Basic Information

Type: gene

Biological Identity

Species

rosa_roxburghii

Chromosome

GWHEROQ00000002

Orthogroup ID

OG0004175

Physical Location & Seq

Genomic Coordinates Reverse (-)

41595264 .. 41596641

Gene Structure 1378 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rroxscaffold_2G00115380.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 531 bp

ATGTTTTTCCATATAGTCTTGGAGAGGAACATGCAGCTTCACCCTCGTCACTTTGGCCGCAATCTCCGGGAGAATTTGGTAGCCAAGCTCATGAAAGATGTTGAAGGGACTTGCAGTGGCCAACATGGGTTTGTGGTTGCCATTACGGGGATTGAGAACATCGGAAAAGGGCTGATTCGTGATGGCACAGGGTTTGTTTCATTTCCAGTCAAGTATCAGTGTGTTGTTTTCAGACCATTTAAAGGAGAGATCTTAGAAGCCGTGGTTACAATGGTGAACAAGATGGGTTTTTTTGCTGAGGCTGGTCCTGTTCAAATCTTTGTTTCGAACCATTTGATACCGGATGATATGGAGTTTCAGTCTGGTGATATGCCAAACTATACAACGTCAGACGGATCTGTTAAGATTCAGAAAGATAGCGAAGTTCGGTTGAAGATAATTGGAACCCGAGTGGATGCAACAGAAATTTTCTGCATTGGTACTATCAAAGATGATTTCTTGGGTGTCATAAACGATCCTGCGAGTGTTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000291 GO:0000428 GO:0000932 GO:0000956 GO:0003674 GO:0003676 GO:0003677 GO:0003697 GO:0003723 GO:0003727 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005665 GO:0005737 GO:0006139 GO:0006351 GO:0006352 GO:0006366 GO:0006367 GO:0006401 GO:0006402 GO:0006417 GO:0006446 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0009056 GO:0009057 GO:0009058 GO:0009059 GO:0009889 GO:0009891 GO:0009892 GO:0009893 GO:0009894 GO:0009896 GO:0009987 GO:0010467 GO:0010468 GO:0010556 GO:0010557 GO:0010604 GO:0010605 GO:0010608 GO:0010628 GO:0010629 GO:0016070 GO:0016071 GO:0016591 GO:0018130 GO:0019219 GO:0019222 GO:0019438 GO:0019439 GO:0030880 GO:0031323 GO:0031325 GO:0031326 GO:0031328 GO:0031329 GO:0031331 GO:0031369 GO:0031974 GO:0031981 GO:0032268 GO:0032270 GO:0032774 GO:0032991 GO:0034248 GO:0034250 GO:0034641 GO:0034645 GO:0034654 GO:0034655 GO:0035770 GO:0036464 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044248 GO:0044249 GO:0044260 GO:0044265 GO:0044270 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045727 GO:0045935 GO:0045948 GO:0046483 GO:0046700 GO:0048518 GO:0048519 GO:0048522 GO:0050789 GO:0050794 GO:0051171 GO:0051173 GO:0051246 GO:0051247 GO:0051252 GO:0051254 GO:0055029 GO:0060211 GO:0060213 GO:0060255 GO:0061013 GO:0061014 GO:0061695 GO:0065007 GO:0070013 GO:0071704 GO:0080090 GO:0090304 GO:0097159 GO:0097659 GO:1900151 GO:1900153 GO:1901360 GO:1901361 GO:1901362 GO:1901363 GO:1901575 GO:1901576 GO:1902494 GO:1903311 GO:1903313 GO:1990234 GO:1990904 GO:2000112

KEGG Pathways

Metabolic & Signaling

ko00230 ko00240 ko01100 ko03020 ko05016 ko05169 map00230 map00240 map01100 map03020 map05016 map05169

Pfam Domains

Protein Families

S1 SHS2_Rpb7-N

Protein Analysis

176

Amino Acids

19.55

Weight (kDa)

5.94

Isoelectric Point (pI)

27.12

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SHS2_Rpb7-N	PF03876	8 - 64	1e-14	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397
S1	PF00575	79 - 156	2.3e-14	S1 RNA binding domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

