Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0016024

Physical Location & Seq

Genomic Coordinates Reverse (-)

49685385 .. 49688357

Gene Structure 2973 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG276100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1092 bp

ATGCTTAAAGAGCAACCCTTTTATCAACCGAAAGAAGGCACTTACATGAGGCTCCTTCTTCTGCTCGGACGGTCTGGCCAACCTCAGCGTGCCCAGAGTCTTTTCGACGAAATGGTTGAAGAAGGGTGTCAACCAACCGCTGAACTGTACACAGCCCTGCTTACAGCTTACTGCAGGAGCAATCTTATTCATGACGCGTTTTCTGTTCTTAACCAGATGAAGACGTTCCCTCAGTGCCAGCCGGATGTTTTTACATACAGTACCTTGATAAAGGCTTGCATTGATAATTTGCAGTTTGAATTAGTTGAGTCTTTGTATGAAGAAATGGCTGCACGGTCAATCACTCCAAACACAGTCACCCAAAACGTAGTCCTGAGTGGGTATGGTAAGGCCGGGATGTATGACCAGATGGAAAGAGTGTTGTCAGGAATGCTGGAGGGTGAAAGTTGCAAGCCCGATGTTTGGACGATGAATGTTATCCTTACTATTTTTGGTAACAAGGGTCAGATAGAGATGATGGAGAGATGGTATCAGAAATTCCGTGATTTTGGGATTGAGCCAGAAACTCGCACTTTTAATATTCTGATTAATGCTTATGGGAAGAAGAAATTGTATGATAAAATGTCTACTGTGATGGAGTACATGCGCAAGCTTCACTTTCCGTGGACAACCGCAACTTACAATAATGTTATTGAGGCTTTTGCGGATGTGGGAGATGCAAAAAACATGGAGTACACATTTGATCAGATGCGTGCTGAGGACATGAAAGCAGACACCAAAACTTTCTGCTGCCTAATAAGAGGGTATGCCAATGCAGGTCTTTTCCATAAGGTGATTAGCAGTGTTCAGTTGGCTGGAAAGTTTGAGATACCTGAAAATACCACCTTTTTTAATGCAGTGATATCTGCATGTGCAAAGGCAGATGATTTGATGGAGATGGAGAGAGTTTTTAACCGGATGAAAGAAAAGCAAGTCTCGCCAGATTCCTCGACATATGCCGTCATGGTTGAGGCATATAGAAAGGAAGGTATGAACGACAAAATCTACTATTTGGAGCAGGAGATTAGTGCTGATGGTATTCAAACCGATTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004519 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006139 GO:0006725 GO:0006807 GO:0007275 GO:0008150 GO:0008152 GO:0009451 GO:0009507 GO:0009536 GO:0009553 GO:0009555 GO:0009790 GO:0009791 GO:0009793 GO:0009856 GO:0009987 GO:0010154 GO:0016070 GO:0016787 GO:0016788 GO:0019843 GO:0022414 GO:0032501 GO:0032502 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044444 GO:0044464 GO:0044706 GO:0046483 GO:0048229 GO:0048316 GO:0048608 GO:0048731 GO:0048856 GO:0048868 GO:0051704 GO:0061458 GO:0071704 GO:0090304 GO:0090305 GO:0097159 GO:1901360 GO:1901363

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PPR PPR_2 PPR_3

Protein Analysis

363

Amino Acids

41.7

Weight (kDa)

5.03

Isoelectric Point (pI)

