Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0002901

Physical Location & Seq

Genomic Coordinates Forward (+)

10690077 .. 10692836

Gene Structure 2760 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG126300.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 483 bp

ATGTCAATTCATGAAAGAAAAGCTAGTTTAAAAGAGTTCTACAGTGTAATATTTCCCTCATTATTGCAACTTCAAAGGGGAATGACTGATGTAGAAGACCGGAAACAGAAAGAAATCTGTTCCAAGTACAAGAGAAAAGATGAGACGGACAAAGGAAAGCTCTCCGAAATTGAGTTGGAGCGAGAAGAAGAATGTGGTATTTGTATGGAGATGAACAGCAAGGTCGTATTGCCCAATTGCAGTCACTCTTTGTGTATAAAGTGCTATCGGAACTGGCGGACACGCTCTCAGTCCTGCCCCTTCTGCCGAGACAGCCTCAAAAGAGTTGACTCATGTGAACTTTGGATCTACACTGGCAACAATGAGATTGTTGACATGTCTGCAATCTCTAGGGAGAATTTGAAGAGACTATTTATCTACATTGATAAGCTGCCTCTTCTTGTTCCAAAGCATGGGGTTGTTTCTTATGACCTTTATCGATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001101 GO:0003674 GO:0003824 GO:0004842 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0006464 GO:0006508 GO:0006511 GO:0006807 GO:0006950 GO:0006970 GO:0008150 GO:0008152 GO:0009056 GO:0009057 GO:0009628 GO:0009651 GO:0009719 GO:0009725 GO:0009737 GO:0009787 GO:0009789 GO:0009966 GO:0009967 GO:0009987 GO:0010033 GO:0010646 GO:0010647 GO:0016567 GO:0016740 GO:0019538 GO:0019787 GO:0019941 GO:0023051 GO:0023056 GO:0030163 GO:0032446 GO:0033993 GO:0036211 GO:0042221 GO:0043170 GO:0043412 GO:0043632 GO:0044237 GO:0044238 GO:0044248 GO:0044257 GO:0044260 GO:0044265 GO:0044267 GO:0044424 GO:0044444 GO:0044464 GO:0048518 GO:0048522 GO:0048583 GO:0048584 GO:0050789 GO:0050794 GO:0050896 GO:0051603 GO:0061630 GO:0061659 GO:0065007 GO:0070647 GO:0071704 GO:0097305 GO:0140096 GO:1901419 GO:1901421 GO:1901564 GO:1901565 GO:1901575 GO:1901700 GO:1905957 GO:1905959

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

zf-C3HC4_3

Protein Analysis

160

Amino Acids

18.9

Weight (kDa)

8.54

Isoelectric Point (pI)

58.93

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
zf-C3HC4_3	PF13920	62 - 108	3.4e-10	Zinc finger, C3HC4 type (RING finger)
zf-RING_2	PF13639	64 - 103	2.8e-08	Ring finger domain
zf-RING_5	PF14634	64 - 103	2.3e-06	zinc-RING finger domain
zf-C3HC4_2	PF13923	64 - 102	2.7e-06	Zinc finger, C3HC4 type (RING finger)
zf-C3HC4	PF00097	65 - 102	1e-06	Zinc finger, C3HC4 type (RING finger)

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0002901)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G01520 AT5G01520
fragaria_vesca	FvH4_3g04920 FvH4_6g11510 FvH4_6g11510
malus_domestica	MD04G1151400.v1.1 MD05G1314700.v1.1 MD10G1296100.v1.1 MD12G1165500.v1.1
prunus_persica	Prupe.4G044500_v2.0.a1 Prupe.6G276500_v2.0.a1 Prupe.6G276500_v2.0.a1 Prupe.6G276500_v2.0.a1
pyrus_communis	pycom04g13730 pycom05g29250 pycom10g24860 pycom12g15810
rosa_chinensis	RchiOBHm_Chr3g0463221 RchiOBHm_Chr5g0008081
rosa_laevigata	RLG00000024801 RLG00000031534
rosa_multiflora	Rmu_sc0001626.1_g000003 Rmu_sc0004643.1_g000001 Rmu_sc0017465.1_g000004
rosa_roxburghii	Rroxscaffold_1G00068400 Rroxscaffold_6G00416790
rosa_rugosa	Rorug03G0062500 Rorug03G0062500 Rorug04G0433300
rosa_samantha	Rh3AG120700 Rh3BG125100 Rh3CG127200 Rh3DG126300 Rh5BG058100 Rh5CG068200 Rh5DG057300
rosa_wichuraiana	Rw3G010250 Rw5G005930

