Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr1D

Orthogroup ID

OG0009331

Physical Location & Seq

Genomic Coordinates Reverse (-)

26525788 .. 26529702

Gene Structure 3915 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh1DG127000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1125 bp

ATGTCGTCGACGCTACTGGAGGTGACGCGTGGCGCTCACGAGGAGGTGGAGCGCTTGGAGCGTTTGATAGTGAAGGACTTACAGAACGAGCCGGCGAGCGGCAAGGAACGCTTGGCTCAGAGCCACCGTGTCCGCCTCATGATCGACACCGTCACCTCCACCACAGAAAGACTCATTGAGATCTATGAGGATAACGATAATGCGAGGAAGGACGAGATTGCGGCTCTCGGAGGCCAAACTGCCACCGGCACCAATGTCTTCAGTGCATTCTATGATAGATTGAAAGAGATCCGTGAGTACCATAGGAGACATCCAGCTGCACTAGTTGTTGATGCTAATGAGGAACATGAAGCCCTGCTGAAGGAGGAGCCTCAAGTAGAGTTCAGTGGAGAGGCATTGGCTTCGTTAGGACTGAAGATAGGGGGTACTGTTCAGCAACGTGCAGAGAGGCTTTTACTTACAAAGGATACACCTCTGGAAAAGTTGGACAAGAAGCATTTTGCCAAAGGGTCACGTGGTTCAGCACAGAATGGGGCTGCTGTAGCTCCACAGCAAGTTGGCATGTTAATAGAAATTGCTCTCTTGGAAGCCAAATTGAAAAAACTAAGCGACTTACTGGGTGAGGCTATTGAACGAACAAAAGACAACATTGTTAAGAAACAGGCTTTGACATATGAAGAAATTGCAGCAGAACGTGAGGATGAAGAGACACAGGCTGATACTGAAAGTGATGACGATGAGCAGCAGATTTATAATCCACTCAAATTGCCAATGGGTTGGGATGGGAAGCCCATACCTTACTGGCTGTATAAGCTTCATGGTCTTGGTCAGGAATTCAAGTGTGAGATATGTGGGAATCAGAGTTACTGGGGGCGTAGAGCTTTTGAGCGGCATTTTAAGGAATGGCGCCATCAGCATGGAATGCGTTGCCTTGGCATACCAAACACCAAGAACTTCAATGAGATCACATCAATTGAGGAAGCACAAGAATTGTGGAAGAGGATACAAGCACGGCAAGGAGTGAACAAGTGGCGCCCAGACCTTGAAGAAGAGTATGAAGACAGAGAGGGCAACATCTATAATAAAAAGACATATACTGATCTCCAGCGACAGGGACTAATTTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000245 GO:0000375 GO:0000377 GO:0000389 GO:0000398 GO:0003674 GO:0003676 GO:0003723 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0005681 GO:0005737 GO:0005829 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:0016604 GO:0016607 GO:0022607 GO:0022613 GO:0022618 GO:0031974 GO:0031981 GO:0032991 GO:0034622 GO:0034641 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043900 GO:0043933 GO:0044085 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044451 GO:0044464 GO:0045595 GO:0045694 GO:0046483 GO:0050789 GO:0050793 GO:0050794 GO:0051239 GO:0065003 GO:0065007 GO:0070013 GO:0071013 GO:0071704 GO:0071826 GO:0071840 GO:0090304 GO:0097159 GO:1901360 GO:1901363 GO:1902494 GO:1990904 GO:2000026 GO:2000241

KEGG Pathways

Metabolic & Signaling

ko03040 map03040

Pfam Domains

Protein Families

DUF3449 SF3A3 SF3a60_bindingd Telomere_Sde2_2

Protein Analysis

374

Amino Acids

42.94

Weight (kDa)

5.43

Isoelectric Point (pI)

40.06

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
SF3a60_bindingd	PF12108	80 - 105	2.9e-12	Splicing factor SF3a60 binding domain
SDE2_2C	PF13297	131 - 169	5.5e-14	Replication stress response SDE2 C-terminal
SF3a60_Prp9_C	PF11931	255 - 374	1.9e-57	SF3a60/Prp9 C-terminal

