Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5B

Orthogroup ID

OG0002317

Physical Location & Seq

Genomic Coordinates Reverse (-)

54942893 .. 54945089

Gene Structure 2197 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5BG355100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 369 bp

ATGGACTCGAAGACGGAAAACGTTTTGGAGATGGAGTCATGCCTGGGTCTTCAACTAGGAGGAAACTCTCAATATTTGAAGCTTGAAATTTGCCATATTGCTTCTCTTTGTGATAAATTGGAGTTTCCTTTGTGTTATGGGTATTGGAAAAAGTATGCAGATCATGAGGCACATTTTGGTGTTATTGATAAAATTGTGGAGGTTTATGAACGAGCAGTTCAAGCTGTTACCTATTCAGTTGACATTTGGTTGCATTACTGCACATTTGCCACAACTACTTTTGGAGATCCAGACACTATCAGAAGTGCATCATTATGCAAATTGCTGCTGGGAAGATCTCGTCCAGTTAAGGGCTTAGATGGCCTCTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000243 GO:0000245 GO:0000375 GO:0000377 GO:0000395 GO:0000398 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005681 GO:0005684 GO:0005685 GO:0006139 GO:0006376 GO:0006396 GO:0006397 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0008380 GO:0009987 GO:0010467 GO:0016043 GO:0016070 GO:0016071 GO:0022607 GO:0022613 GO:0022618 GO:0030532 GO:0032991 GO:0034622 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043933 GO:0044085 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0045292 GO:0046483 GO:0065003 GO:0071004 GO:0071010 GO:0071704 GO:0071826 GO:0071840 GO:0090304 GO:0097525 GO:0120114 GO:1901360 GO:1990904

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

No domains found.

Protein Analysis

122

Amino Acids

13.76

Weight (kDa)

5.48

Isoelectric Point (pI)

41.05

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HAT_PRP39_N	PF23240	41 - 98	1.1e-22	PRP39 N-terminal HAT repeat
HAT_Syf1_CNRKL1_N	PF23233	48 - 93	8.9e-06	Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat
HAT_PRP39_C	PF23241	49 - 93	5.5e-06	PRP39 C-terminal HAT 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)

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Publication-ready

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Orthologous Genes (Group: OG0002317)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G04080 AT1G04080 AT1G04080 AT1G04080 AT1G04080
fragaria_vesca	FvH4_2g20550
malus_domestica	MD00G1060100.v1.1
prunus_persica	Prupe.8G215900_v2.0.a1 Prupe.8G215900_v2.0.a1 Prupe.8G215900_v2.0.a1 Prupe.8G215900_v2.0.a1
pyrus_communis	pycom05g17390 pycom10g15270
rosa_chinensis	RchiOBHm_Chr1g0327141 RchiOBHm_Chr6g0282561 RchiOBHm_Chr6g0286711
rosa_laevigata	RLG00000007391 RLG00000012550 RLG00000030995
rosa_multiflora	Rmu_co8283097.1_g000001 Rmu_co8332197.1_g000001 Rmu_sc0001468.1_g000022
rosa_roxburghii	Rroxscaffold_1G00034270 Rroxscaffold_1G00060390 Rroxscaffold_7G00182090
rosa_rugosa	Rorug05G0468800 Rorug06G0182100 Rorug06G0182200
rosa_samantha	Rh2CG306300 Rh5BG355000 Rh5BG355100 Rh5BG357900 Rh6AG023000 Rh6AG294900 Rh6BG204700 Rh6BG298100 Rh6BG298200 Rh6CG298600 Rh6DG290600
rosa_wichuraiana	Rw1G013170 Rw5G035150 Rw6G025370

