 SHS2_Rpb7-N

Protein Analysis

315

Amino Acids

36.35

Weight (kDa)

6.04

Isoelectric Point (pI)

45.53

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHS2_Rpb7-N	PF03876	8 - 64	1.2e-11	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
RNA_pol_Rbc25	PF08292	83 - 168	1.2e-16	RNA polymerase III subunit Rpc25
Cofilin_ADF	PF00241	183 - 314	1.3e-40	Cofilin/tropomyosin-type actin-binding protein

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: OG0010170)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G06790 AT1G06790
fragaria_vesca	FvH4_1g22880
malus_domestica	MD08G1227600.v1.1
prunus_persica	Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.2G103200_v2.0.a1 Prupe.7G016800_v2.0.a1
rosa_chinensis	RchiOBHm_Chr5g0063451
rosa_laevigata	RLG00000022776 RLG00000035635
rosa_multiflora	Rmu_sc0016394.1_g000005
rosa_roxburghii	Rroxscaffold_1G00017270
rosa_rugosa	Rorug05G0357400
rosa_samantha	Rh5AG416500 Rh5BG431600 Rh5CG454900 Rh5DG445100
rosa_wichuraiana	Rw5G039120

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	637
Acc36I	ACCTGC	1 cut(s)	637
AccB7I	CCANNNNNTGG	1 cut(s)	188
AccI	GTMKAC	2 cut(s)	64, 275
AciI	CCGC	2 cut(s)	539, 610
AclWI	GGATC	1 cut(s)	924
AcsI	RAATTY	3 cut(s)	121, 416, 477
AcyI	GRCGYC	1 cut(s)	542
AfiI	CCNNNNNNNGG	5 cut(s)	188, 242, 361, 523, 852
AgsI	TTSAA	6 cut(s)	423, 433, 458, 592, 625, 859
AjnI	CCWGG	1 cut(s)	450
AjuI	GAANNNNNNNTTGG	2 cut(s)	839, 871
AluBI	AGCT	8 cut(s)	88, 97, 677, 684, 713, 843, 889, 945
AluI	AGCT	8 cut(s)	88, 97, 677, 684, 713, 843, 889, 945
Alw21I	GWGCWC	1 cut(s)	27
AlwI	GGATC	1 cut(s)	924
AoxI	GGCC	2 cut(s)	594, 894
ApeKI	GCWGC	2 cut(s)	490, 889
ApoI	RAATTY	3 cut(s)	121, 416, 477
Asp700I	GAANNNNTTC	1 cut(s)	98
AspS9I	GGNCC	2 cut(s)	436, 798
AsuHPI	GGTGA	3 cut(s)	661, 680, 829
AvaII	GGWCC	2 cut(s)	436, 798
Bbv12I	GWGCWC	1 cut(s)	27
BbvI	GCAGC	2 cut(s)	502, 876
BccI	CCATC	3 cut(s)	182, 866, 907
BciT130I	CCWGG	1 cut(s)	452
BciVI	GTATCC	1 cut(s)	887
BfmI	CTRYAG	1 cut(s)	890
BfuAI	ACCTGC	1 cut(s)	637
BfuI	GTATCC	1 cut(s)	887
BglI	GCCNNNNNGGC	1 cut(s)	539