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0009331)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G06160
fragaria_vesca	FvH4_1g22860 FvH4_5g28470 FvH4_7g05370 FvH4_7g06390
malus_domestica	MD01G1219700.v1.1 MD07G1290300.v1.1
prunus_persica	Prupe.2G311500_v2.0.a1
pyrus_communis	pycom01g22950 pycom07g26290
rosa_chinensis	RchiOBHm_Chr1g0331941
rosa_laevigata	RLG00000025855 RLG00000029702
rosa_multiflora	Rmu_sc0004874.1_g000018 Rmu_sc0008128.1_g000009
rosa_roxburghii	Rroxscaffold_4G00318600
rosa_rugosa	Rorug01G0097000
rosa_samantha	Rh1AG121100 Rh1BG092700 Rh1CG115900 Rh1DG127000
rosa_wichuraiana	Rw1G009880

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AanI	TTATAA	1 cut(s)	753
AccB1I	GGYRCC	3 cut(s)	248, 906, 1032
AccBSI	CCGCTC	2 cut(s)	99, 889
AccI	GTMKAC	1 cut(s)	8
AccII	CGCG	1 cut(s)	28
AciI	CCGC	4 cut(s)	99, 133, 221, 889
AclWI	GGATC	1 cut(s)	283
AcsI	RAATTY	1 cut(s)	833
AcuI	CTGAAG	3 cut(s)	244, 380, 434
AcvI	CACGTG	1 cut(s)	515
AcyI	GRCGYC	2 cut(s)	907, 1033
AfaI	GTAC	2 cut(s)	299, 427
AfeI	AGCGCT	1 cut(s)	53
AfiI	CCNNNNNNNGG	3 cut(s)	98, 361, 1111
AflIII	ACRYGT	1 cut(s)	26
AgsI	TTSAA	6 cut(s)	283, 598, 632, 838, 958, 1046
AhlI	ACTAGT	1 cut(s)	322
AluBI	AGCT	4 cut(s)	317, 545, 814, 881
AluI	AGCT	4 cut(s)	317, 545, 814, 881
Alw26I	GTCTC	2 cut(s)	301, 701
AlwI	GGATC	1 cut(s)	283
Aor51HI	AGCGCT	1 cut(s)	53
AoxI	GGCC	1 cut(s)	232
ApeKI	GCWGC	4 cut(s)	317, 536, 686, 742
ApoI	RAATTY	1 cut(s)	833
AspLEI	GCGC	4 cut(s)	35, 54, 909, 1035
AsuHPI	GGTGA	3 cut(s)	34, 145, 632
BanI	GGYRCC	3 cut(s)	248, 906, 1032
BauI	CACGAG	1 cut(s)	38
BbrPI	CACGTG	1 cut(s)	515
BbsI	GAAGAC	2 cut(s)	250, 1065
BbvI	GCAGC	4 cut(s)	304, 523, 698, 754
BccI	CCATC	2 cut(s)	776, 918
BceAI	ACGGC	1 cut(s)	1028
BcgI	CGANNNNNNTGC	2 cut(s)	384, 418
BciVI	GTATCC	2 cut(s)	460, 996
BcoDI	GTCTC	2 cut(s)	301, 701
BcuI	ACTAGT	1 cut(s)	322
BfaI	CTAG	1 cut(s)	323
BfmI	CTRYAG	1 cut(s)	540
BfoI	RGCGCY	4 cut(s)	36, 55, 910, 1036
BfuI	GTATCC	2 cut(s)	460, 996
BglII	AGATCT	1 cut(s)	180
BisI	GCNGC	7 cut(s)	100, 222, 318, 537, 687, 743, 890