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AclI	AACGTT	1 cut(s)	21
AclWI	GGATC	1 cut(s)	281
AcsI	RAATTY	1 cut(s)	87
AfiI	CCNNNNNNNGG	1 cut(s)	350
AgsI	TTSAA	4 cut(s)	53, 79, 86, 221
AjnI	CCWGG	1 cut(s)	42
AluBI	AGCT	2 cut(s)	82, 224
AluI	AGCT	2 cut(s)	82, 224
AlwI	GGATC	1 cut(s)	281
AoxI	GGCC	1 cut(s)	361
ApeKI	GCWGC	1 cut(s)	325
ApoI	RAATTY	1 cut(s)	87
BbsI	GAAGAC	2 cut(s)	17, 41
BbvI	GCAGC	1 cut(s)	312
BccI	CCATC	2 cut(s)	25, 353
BciT130I	CCWGG	1 cut(s)	44
BfaI	CTAG	2 cut(s)	56, 367
BglII	AGATCT	1 cut(s)	335
BisI	GCNGC	1 cut(s)	326
BlsI	GCNGC	1 cut(s)	327
Bme1390I	CCNGG	1 cut(s)	44
BmrFI	CCNGG	1 cut(s)	44
BmsI	GCATC	1 cut(s)	317
BpiI	GAAGAC	2 cut(s)	17, 41
BsaJI	CCNNGG	1 cut(s)	43
BsaXI	ACNNNNNCTCC	2 cut(s)	20, 50
Bsc4I	CCNNNNNNNGG	1 cut(s)	350
Bse1I	ACTGG	1 cut(s)	344
BseBI	CCWGG	1 cut(s)	44
BseDI	CCNNGG	1 cut(s)	43
BseLI	CCNNNNNNNGG	1 cut(s)	350
BseNI	ACTGG	1 cut(s)	344
BseXI	GCAGC	1 cut(s)	312
BseYI	CCCAGC	1 cut(s)	328
BsgI	GTGCAG	1 cut(s)	244
BshFI	GGCC	1 cut(s)	363
BslI	CCNNNNNNNGG	1 cut(s)	350
BsnI	GGCC	1 cut(s)	363
Bsp143I	GATC	3 cut(s)	160, 286, 335
BspANI	GGCC	1 cut(s)	363
BspHI	TCATGA	1 cut(s)	163
BspPI	GGATC	1 cut(s)	281
BsrI	ACTGG	1 cut(s)	344
BssECI	CCNNGG	1 cut(s)	43
BssMI	GATC	3 cut(s)	160, 286, 335
Bst2UI	CCWGG	1 cut(s)	44
BstDEI	CTNAG	1 cut(s)	355
BstKTI	GATC	3 cut(s)	163, 289, 338
BstMBI	GATC	3 cut(s)	160, 286, 335
BstMWI	GCNNNNNNNGC	2 cut(s)	221, 360
BstNI	CCWGG	1 cut(s)	44
BstSCI	CCNGG	1 cut(s)	42
BstV1I	GCAGC	1 cut(s)	312
BstV2I	GAAGAC	2 cut(s)	17, 41
BstX2I	RGATCY	2 cut(s)	286, 335
BstYI	RGATCY	2 cut(s)	286, 335
BsuRI	GGCC	1 cut(s)	363
CciI	TCATGA	1 cut(s)	163
CviAII	CATG	2 cut(s)	39, 164
CviJI	RGCY	4 cut(s)	82, 224, 354, 363
CviKI_1	RGCY	4 cut(s)	82, 224, 354, 363
DdeI	CTNAG	1 cut(s)	355
DpnI	GATC	3 cut(s)	162, 288, 337
DpnII	GATC	3 cut(s)	160, 286, 335
EcoRII	CCWGG	1 cut(s)	42
FaeI	CATG	2 cut(s)	42, 167
FaiI	YATR	7 cut(s)	40, 96, 138, 156, 165, 207, 316
FatI	CATG	2 cut(s)	38, 163
Fnu4HI	GCNGC	1 cut(s)	326
Fsp4HI	GCNGC	1 cut(s)	326
FspBI	CTAG	2 cut(s)	56, 367
GluI	GCNGC	1 cut(s)	326