BisI	GCNGC	3 cut(s)	491, 540, 890
BlpI	GCTNAGC	1 cut(s)	53
BlsI	GCNGC	3 cut(s)	492, 541, 891
Bme1390I	CCNGG	1 cut(s)	452
Bme18I	GGWCC	2 cut(s)	436, 798
BmgT120I	GGNCC	2 cut(s)	436, 798
BmiI	GGNNCC	1 cut(s)	800
BmrFI	CCNGG	1 cut(s)	452
BmrI	ACTGGG	1 cut(s)	311
BmsI	GCATC	1 cut(s)	61
BmuI	ACTGGG	1 cut(s)	311
Bpu1102I	GCTNAGC	1 cut(s)	53
BpuEI	CTTGAG	1 cut(s)	110
BsaBI	GATNNNNATC	1 cut(s)	192
BsaHI	GRCGYC	1 cut(s)	542
BsaJI	CCNNGG	1 cut(s)	846
Bsc4I	CCNNNNNNNGG	5 cut(s)	188, 242, 361, 523, 852
Bse1I	ACTGG	1 cut(s)	306
Bse3DI	GCAATG	2 cut(s)	29, 789
Bse8I	GATNNNNATC	1 cut(s)	192
BseBI	CCWGG	1 cut(s)	452
BseDI	CCNNGG	1 cut(s)	846
BseGI	GGATG	4 cut(s)	193, 370, 565, 877
BseJI	GATNNNNATC	1 cut(s)	192
BseLI	CCNNNNNNNGG	5 cut(s)	188, 242, 361, 523, 852
BseMI	GCAATG	2 cut(s)	29, 789
BseMII	CTCAG	1 cut(s)	900
BseNI	ACTGG	1 cut(s)	306
BseRI	GAGGAG	1 cut(s)	647
BseXI	GCAGC	2 cut(s)	502, 876
BshFI	GGCC	2 cut(s)	596, 896
BsiHKAI	GWGCWC	1 cut(s)	27
BslFI	GGGAC	2 cut(s)	141, 784
BslI	CCNNNNNNNGG	5 cut(s)	188, 242, 361, 523, 852
BsmFI	GGGAC	2 cut(s)	141, 784
BsmI	GAATGC	1 cut(s)	725
BsnI	GGCC	2 cut(s)	596, 896
Bsp1286I	GDGCHC	1 cut(s)	27
Bsp143I	GATC	3 cut(s)	166, 651, 916
Bsp1720I	GCTNAGC	1 cut(s)	53
BspACI	CCGC	2 cut(s)	539, 610
BspANI	GGCC	2 cut(s)	596, 896
BspCNI	CTCAG	1 cut(s)	901
BspLI	GGNNCC	1 cut(s)	800
BspMAI	CTGCAG	1 cut(s)	894
BspMI	ACCTGC	1 cut(s)	637
BspPI	GGATC	1 cut(s)	924
BsrDI	GCAATG	2 cut(s)	29, 789
BsrI	ACTGG	1 cut(s)	306
BssECI	CCNNGG	1 cut(s)	846
BssMI	GATC	3 cut(s)	166, 651, 916
BssNI	GRCGYC	1 cut(s)	542
BssT1I	CCWWGG	1 cut(s)	846
Bst2UI	CCWGG	1 cut(s)	452
Bst4CI	ACNGT	3 cut(s)	11, 208, 767
BstACI	GRCGYC	1 cut(s)	542
BstAPI	GCANNNNNTGC	1 cut(s)	31
BstC8I	GCNNGC	5 cut(s)	675, 703, 841, 894, 943
BstDEI	CTNAG	3 cut(s)	53, 103, 909
BstF5I	GGATG	4 cut(s)	193, 370, 565, 877
BstKTI	GATC	3 cut(s)	169, 654, 919
BstMBI	GATC	3 cut(s)	166, 651, 916
BstMWI	GCNNNNNNNGC	3 cut(s)	31, 94, 539
BstNI	CCWGG	1 cut(s)	452
BstSCI	CCNGG	1 cut(s)	450
BstSFI	CTRYAG	1 cut(s)	890
BstV1I	GCAGC	2 cut(s)	502, 876
BstX2I	RGATCY	1 cut(s)	916
