Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2D

Orthogroup ID

OG0004622

Physical Location & Seq

Genomic Coordinates Forward (+)

39531819 .. 39538852

Gene Structure 7034 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2DG318100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 357 bp

ATGGCTGTTCATGTACCTTTATCTTTGGAGGCTCAAGCAGAGGCTTGTTTACTTATGTTTTCTCTTATGAATCTCTTGTCTCCAGCTATTGGGGATCCTATTTCCGTACCAAACCAAGATATGCTTATCGGGCTCTATGTATTAACGAGCAGGAATCGCCGAGGTATTTGTGCAAATAGGTATAATCCGTGTAGTCGCACAAATTCGAATCTTATGAAATTGTTCGAGAAAAATCTTCTATACGAGAACTCTCTTTCACCAAAATGTTGTGCTTTGAAGAATCACAAAATACTTTATATGTGTGCAAGAGATGCTAAAGTTGCTGCAAGTTCATATGGCATGGAGGTCAAGCAATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000428 GO:0001817 GO:0001819 GO:0002376 GO:0003674 GO:0003824 GO:0003899 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005666 GO:0005737 GO:0005829 GO:0006139 GO:0006351 GO:0006725 GO:0006807 GO:0006950 GO:0006952 GO:0006955 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:0032479 GO:0032481 GO:0032648 GO:0032728 GO:0032774 GO:0032991 GO:0034062 GO:0034641 GO:0034645 GO:0034654 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045087 GO:0046483 GO:0048518 GO:0050789 GO:0050896 GO:0051239 GO:0051240 GO:0055029 GO:0061695 GO:0065007 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 ko04623 ko05169 map00230 map00240 map01100 map03020 map04623 map05169

Pfam Domains

Protein Families

RNA_pol_Rpb1_1 RNA_pol_Rpb1_2 RNA_pol_Rpb1_3 RNA_pol_Rpb1_4 RNA_pol_Rpb1_5

Protein Analysis

118

Amino Acids

13.13

Weight (kDa)

8.99

Isoelectric Point (pI)

41.1

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RNA_pol_Rpb1_3	PF04983	24 - 70	5.3e-07	RNA polymerase Rpb1, domain 3

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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Orthologous Genes (Group: OG0004622)

Species	Orthologous Gene IDs
arabidopsis_thaliana	ATCG00170
malus_domestica	MD01G1014400.v1.1
pyrus_communis	pycom12397g00020 pycom12397g00340
rosa_chinensis	RchiOBHm_Chr4g0421201
rosa_laevigata	RLG00000000048 RLG00000000088 RLG00000000117 RLG00000000174 RLG00000000232 RLG00000000233 RLG00000000247 RLG00000000283 RLG00000000313 RLG00000000317 RLG00000000339
rosa_multiflora	Rmu_sc0001741.1_g000011
rosa_roxburghii	Rroxscaffold_2G00119090 Rroxscaffold_2G00119100
rosa_rugosa	RorugMtG0001800
rosa_samantha	Rh2AG294100 Rh2AG294200 Rh2DG057700 Rh2DG318000 Rh2DG318100 Rh4CG233400 Rh4CG244200 Rh7BG354800 Rh7CG382200
rosa_wichuraiana	Rw4G006960 Rw4G006970