Font Size (px)

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0004175)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G59180
fragaria_vesca	FvH4_2g24550 FvH4_6g26920 FvH4_6g26920 FvH4_6g26920
malus_domestica	MD06G1239600.v1.1 MD14G1245600.v1.1
prunus_persica	Prupe.4G244700_v2.0.a1 Prupe.5G243500_v2.0.a1
pyrus_communis	pycom06g21510 pycom14g20650
rosa_chinensis	RchiOBHm_Chr2g0128671 RchiOBHm_Chr6g0292371
rosa_laevigata	RLG00000012035 RLG00000019016
rosa_multiflora	Rmu_sc0001354.1_g000012 Rmu_sc0003465.1_g000052 Rmu_sc0005514.1_g000001 Rmu_sc0023058.1_g000002
rosa_roxburghii	Rroxscaffold_2G00115380 Rroxscaffold_2G00115880 Rroxscaffold_7G00175130
rosa_rugosa	Rorug06G0226000
rosa_samantha	Rh2AG333500 Rh2BG341100 Rh2CG320100 Rh2DG357800 Rh6AG339300 Rh6BG346600 Rh6CG353400 Rh6DG339400
rosa_wichuraiana	Rw2G026920 Rw6G029530

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	58
AclWI	GGATC	2 cut(s)	403, 509
AcoI	YGGCCR	2 cut(s)	55, 118
AcsI	RAATTY	2 cut(s)	73, 465
AfaI	GTAC	1 cut(s)	481
AfiI	CCNNNNNNNGG	2 cut(s)	147, 242
AgsI	TTSAA	3 cut(s)	104, 314, 433
AluBI	AGCT	2 cut(s)	37, 88
AluI	AGCT	2 cut(s)	37, 88
AlwI	GGATC	2 cut(s)	403, 509
Ama87I	CYCGRG	1 cut(s)	447
AoxI	GGCC	2 cut(s)	55, 118
ApeKI	GCWGC	1 cut(s)	34
ApoI	RAATTY	2 cut(s)	73, 465
AspS9I	GGNCC	1 cut(s)	305
AsuC2I	CCSGG	1 cut(s)	68
AsuHPI	GGTGA	3 cut(s)	32, 286, 377
AsuII	TTCGAA	1 cut(s)	326
AvaI	CYCGRG	1 cut(s)	447
AvaII	GGWCC	1 cut(s)	305
BalI	TGGCCA	1 cut(s)	120
BbvCI	CCTCAGC	1 cut(s)	297
BbvI	GCAGC	1 cut(s)	46
BccI	CCATC	2 cut(s)	176, 277
BceAI	ACGGC	1 cut(s)	245
BcnI	CCSGG	1 cut(s)	68
BglII	AGATCT	1 cut(s)	249
BisI	GCNGC	2 cut(s)	35, 58
BlsI	GCNGC	2 cut(s)	36, 59
Bme1390I	CCNGG	1 cut(s)	68
Bme18I	GGWCC	1 cut(s)	305
BmeT110I	CYCGRG	1 cut(s)	447
BmgT120I	GGNCC	1 cut(s)	305
BmiI	GGNNCC	1 cut(s)	445
BmrFI	CCNGG	1 cut(s)	68
BmsI	GCATC	1 cut(s)	445
Bpu10I	CCTNAGC	1 cut(s)	297
Bpu14I	TTCGAA	1 cut(s)	326
BpuMI	CCSGG	1 cut(s)	68
BsaJI	CCNNGG	1 cut(s)	261
BsaWI	WCCGGW	1 cut(s)	340
BsaXI	ACNNNNNCTCC	2 cut(s)	344, 374
Bsc4I	CCNNNNNNNGG	2 cut(s)	147, 242
Bse1I	ACTGG	1 cut(s)	206
BseDI	CCNNGG	1 cut(s)	261