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	452
AciI	CCGC	1 cut(s)	277
AclWI	GGATC	1 cut(s)	353
AcsI	RAATTY	1 cut(s)	397
AfaI	GTAC	1 cut(s)	128
AfiI	CCNNNNNNNGG	1 cut(s)	452
AflIII	ACRYGT	1 cut(s)	375
AgsI	TTSAA	2 cut(s)	74, 403
AluBI	AGCT	3 cut(s)	23, 160, 430
AluI	AGCT	3 cut(s)	23, 160, 430
Alw26I	GTCTC	3 cut(s)	137, 303, 400
AlwI	GGATC	1 cut(s)	353
ApeKI	GCWGC	1 cut(s)	430
ApoI	RAATTY	1 cut(s)	397
BbsI	GAAGAC	1 cut(s)	102
BbvI	GCAGC	1 cut(s)	417
BcoDI	GTCTC	3 cut(s)	137, 303, 400
BfaI	CTAG	2 cut(s)	24, 390
BfmI	CTRYAG	1 cut(s)	40
BisI	GCNGC	1 cut(s)	431
BlsI	GCNGC	1 cut(s)	432
BpiI	GAAGAC	1 cut(s)	102
BplI	GAGNNNNNCTC	2 cut(s)	300, 332
Bsa29I	ATCGAT	1 cut(s)	478
BsaWI	WCCGGW	1 cut(s)	99
Bsc4I	CCNNNNNNNGG	1 cut(s)	452
Bse1I	ACTGG	2 cut(s)	278, 358
BseCI	ATCGAT	1 cut(s)	478
BseLI	CCNNNNNNNGG	1 cut(s)	452
BseMII	CTCAG	1 cut(s)	302
BseNI	ACTGG	2 cut(s)	278, 358
BseXI	GCAGC	1 cut(s)	417
BshVI	ATCGAT	1 cut(s)	478
BsiSI	CCGG	1 cut(s)	100
BslI	CCNNNNNNNGG	1 cut(s)	452
BsmAI	GTCTC	3 cut(s)	137, 303, 400
BsmBI	CGTCTC	1 cut(s)	137
Bsp143I	GATC	1 cut(s)	345
BspACI	CCGC	1 cut(s)	277
BspCNI	CTCAG	1 cut(s)	301
BspDI	ATCGAT	1 cut(s)	478
BspHI	TCATGA	1 cut(s)	10
BspPI	GGATC	1 cut(s)	353
BsrI	ACTGG	2 cut(s)	278, 358
BssMI	GATC	1 cut(s)	345
Bst4CI	ACNGT	1 cut(s)	44
Bst6I	CTCTTC	2 cut(s)	398, 441
BstDEI	CTNAG	1 cut(s)	288
BstKTI	GATC	1 cut(s)	348
BstMAI	GTCTC	3 cut(s)	137, 303, 400
BstMBI	GATC	1 cut(s)	345
BstMWI	GCNNNNNNNGC	2 cut(s)	303, 312
BstNSI	RCATGY	1 cut(s)	379
BstSFI	CTRYAG	1 cut(s)	40
BstV1I	GCAGC	1 cut(s)	417
BstV2I	GAAGAC	1 cut(s)	102
BstX2I	RGATCY	1 cut(s)	345
BstYI	RGATCY	1 cut(s)	345
Bsu15I	ATCGAT	1 cut(s)	478
BsuTUI	ATCGAT	1 cut(s)	478
BtsIMutI	CAGTG	2 cut(s)	49, 351
CciI	TCATGA	1 cut(s)	10
ClaI	ATCGAT	1 cut(s)	478
Csp6I	GTAC	1 cut(s)	127
CviAII	CATG	4 cut(s)	11, 333, 376, 452
CviJI	RGCY	4 cut(s)	23, 160, 315, 430
CviKI_1	RGCY	4 cut(s)	23, 160, 315, 430
CviQI	GTAC	1 cut(s)	127
DdeI	CTNAG	1 cut(s)	288
DpnI	GATC	1 cut(s)	347
DpnII	GATC	1 cut(s)	345
DraI	TTTAAA	1 cut(s)	30
Eam1104I	CTCTTC	2 cut(s)	398, 441
EarI	CTCTTC	2 cut(s)	398, 441
EciI	GGCGGA	1 cut(s)	292
Esp3I	CGTCTC	1 cut(s)	137
FaeI	CATG	4 cut(s)	14, 336, 379, 455
FaiI	YATR	7 cut(s)	12, 206, 257, 334, 377, 453, 468
FatI	CATG	4 cut(s)	10, 332, 375, 451
Fnu4HI	GCNGC	1 cut(s)	431