BlsI	GCNGC	7 cut(s)	101, 223, 319, 538, 688, 744, 891
BmiI	GGNNCC	4 cut(s)	250, 369, 908, 1034
BmrI	ACTGGG	2 cut(s)	626, 877
BmsI	GCATC	1 cut(s)	322
BmuI	ACTGGG	2 cut(s)	626, 877
BpiI	GAAGAC	2 cut(s)	250, 1065
BpmI	CTGGAG	2 cut(s)	38, 1088
BpuEI	CTTGAG	1 cut(s)	357
BsaAI	YACGTR	1 cut(s)	515
BsaHI	GRCGYC	2 cut(s)	907, 1033
BsaJI	CCNNGG	1 cut(s)	931
Bsc4I	CCNNNNNNNGG	3 cut(s)	98, 361, 1111
Bse118I	RCCGGY	2 cut(s)	91, 245
Bse1I	ACTGG	4 cut(s)	21, 621, 806, 872
BseDI	CCNNGG	1 cut(s)	931
BseGI	GGATG	3 cut(s)	310, 706, 787
BseLI	CCNNNNNNNGG	3 cut(s)	98, 361, 1111
BseMII	CTCAG	1 cut(s)	131
BseNI	ACTGG	4 cut(s)	21, 621, 806, 872
BseRI	GAGGAG	2 cut(s)	56, 380
BseXI	GCAGC	4 cut(s)	304, 523, 698, 754
BsgI	GTGCAG	2 cut(s)	303, 462
Bsh1236I	CGCG	1 cut(s)	28
BshFI	GGCC	1 cut(s)	234
BshNI	GGYRCC	3 cut(s)	248, 906, 1032
BsiSI	CCGG	2 cut(s)	92, 246
BslI	CCNNNNNNNGG	3 cut(s)	98, 361, 1111
BsmAI	GTCTC	2 cut(s)	301, 701
BsmI	GAATGC	2 cut(s)	266, 927
BsnI	GGCC	1 cut(s)	234
Bsp143I	GATC	5 cut(s)	141, 180, 288, 963, 1099
BspACI	CCGC	4 cut(s)	99, 133, 221, 889
BspANI	GGCC	1 cut(s)	234
BspCNI	CTCAG	1 cut(s)	130
BspFNI	CGCG	1 cut(s)	28
BspHI	TCATGA	1 cut(s)	138
BspLI	GGNNCC	4 cut(s)	250, 369, 908, 1034
BspPI	GGATC	1 cut(s)	283
BspT107I	GGYRCC	3 cut(s)	248, 906, 1032
BsrBI	CCGCTC	2 cut(s)	99, 889
BsrFI	RCCGGY	2 cut(s)	91, 245
BsrI	ACTGG	4 cut(s)	21, 621, 806, 872
BssAI	RCCGGY	2 cut(s)	91, 245
BssECI	CCNNGG	1 cut(s)	931
BssMI	GATC	5 cut(s)	141, 180, 288, 963, 1099
BssNI	GRCGYC	2 cut(s)	907, 1033
BssSI	CACGAG	1 cut(s)	38
BssT1I	CCWWGG	1 cut(s)	931
Bst2BI	CACGAG	1 cut(s)	38
Bst4CI	ACNGT	3 cut(s)	128, 151, 430
Bst6I	CTCTTC	3 cut(s)	699, 992, 1044
BstACI	GRCGYC	2 cut(s)	907, 1033
BstAPI	GCANNNNNTGC	1 cut(s)	922
BstBAI	YACGTR	1 cut(s)	515
BstC8I	GCNNGC	2 cut(s)	93, 97
BstDEI	CTNAG	2 cut(s)	117, 605
BstENI	CCTNNNNNAGG	1 cut(s)	359
BstF5I	GGATG	3 cut(s)	310, 706, 787
BstFNI	CGCG	1 cut(s)	28
BstH2I	RGCGCY	4 cut(s)	36, 55, 910, 1036
BstHHI	GCGC	4 cut(s)	35, 54, 909, 1035
BstKTI	GATC	5 cut(s)	144, 183, 291, 966, 1102
