Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4B

Orthogroup ID

OG0009334

Physical Location & Seq

Genomic Coordinates Reverse (-)

40636398 .. 40639170

Gene Structure 2773 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4BG239900.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 591 bp

ATGGGCACGATGAGTCCCACGCAGCTTGATTACTACGAAGACATGTGGAAGCTTGATTCCGATGCCACATTGGTAGCGTTGGTCAAAGGTGAAGATGGACGGACGGCTTTGGTGTTGGACCGGACGGTGTTCCATCCGCAAGGCGGCGGTCAACCGGCGGACACAGGCTTCGTCGCCGTCGCCGGTTCGGAGGTCAAGTTCGTCGTGCAAGATGTGCGGTCCAAGGACGGTGTAGTTTACCACTACGGTTTGGTTGAGAATTGCGGTGAGGGATGGGAAGCGGAGTTTGAGAAAGGGAGAGAGGTGGTGTTGCATGTTGATGAGTCTAGGCGCAAGCTTAATTCTAGGCTTCACTCAGCTGGGCATTTGCTAGATGTGTGTATGAAGAATGTGGGATTGGGTGATTTAAAGACAGGCAAGGGCTACCATTTCCCTCAAGGGCCATATGTGGAATATATAGGCATAGTTCCACAGAAAGATGTGCAGAGTAAGCAGAAAGAGTTGGAGCTAGAAGCTAATGCATTGATATCGAGAGGAGGGAAGGTGAGTTCTGATACTTGTTTAAAGCTTCTTGCTTGGTATGACATATAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000049 GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004812 GO:0004813 GO:0005488 GO:0006082 GO:0006139 GO:0006396 GO:0006399 GO:0006400 GO:0006412 GO:0006418 GO:0006419 GO:0006518 GO:0006520 GO:0006725 GO:0006807 GO:0008033 GO:0008150 GO:0008152 GO:0009058 GO:0009059 GO:0009451 GO:0009987 GO:0010467 GO:0016070 GO:0016597 GO:0016874 GO:0016875 GO:0019538 GO:0019752 GO:0031406 GO:0034470 GO:0034641 GO:0034645 GO:0034660 GO:0036094 GO:0043038 GO:0043039 GO:0043043 GO:0043167 GO:0043168 GO:0043170 GO:0043177 GO:0043412 GO:0043436 GO:0043603 GO:0043604 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044267 GO:0044271 GO:0044281 GO:0046483 GO:0071704 GO:0090304 GO:0097159 GO:0140098 GO:0140101 GO:1901360 GO:1901363 GO:1901564 GO:1901566 GO:1901576

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

tRNA-synt_2c tRNA_SAD

Protein Analysis

196

Amino Acids

21.62

Weight (kDa)

5.37

Isoelectric Point (pI)

35.43

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
tRNA-synt_2c	PF01411	33 - 109	9.4e-11	tRNA synthetases class II (A)

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: OG0009334)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G16565 AT3G16565 AT3G16565 AT3G16565 AT3G16565 AT3G16565
fragaria_vesca	FvH4_4g17960
malus_domestica	MD13G1169000.v1.1 MD16G1169600.v1.1
prunus_persica	Prupe.1G137400_v2.0.a1
pyrus_communis	pycom13g14460
rosa_chinensis	RchiOBHm_Chr4g0422131
rosa_laevigata	RLG00000007632
rosa_multiflora	Rmu_sc0004902.1_g000006 Rmu_sc0036261.1_g000001
rosa_roxburghii	Rroxscaffold_5G00364210
rosa_rugosa	Rorug04G0177600
rosa_samantha	Rh4AG237100 Rh4BG239900 Rh4CG251800 Rh4DG236000
rosa_wichuraiana	Rw4G020510