43.71

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TPR_24	PF23276	12 - 132	7.7e-06	Fungal tetratrico peptide repeats
PPR_3	PF13812	33 - 96	4.9e-10	Pentatricopeptide repeat domain
PPR_1	PF12854	42 - 74	8.4e-08	PPR repeat
PPR_2	PF13041	47 - 93	1.1e-12	PPR repeat family
PPR_2	PF13041	81 - 129	1.3e-10	PPR repeat family
PPR_3	PF13812	104 - 166	2.5e-06	Pentatricopeptide repeat domain
PPR_2	PF13041	116 - 161	6.5e-07	PPR repeat family
PPR_2	PF13041	152 - 200	1.6e-08	PPR repeat family
PPR_2	PF13041	187 - 235	1.1e-06	PPR repeat family
PPR_2	PF13041	224 - 271	4.3e-07	PPR repeat family
PPR_long	PF17177	285 - 361	4.9e-06	Pentacotripeptide-repeat region of PRORP
PPR_2	PF13041	293 - 339	2.8e-10	PPR repeat family
PPR_3	PF13812	294 - 339	1.4e-06	Pentatricopeptide repeat domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0016024)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G06430
fragaria_vesca	FvH4_4g21400
malus_domestica	MD13G1141500.v1.1 MD16G1137800.v1.1
prunus_persica	Prupe.1G106700_v2.0.a1
pyrus_communis	pycom13g12300 pycom16g12170
rosa_chinensis	RchiOBHm_Chr4g0427331
rosa_multiflora	Rmu_sc0008400.1_g000001
rosa_rugosa	Rorug04G0216700
rosa_samantha	Rh4AG273000 Rh4BG278700 Rh4CG294000 Rh4DG276100
rosa_wichuraiana	Rw4G023690