BseGI	GGATG	2 cut(s)	349, 460
BseLI	CCNNNNNNNGG	2 cut(s)	147, 242
BseMII	CTCAG	1 cut(s)	288
BseNI	ACTGG	1 cut(s)	206
BseXI	GCAGC	1 cut(s)	46
BshFI	GGCC	2 cut(s)	57, 120
BsiHKCI	CYCGRG	1 cut(s)	447
BsiSI	CCGG	2 cut(s)	67, 341
BslFI	GGGAC	1 cut(s)	121
BslI	CCNNNNNNNGG	2 cut(s)	147, 242
BsmFI	GGGAC	1 cut(s)	121
BsnI	GGCC	2 cut(s)	57, 120
BsoBI	CYCGRG	1 cut(s)	447
Bsp119I	TTCGAA	1 cut(s)	326
Bsp143I	GATC	3 cut(s)	249, 395, 514
BspACI	CCGC	1 cut(s)	58
BspANI	GGCC	2 cut(s)	57, 120
BspCNI	CTCAG	1 cut(s)	289
BspHI	TCATGA	1 cut(s)	90
BspLI	GGNNCC	1 cut(s)	445
BspPI	GGATC	2 cut(s)	403, 509
BspT104I	TTCGAA	1 cut(s)	326
BsrI	ACTGG	1 cut(s)	206
BssECI	CCNNGG	1 cut(s)	261
BssMI	GATC	3 cut(s)	249, 395, 514
BstBI	TTCGAA	1 cut(s)	326
BstDEI	CTNAG	2 cut(s)	253, 297
BstDSI	CCRYGG	1 cut(s)	261
BstF5I	GGATG	2 cut(s)	349, 460
BstKTI	GATC	3 cut(s)	252, 398, 517
BstMBI	GATC	3 cut(s)	249, 395, 514
BstNSI	RCATGY	1 cut(s)	34
BstSCI	CCNGG	1 cut(s)	66
BstV1I	GCAGC	1 cut(s)	46
BstX2I	RGATCY	2 cut(s)	249, 395
BstYI	RGATCY	2 cut(s)	249, 395
BsuRI	GGCC	2 cut(s)	57, 120
BtgI	CCRYGG	1 cut(s)	261
BtsCI	GGATG	2 cut(s)	349, 460
BtsI	GCAGTG	1 cut(s)	121
BtsIMutI	CAGTG	2 cut(s)	121, 224
CciI	TCATGA	1 cut(s)	90
Cfr13I	GGNCC	1 cut(s)	305
Csp6I	GTAC	1 cut(s)	480
CviAII	CATG	3 cut(s)	31, 91, 125
CviJI	RGCY	8 cut(s)	37, 57, 83, 88, 120, 172, 260, 302
CviKI_1	RGCY	8 cut(s)	37, 57, 83, 88, 120, 172, 260, 302
CviQI	GTAC	1 cut(s)	480
DdeI	CTNAG	2 cut(s)	253, 297
DpnI	GATC	3 cut(s)	251, 397, 516
DpnII	GATC	3 cut(s)	249, 395, 514
DraI	TTTAAA	1 cut(s)	241
EaeI	YGGCCR	2 cut(s)	55, 118
Eco47I	GGWCC	1 cut(s)	305
Eco88I	CYCGRG	1 cut(s)	447
FaeI	CATG	3 cut(s)	34, 94, 128
FaiI	YATR	9 cut(s)	12, 14, 32, 92, 126, 350, 371, 381, 509
FaqI	GGGAC	1 cut(s)	121
FatI	CATG	3 cut(s)	30, 90, 124
Fnu4HI	GCNGC	2 cut(s)	35, 58
FokI	GGATG	2 cut(s)	356, 467
Fsp4HI	GCNGC	2 cut(s)	35, 58
GluI	GCNGC	2 cut(s)	35, 58
HaeIII	GGCC	2 cut(s)	57, 120
HapII	CCGG	2 cut(s)	67, 341
Hin1II	CATG	3 cut(s)	34, 94, 128
HinfI	GANTC	2 cut(s)	175, 406
HpaII	CCGG	2 cut(s)	67, 341
HphI	GGTGA	3 cut(s)	32, 286, 377
Hpy166II	GTNNAC	1 cut(s)	277
Hpy188I	TCNGA	4 cut(s)	164, 233, 391, 411