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	89
AclWI	GGATC	2 cut(s)	89, 102
AcsI	RAATTY	1 cut(s)	202
AfaI	GTAC	2 cut(s)	15, 108
AfiI	CCNNNNNNNGG	1 cut(s)	89
AgsI	TTSAA	1 cut(s)	277
AluBI	AGCT	1 cut(s)	86
AluI	AGCT	1 cut(s)	86
Alw26I	GTCTC	1 cut(s)	84
AlwI	GGATC	2 cut(s)	89, 102
ApeKI	GCWGC	1 cut(s)	323
ApoI	RAATTY	1 cut(s)	202
Asp700I	GAANNNNTTC	1 cut(s)	221
AsuHPI	GGTGA	1 cut(s)	249
AsuII	TTCGAA	1 cut(s)	206
BamHI	GGATCC	1 cut(s)	94
BanII	GRGCYC	1 cut(s)	135
BbvI	GCAGC	1 cut(s)	310
BcoDI	GTCTC	1 cut(s)	84
BisI	GCNGC	1 cut(s)	324
BlsI	GCNGC	1 cut(s)	325
BmiI	GGNNCC	1 cut(s)	96
BmsI	GCATC	1 cut(s)	301
BpmI	CTGGAG	1 cut(s)	66
Bpu14I	TTCGAA	1 cut(s)	206
BpuEI	CTTGAG	1 cut(s)	18
BsaJI	CCNNGG	1 cut(s)	160
Bsc4I	CCNNNNNNNGG	1 cut(s)	89
BseDI	CCNNGG	1 cut(s)	160
BseLI	CCNNNNNNNGG	1 cut(s)	89
BseXI	GCAGC	1 cut(s)	310
BslI	CCNNNNNNNGG	1 cut(s)	89
BsmAI	GTCTC	1 cut(s)	84
Bsp119I	TTCGAA	1 cut(s)	206
Bsp1286I	GDGCHC	1 cut(s)	135
Bsp143I	GATC	1 cut(s)	94
BspLI	GGNNCC	1 cut(s)	96
BspPI	GGATC	2 cut(s)	89, 102
BspT104I	TTCGAA	1 cut(s)	206
BssECI	CCNNGG	1 cut(s)	160
BssMI	GATC	1 cut(s)	94
BstAPI	GCANNNNNTGC	1 cut(s)	311
BstBI	TTCGAA	1 cut(s)	206
BstKTI	GATC	1 cut(s)	97
BstMAI	GTCTC	1 cut(s)	84
BstMBI	GATC	1 cut(s)	94
BstMWI	GCNNNNNNNGC	4 cut(s)	130, 156, 311, 320
BstV1I	GCAGC	1 cut(s)	310
BstX2I	RGATCY	1 cut(s)	94
BstYI	RGATCY	1 cut(s)	94
Csp6I	GTAC	2 cut(s)	14, 107
CviAII	CATG	2 cut(s)	11, 340
CviJI	RGCY	5 cut(s)	5, 32, 44, 86, 133
CviKI_1	RGCY	5 cut(s)	5, 32, 44, 86, 133
CviQI	GTAC	2 cut(s)	14, 107
DpnI	GATC	1 cut(s)	96
DpnII	GATC	1 cut(s)	94
Eco24I	GRGCYC	1 cut(s)	135
EcoT38I	GRGCYC	1 cut(s)	135
FaeI	CATG	2 cut(s)	14, 343
FalI	AAGNNNNNCTT	2 cut(s)	108, 140
FatI	CATG	2 cut(s)	10, 339
FauNDI	CATATG	1 cut(s)	334
Fnu4HI	GCNGC	1 cut(s)	324
FriOI	GRGCYC	1 cut(s)	135
Fsp4HI	GCNGC	1 cut(s)	324
GluI	GCNGC	1 cut(s)	324
GsuI	CTGGAG	1 cut(s)	66
Hin1II	CATG	2 cut(s)	14, 343
HinfI	GANTC	4 cut(s)	70, 154, 208, 280
HphI	GGTGA	1 cut(s)	249
Hpy166II	GTNNAC	1 cut(s)	50
Hpy188III	TCNNGA	1 cut(s)	226
Hpy8I	GTNNAC	1 cut(s)	50
HpyCH4V	TGCA	3 cut(s)	173, 305, 326
HpyF10VI	GCNNNNNNNGC	4 cut(s)	130, 156, 311, 320
Hsp92II	CATG	2 cut(s)	14, 343
Kzo9I	GATC	1 cut(s)	94
LpnPI	CCDG	2 cut(s)	96, 136
Lsp1109I	GCAGC	1 cut(s)	310
LweI	GCATC	1 cut(s)	301
MalI	GATC	1 cut(s)	96
MboI	GATC	1 cut(s)	94
MboII	GAAGA	2 cut(s)	227, 289
MflI	RGATCY	1 cut(s)	94
MhlI	GDGCHC	1 cut(s)	135
MluCI	AATT	2 cut(s)	202, 218
MnlI	CCTC	4 cut(s)	22, 34, 155, 337
MroXI	GAANNNNTTC	1 cut(s)	221
MseI	TTAA	1 cut(s)	143
MslI	CAYNNNNRTG	1 cut(s)	262
MwoI	GCNNNNNNNGC	4 cut(s)	130, 156, 311, 320
NdeI	CATATG	1 cut(s)	334
NdeII	GATC	1 cut(s)	94
NlaIII	CATG	2 cut(s)	14, 343
NlaIV	GGNNCC	1 cut(s)	96
NmeAIII	GCCGAG	1 cut(s)	185
NspV	TTCGAA	1 cut(s)	206
PdmI	GAANNNNTTC	1 cut(s)	221
PfeI	GAWTC	4 cut(s)	70, 154, 208, 280
PflMI	CCANNNNNTGG	1 cut(s)	89
PkrI	GCNGC	1 cut(s)	325
PspN4I	GGNNCC	1 cut(s)	96
PsuI	RGATCY	1 cut(s)	94
RsaI	GTAC	2 cut(s)	15, 108
RsaNI	GTAC	2 cut(s)	14, 107
RseI	CAYNNNNRTG	1 cut(s)	262
SaqAI	TTAA	1 cut(s)	143
SatI	GCNGC	1 cut(s)	324
Sau3AI	GATC	1 cut(s)	94
SduI	GDGCHC	1 cut(s)	135
SetI	ASST	5 cut(s)	19, 88, 166, 182, 348
SfaNI	GCATC	1 cut(s)	301
SfuI	TTCGAA	1 cut(s)	206
SmiMI	CAYNNNNRTG	1 cut(s)	262
SmlI	CTYRAG	1 cut(s)	33
SmoI	CTYRAG	1 cut(s)	33
Sse9I	AATT	2 cut(s)	202, 218
TaqI	TCGA	2 cut(s)	206, 225
TasI	AATT	2 cut(s)	202, 218
TfiI	GAWTC	4 cut(s)	70, 154, 208, 280
Tru1I	TTAA	1 cut(s)	143
Tru9I	TTAA	1 cut(s)	143
TseI	GCWGC	1 cut(s)	323
TspDTI	ATGAA	3 cut(s)	83, 230, 321
TspGWI	ACGGA	2 cut(s)	94, 177
Van91I	CCANNNNNTGG	1 cut(s)	89
XapI	RAATTY	1 cut(s)	202
XmnI	GAANNNNTTC	1 cut(s)	221

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