BstMAI	GTCTC	2 cut(s)	301, 701
BstMBI	GATC	5 cut(s)	141, 180, 288, 963, 1099
BstMWI	GCNNNNNNNGC	6 cut(s)	58, 108, 542, 811, 913, 922
BstNSI	RCATGY	1 cut(s)	565
BstSFI	CTRYAG	1 cut(s)	540
BstUI	CGCG	1 cut(s)	28
BstV1I	GCAGC	4 cut(s)	304, 523, 698, 754
BstV2I	GAAGAC	2 cut(s)	250, 1065
BstX2I	RGATCY	2 cut(s)	180, 288
BstXI	CCANNNNNNTGG	2 cut(s)	777, 917
BstYI	RGATCY	2 cut(s)	180, 288
BsuI	GTATCC	2 cut(s)	460, 996
BsuRI	GGCC	1 cut(s)	234
BtsCI	GGATG	3 cut(s)	310, 706, 787
BtsIMutI	CAGTG	2 cut(s)	268, 391
Cac8I	GCNNGC	2 cut(s)	93, 97
CciI	TCATGA	1 cut(s)	138
CfoI	GCGC	4 cut(s)	35, 54, 909, 1035
Cfr10I	RCCGGY	2 cut(s)	91, 245
CseI	GACGC	2 cut(s)	19, 34
Csp6I	GTAC	2 cut(s)	298, 426
CspCI	CAANNNNNGTGG	4 cut(s)	747, 782, 974, 1009
CviAII	CATG	5 cut(s)	139, 347, 562, 818, 917
CviQI	GTAC	2 cut(s)	298, 426
DdeI	CTNAG	2 cut(s)	117, 605
DinI	GGCGCC	2 cut(s)	908, 1034
DpnI	GATC	5 cut(s)	143, 182, 290, 965, 1101
DpnII	GATC	5 cut(s)	141, 180, 288, 963, 1099
Eam1104I	CTCTTC	3 cut(s)	699, 992, 1044
EarI	CTCTTC	3 cut(s)	699, 992, 1044
EciI	GGCGGA	1 cut(s)	122
Eco130I	CCWWGG	1 cut(s)	931
Eco47III	AGCGCT	1 cut(s)	53
Eco57I	CTGAAG	3 cut(s)	244, 380, 434
Eco72I	CACGTG	1 cut(s)	515
EcoNI	CCTNNNNNAGG	1 cut(s)	359
EcoRI	GAATTC	1 cut(s)	833
EcoT14I	CCWWGG	1 cut(s)	931
EgeI	GGCGCC	2 cut(s)	908, 1034
EheI	GGCGCC	2 cut(s)	908, 1034
ErhI	CCWWGG	1 cut(s)	931
FaeI	CATG	5 cut(s)	142, 350, 565, 821, 920
FalI	AAGNNNNNCTT	2 cut(s)	95, 127
FatI	CATG	5 cut(s)	138, 346, 561, 817, 916
FauNDI	CATATG	1 cut(s)	673
FblI	GTMKAC	1 cut(s)	8
Fnu4HI	GCNGC	7 cut(s)	100, 222, 318, 537, 687, 743, 890
FokI	GGATG	3 cut(s)	297, 713, 794
Fsp4HI	GCNGC	7 cut(s)	100, 222, 318, 537, 687, 743, 890
FspBI	CTAG	1 cut(s)	323
GlaI	GCGC	4 cut(s)	34, 53, 908, 1034
GluI	GCNGC	7 cut(s)	100, 222, 318, 537, 687, 743, 890
GsuI	CTGGAG	2 cut(s)	38, 1088
HaeII	RGCGCY	4 cut(s)	36, 55, 910, 1036
HaeIII	GGCC	1 cut(s)	234
HapII	CCGG	2 cut(s)	92, 246
HgaI	GACGC	2 cut(s)	19, 34
HhaI	GCGC	4 cut(s)	35, 54, 909, 1035
Hin1I	GRCGYC	2 cut(s)	907, 1033
Hin1II	CATG	5 cut(s)	142, 350, 565, 821, 920