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc16I	TGCGCA	1 cut(s)	647
Acc36I	ACCTGC	1 cut(s)	806
AccI	GTMKAC	1 cut(s)	626
AccII	CGCG	1 cut(s)	197
AciI	CCGC	3 cut(s)	138, 672, 704
AcoI	YGGCCR	1 cut(s)	76
AcsI	RAATTY	1 cut(s)	536
AfaI	GTAC	4 cut(s)	149, 262, 641, 734
AfiI	CCNNNNNNNGG	2 cut(s)	35, 462
AflIII	ACRYGT	1 cut(s)	195
AgsI	TTSAA	3 cut(s)	119, 299, 1082
AluBI	AGCT	2 cut(s)	167, 652
AluI	AGCT	2 cut(s)	167, 652
Alw26I	GTCTC	1 cut(s)	979
AoxI	GGCC	2 cut(s)	76, 390
ApeKI	GCWGC	2 cut(s)	329, 789
ApoI	RAATTY	1 cut(s)	536
AseI	ATTAAT	1 cut(s)	588
Asp700I	GAANNNNTTC	1 cut(s)	224
AspLEI	GCGC	1 cut(s)	648
AsuC2I	CCSGG	1 cut(s)	394
AsuHPI	GGTGA	3 cut(s)	349, 452, 844
BaeGI	GKGCMC	1 cut(s)	94
BalI	TGGCCA	1 cut(s)	78
BbsI	GAAGAC	1 cut(s)	227
BbvCI	CCTCAGC	2 cut(s)	84, 756
BbvI	GCAGC	2 cut(s)	316, 776
BccI	CCATC	7 cut(s)	403, 511, 519, 628, 925, 931, 1067
BceAI	ACGGC	1 cut(s)	983
BclI	TGATCA	1 cut(s)	742
BcnI	CCSGG	1 cut(s)	394
BcoDI	GTCTC	1 cut(s)	979
BfmI	CTRYAG	1 cut(s)	172
BfuAI	ACCTGC	1 cut(s)	806
BisI	GCNGC	2 cut(s)	330, 790
BlsI	GCNGC	2 cut(s)	331, 791
Bme1390I	CCNGG	1 cut(s)	394
BmiI	GGNNCC	1 cut(s)	53
BmrFI	CCNGG	1 cut(s)	394
BmsI	GCATC	2 cut(s)	706, 738
BpiI	GAAGAC	1 cut(s)	227
BpmI	CTGGAG	1 cut(s)	455
Bpu10I	CCTNAGC	2 cut(s)	84, 756
BpuMI	CCSGG	1 cut(s)	394
BsaJI	CCNNGG	1 cut(s)	662
BsaWI	WCCGGW	1 cut(s)	954
BsaXI	ACNNNNNCTCC	2 cut(s)	512, 542
Bsc4I	CCNNNNNNNGG	2 cut(s)	35, 462
BseDI	CCNNGG	1 cut(s)	662
BseGI	GGATG	4 cut(s)	250, 402, 712, 963
BseLI	CCNNNNNNNGG	2 cut(s)	35, 462
BseMII	CTCAG	4 cut(s)	98, 245, 365, 747
BseSI	GKGCMC	1 cut(s)	94
BseXI	GCAGC	2 cut(s)	316, 776
BsgI	GTGCAG	1 cut(s)	315
Bsh1236I	CGCG	1 cut(s)	197
BshFI	GGCC	2 cut(s)	78, 392
BsiSI	CCGG	3 cut(s)	242, 393, 955
BslI	CCNNNNNNNGG	2 cut(s)	35, 462
BsmAI	GTCTC	1 cut(s)	979
BsmI	GAATGC	1 cut(s)	435
BsnI	GGCC	2 cut(s)	78, 392
Bsp1286I	GDGCHC	1 cut(s)	94
Bsp1407I	TGTACA	1 cut(s)	147
Bsp143I	GATC	1 cut(s)	742
BspACI	CCGC	3 cut(s)	138, 672, 704
BspANI	GGCC	2 cut(s)	78, 392
BspCNI	CTCAG	4 cut(s)	97, 244, 366, 748
BspFNI	CGCG	1 cut(s)	197
BspHI	TCATGA	1 cut(s)	190
BspLI	GGNNCC	1 cut(s)	53
BspMAI	CTGCAG	1 cut(s)	176
BspMI	ACCTGC	1 cut(s)	806
BsrGI	TGTACA	1 cut(s)	147
BssECI	CCNNGG	1 cut(s)	662
BssMI	GATC	1 cut(s)	742
Bst4CI	ACNGT	6 cut(s)	72, 147, 260, 336, 355, 631
BstAUI	TGTACA	1 cut(s)	147
BstC8I	GCNNGC	6 cut(s)	90, 239, 277, 452, 650, 753
BstDEI	CTNAG	4 cut(s)	84, 231, 374, 756
BstDSI	CCRYGG	1 cut(s)	662
BstF5I	GGATG	4 cut(s)	250, 402, 712, 963