BstYI	RGATCY	1 cut(s)	916
BsuI	GTATCC	1 cut(s)	887
BsuRI	GGCC	2 cut(s)	596, 896
BtsCI	GGATG	4 cut(s)	193, 370, 565, 877
BtsI	GCAGTG	1 cut(s)	696
BtsIMutI	CAGTG	4 cut(s)	218, 299, 696, 897
BveI	ACCTGC	1 cut(s)	637
Cac8I	GCNNGC	5 cut(s)	675, 703, 841, 894, 943
Cfr13I	GGNCC	2 cut(s)	436, 798
CseI	GACGC	2 cut(s)	23, 531
CviAII	CATG	2 cut(s)	351, 795
DdeI	CTNAG	3 cut(s)	53, 103, 909
DpnI	GATC	3 cut(s)	168, 653, 918
DpnII	GATC	3 cut(s)	166, 651, 916
Eco130I	CCWWGG	1 cut(s)	846
Eco32I	GATATC	1 cut(s)	151
Eco47I	GGWCC	2 cut(s)	436, 798
EcoRII	CCWGG	1 cut(s)	450
EcoRV	GATATC	1 cut(s)	151
EcoT14I	CCWWGG	1 cut(s)	846
ErhI	CCWWGG	1 cut(s)	846
FaeI	CATG	2 cut(s)	354, 798
FalI	AAGNNNNNCTT	2 cut(s)	86, 118
FaqI	GGGAC	2 cut(s)	141, 784
FatI	CATG	2 cut(s)	350, 794
FblI	GTMKAC	2 cut(s)	64, 275
Fnu4HI	GCNGC	3 cut(s)	491, 540, 890
FokI	GGATG	4 cut(s)	180, 377, 572, 884
Fsp4HI	GCNGC	3 cut(s)	491, 540, 890
GluI	GCNGC	3 cut(s)	491, 540, 890
HaeIII	GGCC	2 cut(s)	596, 896
HgaI	GACGC	2 cut(s)	23, 531
Hin1I	GRCGYC	1 cut(s)	542
Hin1II	CATG	2 cut(s)	354, 798
HinfI	GANTC	3 cut(s)	272, 368, 447
HphI	GGTGA	3 cut(s)	661, 680, 829
Hpy166II	GTNNAC	5 cut(s)	65, 216, 276, 290, 466
Hpy188I	TCNGA	3 cut(s)	409, 771, 932
Hpy188III	TCNNGA	5 cut(s)	118, 546, 625, 859, 920
Hpy8I	GTNNAC	5 cut(s)	65, 216, 276, 290, 466
Hpy99I	CGWCG	1 cut(s)	547
HpyAV	CCTTC	7 cut(s)	54, 68, 355, 414, 427, 586, 716
HpyCH4III	ACNGT	3 cut(s)	11, 208, 767
HpyCH4IV	ACGT	1 cut(s)	292
HpyCH4V	TGCA	9 cut(s)	74, 135, 260, 570, 701, 723, 794, 839, 892
HpyF10VI	GCNNNNNNNGC	3 cut(s)	31, 94, 539
HpyF3I	CTNAG	3 cut(s)	53, 103, 909
HpySE526I	ACGT	1 cut(s)	292
Hsp92I	GRCGYC	1 cut(s)	542
Hsp92II	CATG	2 cut(s)	354, 798
Kzo9I	GATC	3 cut(s)	166, 651, 916
LmnI	GCTCC	1 cut(s)	848
Lsp1109I	GCAGC	2 cut(s)	502, 876
LweI	GCATC	1 cut(s)	61
MaeII	ACGT	1 cut(s)	292
MaeIII	GTNAC	3 cut(s)	265, 297, 751
MalI	GATC	3 cut(s)	168, 653, 918
MboI	GATC	3 cut(s)	166, 651, 916
MboII	GAAGA	2 cut(s)	701, 778
MfeI	CAATTG	2 cut(s)	423, 483
MflI	RGATCY	1 cut(s)	916
MhlI	GDGCHC	1 cut(s)	27
MluCI	AATT	9 cut(s)	18, 121, 252, 416, 423, 477, 483, 662, 866