Hin6I	GCGC	4 cut(s)	33, 52, 907, 1033
HinP1I	GCGC	4 cut(s)	33, 52, 907, 1033
HincII	GTYRAC	1 cut(s)	9
HindII	GTYRAC	1 cut(s)	9
HindIII	AAGCTT	1 cut(s)	812
HinfI	GANTC	2 cut(s)	171, 856
HpaII	CCGG	2 cut(s)	92, 246
HphI	GGTGA	3 cut(s)	34, 145, 632
Hpy166II	GTNNAC	2 cut(s)	9, 1024
Hpy188I	TCNGA	3 cut(s)	120, 230, 861
Hpy188III	TCNNGA	4 cut(s)	38, 139, 476, 830
Hpy8I	GTNNAC	2 cut(s)	9, 1024
Hpy99I	CGWCG	2 cut(s)	10, 13
HpyAV	CCTTC	3 cut(s)	67, 202, 355
HpyCH4III	ACNGT	3 cut(s)	128, 151, 430
HpyCH4IV	ACGT	3 cut(s)	439, 514, 694
HpyCH4V	TGCA	4 cut(s)	266, 320, 443, 686
HpyF10VI	GCNNNNNNNGC	6 cut(s)	58, 108, 542, 811, 913, 922
HpyF3I	CTNAG	2 cut(s)	117, 605
HpySE526I	ACGT	3 cut(s)	439, 514, 694
Hsp92I	GRCGYC	2 cut(s)	907, 1033
Hsp92II	CATG	5 cut(s)	142, 350, 565, 821, 920
HspAI	GCGC	4 cut(s)	33, 52, 907, 1033
KasI	GGCGCC	2 cut(s)	906, 1032
KroI	GCCGGC	1 cut(s)	91
KroNI	GCCGGC	1 cut(s)	93
Kzo9I	GATC	5 cut(s)	141, 180, 288, 963, 1099
LmnI	GCTCC	4 cut(s)	49, 58, 367, 550
Lsp1109I	GCAGC	4 cut(s)	304, 523, 698, 754
LweI	GCATC	1 cut(s)	322
MaeI	CTAG	1 cut(s)	323
MaeII	ACGT	3 cut(s)	439, 514, 694
MaeIII	GTNAC	4 cut(s)	22, 151, 510, 863
MalI	GATC	5 cut(s)	143, 182, 290, 965, 1101
MbiI	CCGCTC	2 cut(s)	99, 889
MboI	GATC	5 cut(s)	141, 180, 288, 963, 1099
MboII	GAAGA	8 cut(s)	250, 427, 689, 716, 1009, 1058, 1061, 1070
MfeI	CAATTG	1 cut(s)	972
MflI	RGATCY	2 cut(s)	180, 288
MluCI	AATT	8 cut(s)	573, 593, 681, 764, 833, 972, 989, 1119
MluI	ACGCGT	1 cut(s)	26
Mly113I	GGCGCC	2 cut(s)	907, 1033
MlyI	GAGTC	1 cut(s)	165
MmeI	TCCRAC	1 cut(s)	465
MroNI	GCCGGC	1 cut(s)	91
MseI	TTAA	4 cut(s)	566, 654, 897, 1123
MslI	CAYNNNNRTG	1 cut(s)	915
MspA1I	CMGCKG	1 cut(s)	317
MspI	CCGG	2 cut(s)	92, 246
MunI	CAATTG	1 cut(s)	972
Mva1269I	GAATGC	2 cut(s)	266, 927
MvnI	CGCG	1 cut(s)	28
MwoI	GCNNNNNNNGC	6 cut(s)	58, 108, 542, 811, 913, 922
NaeI	GCCGGC	1 cut(s)	93
NarI	GGCGCC	2 cut(s)	907, 1033
NdeI	CATATG	1 cut(s)	673
NdeII	GATC	5 cut(s)	141, 180, 288, 963, 1099
NgoMIV	GCCGGC	1 cut(s)	91
NlaIII	CATG	5 cut(s)	142, 350, 565, 821, 920