BstFNI	CGCG	1 cut(s)	197
BstHHI	GCGC	1 cut(s)	648
BstKTI	GATC	1 cut(s)	745
BstMAI	GTCTC	1 cut(s)	979
BstMBI	GATC	1 cut(s)	742
BstMWI	GCNNNNNNNGC	2 cut(s)	10, 976
BstNSI	RCATGY	2 cut(s)	646, 912
BstSCI	CCNGG	1 cut(s)	392
BstSFI	CTRYAG	1 cut(s)	172
BstSLI	GKGCMC	1 cut(s)	94
BstUI	CGCG	1 cut(s)	197
BstV1I	GCAGC	2 cut(s)	316, 776
BstV2I	GAAGAC	1 cut(s)	227
BsuRI	GGCC	2 cut(s)	78, 392
BtgI	CCRYGG	1 cut(s)	662
BtsCI	GGATG	4 cut(s)	250, 402, 712, 963
BtsI	GCAGTG	2 cut(s)	847, 903
BtsIMutI	CAGTG	3 cut(s)	239, 847, 903
BveI	ACCTGC	1 cut(s)	806
Cac8I	GCNNGC	6 cut(s)	90, 239, 277, 452, 650, 753
CciI	TCATGA	1 cut(s)	190
CfoI	GCGC	1 cut(s)	648
CseI	GACGC	1 cut(s)	203
Csp6I	GTAC	4 cut(s)	148, 261, 640, 733
CviAII	CATG	7 cut(s)	46, 191, 643, 727, 763, 909, 1003
CviQI	GTAC	4 cut(s)	148, 261, 640, 733
DdeI	CTNAG	4 cut(s)	84, 231, 374, 756
DpnI	GATC	1 cut(s)	744
DpnII	GATC	1 cut(s)	742
EaeI	YGGCCR	1 cut(s)	76
Eco32I	GATATC	1 cut(s)	903
EcoRV	GATATC	1 cut(s)	903
FaeI	CATG	7 cut(s)	49, 194, 646, 730, 766, 912, 1006
FalI	AAGNNNNNCTT	2 cut(s)	641, 673
FatI	CATG	7 cut(s)	45, 190, 642, 726, 762, 908, 1002
FauNDI	CATATG	1 cut(s)	994
FbaI	TGATCA	1 cut(s)	742
FblI	GTMKAC	1 cut(s)	626
Fnu4HI	GCNGC	2 cut(s)	330, 790
FokI	GGATG	4 cut(s)	257, 409, 719, 970
Fsp4HI	GCNGC	2 cut(s)	330, 790
FspI	TGCGCA	1 cut(s)	647
GlaI	GCGC	1 cut(s)	647
GluI	GCNGC	2 cut(s)	330, 790
GsuI	CTGGAG	1 cut(s)	455
HaeIII	GGCC	2 cut(s)	78, 392
HapII	CCGG	3 cut(s)	242, 393, 955
HgaI	GACGC	1 cut(s)	203
HhaI	GCGC	1 cut(s)	648
Hin1II	CATG	7 cut(s)	49, 194, 646, 730, 766, 912, 1006
Hin6I	GCGC	1 cut(s)	646
HinP1I	GCGC	1 cut(s)	646
HincII	GTYRAC	1 cut(s)	131
HindII	GTYRAC	1 cut(s)	131
HindIII	AAGCTT	1 cut(s)	650
HinfI	GANTC	3 cut(s)	97, 308, 983
HpaII	CCGG	3 cut(s)	242, 393, 955
HphI	GGTGA	3 cut(s)	349, 452, 844
Hpy166II	GTNNAC	5 cut(s)	131, 150, 627, 666, 735
Hpy188I	TCNGA	5 cut(s)	68, 507, 534, 585, 747
Hpy188III	TCNNGA	3 cut(s)	191, 373, 426
Hpy8I	GTNNAC	5 cut(s)	131, 150, 627, 666, 735
Hpy99I	CGWCG	1 cut(s)	110
HpyAV	CCTTC	4 cut(s)	29, 65, 116, 1019
HpyCH4III	ACNGT	6 cut(s)	72, 147, 260, 336, 355, 631
HpyCH4IV	ACGT	2 cut(s)	224, 366
HpyF10VI	GCNNNNNNNGC	2 cut(s)	10, 976
HpyF3I	CTNAG	4 cut(s)	84, 231, 374, 756
HpySE526I	ACGT	2 cut(s)	224, 366
Hsp92II	CATG	7 cut(s)	49, 194, 646, 730, 766, 912, 1006
HspAI	GCGC	1 cut(s)	646
Ksp22I	TGATCA	1 cut(s)	742
Kzo9I	GATC	1 cut(s)	742
LmnI	GCTCC	3 cut(s)	57, 177, 1054
Lsp1109I	GCAGC	2 cut(s)	316, 776
LweI	GCATC	2 cut(s)	706, 738