Hpy188III	TCNNGA	2 cut(s)	91, 179
Hpy8I	GTNNAC	1 cut(s)	277
HpyAV	CCTTC	1 cut(s)	98
HpyCH4IV	ACGT	1 cut(s)	386
HpyCH4V	TGCA	4 cut(s)	34, 114, 458, 474
HpyF3I	CTNAG	2 cut(s)	253, 297
HpySE526I	ACGT	1 cut(s)	386
Hsp92II	CATG	3 cut(s)	34, 94, 128
Kzo9I	GATC	3 cut(s)	249, 395, 514
LpnPI	CCDG	7 cut(s)	80, 174, 219, 288, 321, 348, 354
Lsp1109I	GCAGC	1 cut(s)	46
LweI	GCATC	1 cut(s)	445
MaeII	ACGT	1 cut(s)	386
MaeIII	GTNAC	2 cut(s)	47, 265
MalI	GATC	3 cut(s)	251, 397, 516
MboI	GATC	3 cut(s)	249, 395, 514
MboII	GAAGA	1 cut(s)	445
MflI	RGATCY	2 cut(s)	249, 395
MlsI	TGGCCA	1 cut(s)	120
MluCI	AATT	3 cut(s)	73, 438, 465
MluNI	TGGCCA	1 cut(s)	120
MnlI	CCTC	3 cut(s)	18, 54, 292
Mox20I	TGGCCA	1 cut(s)	120
MscI	TGGCCA	1 cut(s)	120
MseI	TTAA	2 cut(s)	240, 402
Msp20I	TGGCCA	1 cut(s)	120
MspI	CCGG	2 cut(s)	67, 341
MspR9I	CCNGG	1 cut(s)	68
NciI	CCSGG	1 cut(s)	68
NdeII	GATC	3 cut(s)	249, 395, 514
NlaIII	CATG	3 cut(s)	34, 94, 128
NlaIV	GGNNCC	1 cut(s)	445
NmuCI	GTSAC	1 cut(s)	47
NspI	RCATGY	1 cut(s)	34
NspV	TTCGAA	1 cut(s)	326
PagI	TCATGA	1 cut(s)	90
PfeI	GAWTC	2 cut(s)	175, 406
PfoI	TCCNGGA	1 cut(s)	66
PkrI	GCNGC	2 cut(s)	36, 59
PspN4I	GGNNCC	1 cut(s)	445
PspPI	GGNCC	1 cut(s)	305
PsuI	RGATCY	2 cut(s)	249, 395
RsaI	GTAC	1 cut(s)	481
RsaNI	GTAC	1 cut(s)	480
SaqAI	TTAA	2 cut(s)	240, 402
SatI	GCNGC	2 cut(s)	35, 58
Sau3AI	GATC	3 cut(s)	249, 395, 514
Sau96I	GGNCC	1 cut(s)	305
ScrFI	CCNGG	1 cut(s)	68
SetI	ASST	3 cut(s)	39, 90, 389
SfaNI	GCATC	1 cut(s)	445
SfuI	TTCGAA	1 cut(s)	326
SinI	GGWCC	1 cut(s)	305
Sse9I	AATT	3 cut(s)	73, 438, 465
SsiI	CCGC	1 cut(s)	58
StyD4I	CCNGG	1 cut(s)	66
TaiI	ACGT	1 cut(s)	389
TaqI	TCGA	1 cut(s)	326
TasI	AATT	3 cut(s)	73, 438, 465
TauI	GCSGC	1 cut(s)	60
TfiI	GAWTC	2 cut(s)	175, 406
Tru1I	TTAA	2 cut(s)	240, 402
Tru9I	TTAA	2 cut(s)	240, 402
TscAI	CASTG	2 cut(s)	121, 224
TseFI	GTSAC	1 cut(s)	47
TseI	GCWGC	1 cut(s)	34
Tsp45I	GTSAC	1 cut(s)	47
TspDTI	ATGAA	2 cut(s)	107, 189
TspGWI	ACGGA	1 cut(s)	408
TspRI	CASTG	2 cut(s)	121, 224
VpaK11BI	GGWCC	1 cut(s)	305
XapI	RAATTY	2 cut(s)	73, 465
XceI	RCATGY	1 cut(s)	34

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