NlaIV	GGNNCC	4 cut(s)	250, 369, 908, 1034
NmuCI	GTSAC	3 cut(s)	22, 151, 510
NspI	RCATGY	1 cut(s)	565
PagI	TCATGA	1 cut(s)	138
PctI	GAATGC	2 cut(s)	266, 927
PdiI	GCCGGC	1 cut(s)	93
PfeI	GAWTC	1 cut(s)	856
PflFI	GACNNNGTC	1 cut(s)	149
PkrI	GCNGC	7 cut(s)	101, 223, 319, 538, 688, 744, 891
PleI	GAGTC	1 cut(s)	165
PluTI	GGCGCC	2 cut(s)	910, 1036
PmaCI	CACGTG	1 cut(s)	515
PmlI	CACGTG	1 cut(s)	515
PpsI	GAGTC	1 cut(s)	165
Ppu21I	YACGTR	1 cut(s)	515
PsiI	TTATAA	1 cut(s)	753
PspCI	CACGTG	1 cut(s)	515
PspN4I	GGNNCC	4 cut(s)	250, 369, 908, 1034
PsuI	RGATCY	2 cut(s)	180, 288
PsyI	GACNNNGTC	1 cut(s)	149
PvuII	CAGCTG	1 cut(s)	317
RsaI	GTAC	2 cut(s)	299, 427
RsaNI	GTAC	2 cut(s)	298, 426
RseI	CAYNNNNRTG	1 cut(s)	915
SalI	GTCGAC	1 cut(s)	7
SaqAI	TTAA	4 cut(s)	566, 654, 897, 1123
SatI	GCNGC	7 cut(s)	100, 222, 318, 537, 687, 743, 890
Sau3AI	GATC	5 cut(s)	141, 180, 288, 963, 1099
SchI	GAGTC	1 cut(s)	165
SfaNI	GCATC	1 cut(s)	322
SfcI	CTRYAG	1 cut(s)	540
SfoI	GGCGCC	2 cut(s)	908, 1034
SgrDI	CGTCGACG	1 cut(s)	7
SmiMI	CAYNNNNRTG	1 cut(s)	915
SmlI	CTYRAG	1 cut(s)	372
SmoI	CTYRAG	1 cut(s)	372
SpeI	ACTAGT	1 cut(s)	322
Sse9I	AATT	8 cut(s)	573, 593, 681, 764, 833, 972, 989, 1119
SsiI	CCGC	4 cut(s)	99, 133, 221, 889
SspDI	GGCGCC	2 cut(s)	906, 1032
SspMI	CTAG	1 cut(s)	323
StyI	CCWWGG	1 cut(s)	931
TaaI	ACNGT	3 cut(s)	128, 151, 430
TaiI	ACGT	3 cut(s)	442, 517, 697
TaqI	TCGA	2 cut(s)	8, 144
TasI	AATT	8 cut(s)	573, 593, 681, 764, 833, 972, 989, 1119
TauI	GCSGC	3 cut(s)	102, 224, 892
TfiI	GAWTC	1 cut(s)	856
Tru1I	TTAA	4 cut(s)	566, 654, 897, 1123
Tru9I	TTAA	4 cut(s)	566, 654, 897, 1123
TscAI	CASTG	2 cut(s)	268, 391
TseFI	GTSAC	3 cut(s)	22, 151, 510
TseI	GCWGC	4 cut(s)	317, 536, 686, 742
Tsp45I	GTSAC	3 cut(s)	22, 151, 510
TspDTI	ATGAA	5 cut(s)	363, 690, 717, 806, 1071
TspGWI	ACGGA	1 cut(s)	281
TspRI	CASTG	2 cut(s)	268, 391
Tth111I	GACNNNGTC	1 cut(s)	149
XagI	CCTNNNNNAGG	1 cut(s)	359
XapI	RAATTY	1 cut(s)	833
XceI	RCATGY	1 cut(s)	565
XmiI	GTMKAC	1 cut(s)	8
XspI	CTAG	1 cut(s)	323

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