Fsp4HI	GCNGC	1 cut(s)	431
FspBI	CTAG	2 cut(s)	24, 390
GluI	GCNGC	1 cut(s)	431
HapII	CCGG	1 cut(s)	100
Hin1II	CATG	4 cut(s)	14, 336, 379, 455
HincII	GTYRAC	2 cut(s)	328, 373
HindII	GTYRAC	2 cut(s)	328, 373
HinfI	GANTC	1 cut(s)	329
HpaII	CCGG	1 cut(s)	100
Hpy166II	GTNNAC	3 cut(s)	328, 338, 373
Hpy188I	TCNGA	2 cut(s)	166, 270
Hpy188III	TCNNGA	1 cut(s)	11
Hpy8I	GTNNAC	3 cut(s)	328, 338, 373
HpyAV	CCTTC	1 cut(s)	310
HpyCH4III	ACNGT	1 cut(s)	44
HpyCH4V	TGCA	3 cut(s)	67, 240, 383
HpyF10VI	GCNNNNNNNGC	2 cut(s)	303, 312
HpyF3I	CTNAG	1 cut(s)	288
Hsp92II	CATG	4 cut(s)	14, 336, 379, 455
Kzo9I	GATC	1 cut(s)	345
LmnI	GCTCC	1 cut(s)	178
LpnPI	CCDG	4 cut(s)	113, 259, 307, 339
Lsp1109I	GCAGC	1 cut(s)	417
MaeI	CTAG	2 cut(s)	24, 390
MaeIII	GTNAC	1 cut(s)	242
MalI	GATC	1 cut(s)	347
MboI	GATC	1 cut(s)	345
MboII	GAAGA	5 cut(s)	107, 197, 200, 415, 428
MfeI	CAATTG	1 cut(s)	235
MflI	RGATCY	1 cut(s)	345
MluCI	AATT	4 cut(s)	6, 168, 235, 397
MlyI	GAGTC	1 cut(s)	323
MmeI	TCCRAC	1 cut(s)	156
MnlI	CCTC	3 cut(s)	67, 326, 444
MseI	TTAA	1 cut(s)	29
MspI	CCGG	1 cut(s)	100
MunI	CAATTG	1 cut(s)	235
MwoI	GCNNNNNNNGC	2 cut(s)	303, 312
NdeII	GATC	1 cut(s)	345
NlaIII	CATG	4 cut(s)	14, 336, 379, 455
NmeAIII	GCCGAG	1 cut(s)	332
NmuCI	GTSAC	1 cut(s)	242
NspI	RCATGY	1 cut(s)	379
PagI	TCATGA	1 cut(s)	10
PciI	ACATGT	1 cut(s)	375
PflMI	CCANNNNNTGG	1 cut(s)	452
PkrI	GCNGC	1 cut(s)	432
PleI	GAGTC	1 cut(s)	323
PpsI	GAGTC	1 cut(s)	323
PscI	ACATGT	1 cut(s)	375
PsuI	RGATCY	1 cut(s)	345
RsaI	GTAC	1 cut(s)	128
RsaNI	GTAC	1 cut(s)	127
SaqAI	TTAA	1 cut(s)	29
SatI	GCNGC	1 cut(s)	431
Sau3AI	GATC	1 cut(s)	345
SchI	GAGTC	1 cut(s)	323
SetI	ASST	5 cut(s)	25, 162, 225, 432, 474
SfcI	CTRYAG	1 cut(s)	40
Sse9I	AATT	4 cut(s)	6, 168, 235, 397
SsiI	CCGC	1 cut(s)	277
SspI	AATATT	1 cut(s)	51
SspMI	CTAG	2 cut(s)	24, 390
TaaI	ACNGT	1 cut(s)	44
TaqI	TCGA	1 cut(s)	478
TasI	AATT	4 cut(s)	6, 168, 235, 397
TatI	WGTACW	1 cut(s)	126
Tru1I	TTAA	1 cut(s)	29
Tru9I	TTAA	1 cut(s)	29
TscAI	CASTG	2 cut(s)	49, 358
TseFI	GTSAC	1 cut(s)	242
TseI	GCWGC	1 cut(s)	430
Tsp45I	GTSAC	1 cut(s)	242
TspDTI	ATGAA	2 cut(s)	27, 227
TspGWI	ACGGA	1 cut(s)	161
TspRI	CASTG	2 cut(s)	49, 358
Van91I	CCANNNNNTGG	1 cut(s)	452
XapI	RAATTY	1 cut(s)	397
XceI	RCATGY	1 cut(s)	379
XspI	CTAG	2 cut(s)	24, 390

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