MaeII	ACGT	2 cut(s)	224, 366
MaeIII	GTNAC	2 cut(s)	355, 494
MalI	GATC	1 cut(s)	744
MboI	GATC	1 cut(s)	742
MboII	GAAGA	6 cut(s)	50, 131, 232, 332, 613, 616
MhlI	GDGCHC	1 cut(s)	94
MlsI	TGGCCA	1 cut(s)	78
MluCI	AATT	4 cut(s)	286, 299, 536, 608
MluI	ACGCGT	1 cut(s)	195
MluNI	TGGCCA	1 cut(s)	78
MlyI	GAGTC	2 cut(s)	106, 317
MnlI	CCTC	9 cut(s)	42, 93, 240, 430, 688, 751, 794, 997, 1003
Mox20I	TGGCCA	1 cut(s)	78
MroXI	GAANNNNTTC	1 cut(s)	224
MscI	TGGCCA	1 cut(s)	78
MseI	TTAA	6 cut(s)	6, 210, 576, 588, 891, 951
MslI	CAYNNNNRTG	1 cut(s)	44
Msp20I	TGGCCA	1 cut(s)	78
MspA1I	CMGCKG	1 cut(s)	140
MspI	CCGG	3 cut(s)	242, 393, 955
MspR9I	CCNGG	1 cut(s)	394
Mva1269I	GAATGC	1 cut(s)	435
MvnI	CGCG	1 cut(s)	197
MwoI	GCNNNNNNNGC	2 cut(s)	10, 976
NciI	CCSGG	1 cut(s)	394
NdeI	CATATG	1 cut(s)	994
NdeII	GATC	1 cut(s)	742
NlaIII	CATG	7 cut(s)	49, 194, 646, 730, 766, 912, 1006
NlaIV	GGNNCC	1 cut(s)	53
NmuCI	GTSAC	1 cut(s)	355
NsbI	TGCGCA	1 cut(s)	647
NspI	RCATGY	2 cut(s)	646, 912
PagI	TCATGA	1 cut(s)	190
PctI	GAATGC	1 cut(s)	435
PdmI	GAANNNNTTC	1 cut(s)	224
PfeI	GAWTC	1 cut(s)	983
PkrI	GCNGC	2 cut(s)	331, 791
PleI	GAGTC	2 cut(s)	105, 316
PpsI	GAGTC	2 cut(s)	105, 316
PshBI	ATTAAT	1 cut(s)	588
PspN4I	GGNNCC	1 cut(s)	53
PstI	CTGCAG	1 cut(s)	176
RsaI	GTAC	4 cut(s)	149, 262, 641, 734
RsaNI	GTAC	4 cut(s)	148, 261, 640, 733
RseI	CAYNNNNRTG	1 cut(s)	44
SaqAI	TTAA	6 cut(s)	6, 210, 576, 588, 891, 951
SatI	GCNGC	2 cut(s)	330, 790
Sau3AI	GATC	1 cut(s)	742
SchI	GAGTC	2 cut(s)	106, 317
ScrFI	CCNGG	1 cut(s)	394
SduI	GDGCHC	1 cut(s)	94
SfaNI	GCATC	2 cut(s)	706, 738
SfcI	CTRYAG	1 cut(s)	172
SmiMI	CAYNNNNRTG	1 cut(s)	44
Sse9I	AATT	4 cut(s)	286, 299, 536, 608
SsiI	CCGC	3 cut(s)	138, 672, 704
SspI	AATATT	1 cut(s)	580
StyD4I	CCNGG	1 cut(s)	392
TaaI	ACNGT	6 cut(s)	72, 147, 260, 336, 355, 631
TaiI	ACGT	2 cut(s)	227, 369
TaqI	TCGA	2 cut(s)	105, 989
TasI	AATT	4 cut(s)	286, 299, 536, 608
TatI	WGTACW	3 cut(s)	147, 639, 732
TfiI	GAWTC	1 cut(s)	983
Tru1I	TTAA	6 cut(s)	6, 210, 576, 588, 891, 951
Tru9I	TTAA	6 cut(s)	6, 210, 576, 588, 891, 951
TscAI	CASTG	3 cut(s)	239, 847, 903
TseFI	GTSAC	1 cut(s)	355
TseI	GCWGC	2 cut(s)	329, 789
Tsp45I	GTSAC	1 cut(s)	355
TspDTI	ATGAA	7 cut(s)	179, 233, 333, 485, 779, 974, 1046
TspGWI	ACGGA	2 cut(s)	530, 651
TspRI	CASTG	3 cut(s)	239, 847, 903
VspI	ATTAAT	1 cut(s)	588
XapI	RAATTY	1 cut(s)	536
XceI	RCATGY	2 cut(s)	646, 912
XmiI	GTMKAC	1 cut(s)	626
XmnI	GAANNNNTTC	1 cut(s)	224

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