GsaI	CCCAGC	1 cut(s)	332
HaeIII	GGCC	1 cut(s)	363
Hin1II	CATG	2 cut(s)	42, 167
HincII	GTYRAC	1 cut(s)	241
HindII	GTYRAC	1 cut(s)	241
HindIII	AAGCTT	1 cut(s)	80
HinfI	GANTC	2 cut(s)	5, 35
Hpy166II	GTNNAC	1 cut(s)	241
Hpy188I	TCNGA	1 cut(s)	302
Hpy188III	TCNNGA	2 cut(s)	164, 290
Hpy8I	GTNNAC	1 cut(s)	241
HpyCH4IV	ACGT	1 cut(s)	21
HpyCH4V	TGCA	5 cut(s)	158, 253, 261, 308, 318
HpyF10VI	GCNNNNNNNGC	2 cut(s)	221, 360
HpyF3I	CTNAG	1 cut(s)	355
HpySE526I	ACGT	1 cut(s)	21
Hsp92II	CATG	2 cut(s)	42, 167
Kzo9I	GATC	3 cut(s)	160, 286, 335
LpnPI	CCDG	5 cut(s)	29, 56, 303, 314, 357
Lsp1109I	GCAGC	1 cut(s)	312
LweI	GCATC	1 cut(s)	317
MaeI	CTAG	2 cut(s)	56, 367
MaeII	ACGT	1 cut(s)	21
MaeIII	GTNAC	1 cut(s)	226
MalI	GATC	3 cut(s)	162, 288, 337
MboI	GATC	3 cut(s)	160, 286, 335
MboII	GAAGA	3 cut(s)	22, 41, 345
MflI	RGATCY	2 cut(s)	286, 335
MluCI	AATT	4 cut(s)	87, 116, 192, 320
MlyI	GAGTC	1 cut(s)	44
MnlI	CCTC	3 cut(s)	53, 160, 193
MseI	TTAA	1 cut(s)	348
MslI	CAYNNNNRTG	2 cut(s)	177, 313
MspR9I	CCNGG	1 cut(s)	44
MvaI	CCWGG	1 cut(s)	44
MwoI	GCNNNNNNNGC	2 cut(s)	221, 360
NdeII	GATC	3 cut(s)	160, 286, 335
NlaIII	CATG	2 cut(s)	42, 167
PagI	TCATGA	1 cut(s)	163
PkrI	GCNGC	1 cut(s)	327
PleI	GAGTC	1 cut(s)	43
PpsI	GAGTC	1 cut(s)	43
Psp1406I	AACGTT	1 cut(s)	21
Psp6I	CCWGG	1 cut(s)	42
PspFI	CCCAGC	1 cut(s)	328
PspGI	CCWGG	1 cut(s)	42
PsuI	RGATCY	2 cut(s)	286, 335
RseI	CAYNNNNRTG	2 cut(s)	177, 313
SaqAI	TTAA	1 cut(s)	348
SatI	GCNGC	1 cut(s)	326
Sau3AI	GATC	3 cut(s)	160, 286, 335
SchI	GAGTC	1 cut(s)	44
ScrFI	CCNGG	1 cut(s)	44
SetI	ASST	5 cut(s)	24, 84, 204, 226, 233
SfaNI	GCATC	1 cut(s)	317
SmiMI	CAYNNNNRTG	2 cut(s)	177, 313
Sse9I	AATT	4 cut(s)	87, 116, 192, 320
SspI	AATATT	1 cut(s)	74
SspMI	CTAG	2 cut(s)	56, 367
StyD4I	CCNGG	1 cut(s)	42
TaiI	ACGT	1 cut(s)	24
TaqI	TCGA	1 cut(s)	8
TasI	AATT	4 cut(s)	87, 116, 192, 320
Tru1I	TTAA	1 cut(s)	348
Tru9I	TTAA	1 cut(s)	348
TseI	GCWGC	1 cut(s)	325
TspDTI	ATGAA	1 cut(s)	222
TspGWI	ACGGA	1 cut(s)	29
XapI	RAATTY	1 cut(s)	87
XspI	CTAG	2 cut(s)	56, 367

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