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	7 cut(s)	137, 144, 147, 158, 217, 264, 281
AfiI	CCNNNNNNNGG	1 cut(s)	143
AflIII	ACRYGT	1 cut(s)	42
AjuI	GAANNNNNNNTTGG	2 cut(s)	380, 412
AloI	GAACNNNNNNTCC	4 cut(s)	182, 214, 532, 564
AluBI	AGCT	7 cut(s)	25, 52, 337, 359, 508, 515, 568
AluI	AGCT	7 cut(s)	25, 52, 337, 359, 508, 515, 568
AoxI	GGCC	1 cut(s)	440
ApeKI	GCWGC	1 cut(s)	22
ArsI	GACNNNNNNTTYG	2 cut(s)	152, 184
AspLEI	GCGC	1 cut(s)	333
AspS9I	GGNCC	3 cut(s)	118, 219, 440
AsuHPI	GGTGA	4 cut(s)	101, 278, 413, 556
AvaII	GGWCC	2 cut(s)	118, 219
BaeGI	GKGCMC	1 cut(s)	8
BbsI	GAAGAC	1 cut(s)	45
BbvI	GCAGC	1 cut(s)	34
BccI	CCATC	3 cut(s)	89, 141, 267
BceAI	ACGGC	2 cut(s)	120, 161
BcgI	CGANNNNNNTGC	2 cut(s)	510, 544
BfaI	CTAG	4 cut(s)	327, 345, 371, 509
BisI	GCNGC	2 cut(s)	23, 145
BlsI	GCNGC	2 cut(s)	24, 146
Bme18I	GGWCC	2 cut(s)	118, 219
BmgT120I	GGNCC	3 cut(s)	118, 219, 440
BmsI	GCATC	1 cut(s)	52
BpiI	GAAGAC	1 cut(s)	45
BpuEI	CTTGAG	1 cut(s)	420
BsaJI	CCNNGG	1 cut(s)	222
BsaWI	WCCGGW	1 cut(s)	120
BsaXI	ACNNNNNCTCC	4 cut(s)	182, 212, 528, 558
Bsc4I	CCNNNNNNNGG	1 cut(s)	143
Bse118I	RCCGGY	2 cut(s)	154, 182
BseDI	CCNNGG	1 cut(s)	222
BseGI	GGATG	2 cut(s)	133, 278
BseLI	CCNNNNNNNGG	1 cut(s)	143
BseMII	CTCAG	1 cut(s)	369
BseRI	GAGGAG	1 cut(s)	549
BseSI	GKGCMC	1 cut(s)	8
BseXI	GCAGC	1 cut(s)	34
BseYI	CCCAGC	1 cut(s)	359
BsgI	GTGCAG	1 cut(s)	503
BshFI	GGCC	1 cut(s)	442
BsiSI	CCGG	3 cut(s)	121, 155, 183
BslI	CCNNNNNNNGG	1 cut(s)	143
BsnI	GGCC	1 cut(s)	442
Bsp1286I	GDGCHC	1 cut(s)	8
BspACI	CCGC	7 cut(s)	137, 144, 147, 158, 217, 264, 281
BspANI	GGCC	1 cut(s)	442
BspCNI	CTCAG	1 cut(s)	368
BsrFI	RCCGGY	2 cut(s)	154, 182
BssAI	RCCGGY	2 cut(s)	154, 182
BssECI	CCNNGG	1 cut(s)	222
BssT1I	CCWWGG	1 cut(s)	222
Bst4CI	ACNGT	3 cut(s)	127, 230, 248
BstAPI	GCANNNNNTGC	1 cut(s)	214
BstC8I	GCNNGC	1 cut(s)	335
BstDEI	CTNAG	1 cut(s)	355
BstF5I	GGATG	2 cut(s)	133, 278
BstHHI	GCGC	1 cut(s)	333
BstMWI	GCNNNNNNNGC	2 cut(s)	214, 490
BstNSI	RCATGY	2 cut(s)	46, 317
BstSLI	GKGCMC	1 cut(s)	8
BstV1I	GCAGC	1 cut(s)	34
BstV2I	GAAGAC	1 cut(s)	45
BsuRI	GGCC	1 cut(s)	442
BtsCI	GGATG	2 cut(s)	133, 278
Cac8I	GCNNGC	1 cut(s)	335
CfoI	GCGC	1 cut(s)	333
Cfr10I	RCCGGY	2 cut(s)	154, 182
Cfr13I	GGNCC	3 cut(s)	118, 219, 440
CspCI	CAANNNNNGTGG	2 cut(s)	7, 42
CviAII	CATG	2 cut(s)	43, 314
DdeI	CTNAG	1 cut(s)	355
DraI	TTTAAA	2 cut(s)	408, 564
EciI	GGCGGA	1 cut(s)	173
Eco130I	CCWWGG	1 cut(s)	222
Eco32I	GATATC	1 cut(s)	528
Eco47I	GGWCC	2 cut(s)	118, 219
EcoRV	GATATC	1 cut(s)	528
EcoT14I	CCWWGG	1 cut(s)	222
EcoT22I	ATGCAT	1 cut(s)	523
ErhI	CCWWGG	1 cut(s)	222
FaeI	CATG	2 cut(s)	46, 317
FatI	CATG	2 cut(s)	42, 313
FauNDI	CATATG	1 cut(s)	445
Fnu4HI	GCNGC	2 cut(s)	23, 145
FokI	GGATG	2 cut(s)	120, 285