MlyI	GAGTC	2 cut(s)	281, 362
MmeI	TCCRAC	1 cut(s)	221
MnlI	CCTC	3 cut(s)	51, 517, 625
MroXI	GAANNNNTTC	1 cut(s)	98
MseI	TTAA	3 cut(s)	78, 162, 528
MspA1I	CMGCKG	1 cut(s)	713
MspR9I	CCNGG	1 cut(s)	452
MunI	CAATTG	2 cut(s)	423, 483
Mva1269I	GAATGC	1 cut(s)	725
MvaI	CCWGG	1 cut(s)	452
MwoI	GCNNNNNNNGC	3 cut(s)	31, 94, 539
NdeII	GATC	3 cut(s)	166, 651, 916
NlaIII	CATG	2 cut(s)	354, 798
NlaIV	GGNNCC	1 cut(s)	800
NmuCI	GTSAC	3 cut(s)	265, 297, 751
PaqCI	CACCTGC	1 cut(s)	637
PctI	GAATGC	1 cut(s)	725
PdmI	GAANNNNTTC	1 cut(s)	98
PfeI	GAWTC	1 cut(s)	447
PflMI	CCANNNNNTGG	1 cut(s)	188
PkrI	GCNGC	3 cut(s)	492, 541, 891
PleI	GAGTC	2 cut(s)	280, 362
PpsI	GAGTC	2 cut(s)	280, 362
Psp6I	CCWGG	1 cut(s)	450
PspGI	CCWGG	1 cut(s)	450
PspN4I	GGNNCC	1 cut(s)	800
PspPI	GGNCC	2 cut(s)	436, 798
PstI	CTGCAG	1 cut(s)	894
PsuI	RGATCY	1 cut(s)	916
PvuII	CAGCTG	1 cut(s)	713
SaqAI	TTAA	3 cut(s)	78, 162, 528
SatI	GCNGC	3 cut(s)	491, 540, 890
Sau3AI	GATC	3 cut(s)	166, 651, 916
Sau96I	GGNCC	2 cut(s)	436, 798
SchI	GAGTC	2 cut(s)	281, 362
ScrFI	CCNGG	1 cut(s)	452
SduI	GDGCHC	1 cut(s)	27
SfaNI	GCATC	1 cut(s)	61
SfcI	CTRYAG	1 cut(s)	890
SinI	GGWCC	2 cut(s)	436, 798
SmlI	CTYRAG	1 cut(s)	89
SmoI	CTYRAG	1 cut(s)	89
Sse9I	AATT	9 cut(s)	18, 121, 252, 416, 423, 477, 483, 662, 866
SsiI	CCGC	2 cut(s)	539, 610
StyD4I	CCNGG	1 cut(s)	450
StyI	CCWWGG	1 cut(s)	846
TaaI	ACNGT	3 cut(s)	11, 208, 767
TaiI	ACGT	1 cut(s)	295
TaqI	TCGA	1 cut(s)	119
TasI	AATT	9 cut(s)	18, 121, 252, 416, 423, 477, 483, 662, 866
TauI	GCSGC	1 cut(s)	542
TfiI	GAWTC	1 cut(s)	447
Tru1I	TTAA	3 cut(s)	78, 162, 528
Tru9I	TTAA	3 cut(s)	78, 162, 528
TscAI	CASTG	4 cut(s)	225, 306, 703, 904
TseFI	GTSAC	3 cut(s)	265, 297, 751
TseI	GCWGC	2 cut(s)	490, 889
Tsp45I	GTSAC	3 cut(s)	265, 297, 751
TspDTI	ATGAA	6 cut(s)	163, 429, 604, 702, 732, 778
TspRI	CASTG	4 cut(s)	225, 306, 703, 904
Van91I	CCANNNNNTGG	1 cut(s)	188
VpaK11BI	GGWCC	2 cut(s)	436, 798
XapI	RAATTY	3 cut(s)	121, 416, 477
XmiI	GTMKAC	2 cut(s)	64, 275
XmnI	GAANNNNTTC	1 cut(s)	98

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