Fsp4HI	GCNGC	2 cut(s)	23, 145
FspBI	CTAG	4 cut(s)	327, 345, 371, 509
GlaI	GCGC	1 cut(s)	332
GluI	GCNGC	2 cut(s)	23, 145
GsaI	CCCAGC	1 cut(s)	363
HaeIII	GGCC	1 cut(s)	442
HapII	CCGG	3 cut(s)	121, 155, 183
HhaI	GCGC	1 cut(s)	333
Hin1II	CATG	2 cut(s)	46, 317
Hin6I	GCGC	1 cut(s)	331
HinP1I	GCGC	1 cut(s)	331
HincII	GTYRAC	1 cut(s)	152
HindII	GTYRAC	1 cut(s)	152
HindIII	AAGCTT	3 cut(s)	50, 335, 566
HinfI	GANTC	3 cut(s)	13, 56, 323
HpaII	CCGG	3 cut(s)	121, 155, 183
HphI	GGTGA	4 cut(s)	101, 278, 413, 556
Hpy166II	GTNNAC	2 cut(s)	152, 238
Hpy188I	TCNGA	3 cut(s)	61, 190, 553
Hpy188III	TCNNGA	1 cut(s)	531
Hpy8I	GTNNAC	2 cut(s)	152, 238
Hpy99I	CGWCG	3 cut(s)	176, 182, 206
HpyAV	CCTTC	1 cut(s)	535
HpyCH4III	ACNGT	3 cut(s)	127, 230, 248
HpyCH4V	TGCA	4 cut(s)	208, 313, 484, 521
HpyF10VI	GCNNNNNNNGC	2 cut(s)	214, 490
HpyF3I	CTNAG	1 cut(s)	355
Hsp92II	CATG	2 cut(s)	46, 317
HspAI	GCGC	1 cut(s)	331
LmnI	GCTCC	1 cut(s)	505
LpnPI	CCDG	6 cut(s)	134, 150, 168, 196, 345, 399
Lsp1109I	GCAGC	1 cut(s)	34
LweI	GCATC	1 cut(s)	52
MaeI	CTAG	4 cut(s)	327, 345, 371, 509
MboII	GAAGA	3 cut(s)	50, 104, 397
MhlI	GDGCHC	1 cut(s)	8
MluCI	AATT	2 cut(s)	259, 340
MlyI	GAGTC	2 cut(s)	22, 332
MmeI	TCCRAC	2 cut(s)	96, 483
MnlI	CCTC	6 cut(s)	184, 262, 295, 444, 527, 530
Mph1103I	ATGCAT	1 cut(s)	523
MseI	TTAA	3 cut(s)	339, 407, 563
MslI	CAYNNNNRTG	1 cut(s)	318
MspA1I	CMGCKG	1 cut(s)	359
MspI	CCGG	3 cut(s)	121, 155, 183
MwoI	GCNNNNNNNGC	2 cut(s)	214, 490
NdeI	CATATG	1 cut(s)	445
NlaIII	CATG	2 cut(s)	46, 317
NsiI	ATGCAT	1 cut(s)	523
NspI	RCATGY	2 cut(s)	46, 317
PciI	ACATGT	1 cut(s)	42
PfeI	GAWTC	1 cut(s)	56
PkrI	GCNGC	2 cut(s)	24, 146
PleI	GAGTC	2 cut(s)	21, 331
PpsI	GAGTC	2 cut(s)	21, 331
PscI	ACATGT	1 cut(s)	42
PspFI	CCCAGC	1 cut(s)	359
PspPI	GGNCC	3 cut(s)	118, 219, 440
PvuII	CAGCTG	1 cut(s)	359
RseI	CAYNNNNRTG	1 cut(s)	318
SaqAI	TTAA	3 cut(s)	339, 407, 563
SatI	GCNGC	2 cut(s)	23, 145
Sau96I	GGNCC	3 cut(s)	118, 219, 440
SchI	GAGTC	2 cut(s)	22, 332
SduI	GDGCHC	1 cut(s)	8
SfaNI	GCATC	1 cut(s)	52
SinI	GGWCC	2 cut(s)	118, 219
SmiMI	CAYNNNNRTG	1 cut(s)	318
SmlI	CTYRAG	1 cut(s)	435
SmoI	CTYRAG	1 cut(s)	435
Sse9I	AATT	2 cut(s)	259, 340
SsiI	CCGC	7 cut(s)	137, 144, 147, 158, 217, 264, 281
SspMI	CTAG	4 cut(s)	327, 345, 371, 509
StyI	CCWWGG	1 cut(s)	222
TaaI	ACNGT	3 cut(s)	127, 230, 248
TaqI	TCGA	1 cut(s)	530
TasI	AATT	2 cut(s)	259, 340
TauI	GCSGC	1 cut(s)	147
TfiI	GAWTC	1 cut(s)	56
Tru1I	TTAA	3 cut(s)	339, 407, 563
Tru9I	TTAA	3 cut(s)	339, 407, 563
TseI	GCWGC	1 cut(s)	22
TspDTI	ATGAA	1 cut(s)	398
TspGWI	ACGGA	1 cut(s)	115
VpaK11BI	GGWCC	2 cut(s)	118, 219
XceI	RCATGY	2 cut(s)	46, 317
XspI	CTAG	4 cut(s)	327, 345, 371, 509
Zsp2I	ATGCAT	1 cut(s)	523

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