Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2C

Orthogroup ID

OG0004536

Physical Location & Seq

Genomic Coordinates Forward (+)

3551965 .. 3553035

Gene Structure 1071 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2CG045000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1071 bp

ATGCTGATGGATCAGACCGCCCCAACATCCTCCATTAGACTTGAAGATGCCGATTATCACGAGGTCAAAAACCTCTCTGTCAAGGAAGTAGAGGAGAAACTTGAAGCTCTCAAGAAAAAATTAGATGATGCGGAATTTAGTTTGATTTCACGAGGCAAGTCCAACCAGACCTATCGTGCTTGTAGCGATGGTGTCAAACGTTATGCGCTGAAGGATATAAATAAATGCTTTAAACCAAGAGCTGAAAAAAGAGAAGCCATCCGTTATATGATTGATCTTATTATCCAGTCCTTCAAAGAAGAAAAACGACCTACACTTGCTAAGCTGAACACGTCGAGCTCAGCTCTTGATGACATATGTTGCGCTATAGGTTGCACCAGATCAAGTCTTAATGTAGATCCTAGTGTAAGAGGCGTTGTTGGAGGTCTGCTTTCGATCAAGATTGGAAAGTACAAAACCTTGTGTACACGCAGGGATGATGGGGAACCCATCCCGCCTTTTATGCATTCAGATATTATTTTGAAGAATCGTGGAGCCAAGTTCGTACTGGTGGTGGAAAAGAAATCCGCTTTTAATACTCTCATGCAAGACAAGTTTTACGTTGATTATCCATGTATAATCATCACTGGAATAGGAATGCCGGAGGTGGGGAGCAGAAGTTTTCTAAACGTATTGTCGGAGAAGTTTAAGATTCCAGTGTATGGCCTTTTCGACTGTGATCCAGCTGGCATCGAAATTTTATCGGTTTATGCTGCTGGGTCGTACAATCAATCGTACGATAGTGTGAATTTGACTTGCCCGTTTATGATGTGGTTGGGTGTTTGGCCGAGTGACCTACATGCGCTTAAAATACCCTGCAAGGATTTAACTTCAGAGGAGATTAGAAAGGTAAACACTCTTTTGGAAAAAGATTTTGTGAAAGAGTATCCGACATTGCTTGAGGAGTTGCAACTTATGAAGAAGAAGAAGAGAAAGGCGAACCTTGAAGCTTTGGAGAAGTTTGGGCACACTTGTTTGACCAAGTACTATTTGCCATATAAGTTGAAGTATCTCTTAACTGACACCGACTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000228 GO:0000280 GO:0000706 GO:0000729 GO:0003674 GO:0003676 GO:0003677 GO:0003824 GO:0003916 GO:0003918 GO:0004518 GO:0004519 GO:0004520 GO:0004536 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005694 GO:0006139 GO:0006259 GO:0006281 GO:0006302 GO:0006310 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0006996 GO:0007049 GO:0007127 GO:0007131 GO:0008094 GO:0008134 GO:0008150 GO:0008152 GO:0009987 GO:0016043 GO:0016462 GO:0016787 GO:0016788 GO:0016817 GO:0016818 GO:0016853 GO:0016887 GO:0016889 GO:0016894 GO:0017111 GO:0022402 GO:0022414 GO:0030957 GO:0031974 GO:0031981 GO:0033554 GO:0034641 GO:0035825 GO:0042138 GO:0042623 GO:0042802 GO:0042803 GO:0043170 GO:0043226 GO:0043227 GO:0043228 GO:0043229 GO:0043231 GO:0043232 GO:0043233 GO:0044237 GO:0044238 GO:0044260 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0046983 GO:0048285 GO:0050896 GO:0051321 GO:0051716 GO:0061505 GO:0061982 GO:0070013 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0097159 GO:0140013 GO:0140097 GO:1901360 GO:1901363 GO:1903046

KEGG Pathways

Metabolic & Signaling

ko04113 map04113

Pfam Domains

Protein Families

TP6A_N

Protein Analysis

356

Amino Acids

40.46

Weight (kDa)

8.68

Isoelectric Point (pI)

41.3

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TOP6A-Spo11_Toprim	PF21180	181 - 348	3.6e-53	Topoisomerase 6 subunit A/Spo11, Toprim domain

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: OG0004536)

Species	Orthologous Gene IDs
fragaria_vesca	FvH4_3g43731 FvH4_3g43753
rosa_chinensis	RchiOBHm_Chr2g0086091 RchiOBHm_Chr2g0089291 RchiOBHm_Chr2g0089851 RchiOBHm_Chr5g0083311
rosa_laevigata	RLG00000015741 RLG00000016061 RLG00000017209
rosa_multiflora	Rmu_co8293021.1_g000001 Rmu_co8360049.1_g000001 Rmu_sc0000388.1_g000047 Rmu_sc0002384.1_g000009 Rmu_sc0003382.1_g000021 Rmu_sc0017765.1_g000002 Rmu_ssc0000355.1_g000016
rosa_roxburghii	Rroxscaffold_2G00140180 Rroxscaffold_2G00151540
rosa_rugosa	Rorug01G0465600 Rorug01G0488800 Rorug02G0003700
rosa_samantha	Rh2AG015000 Rh2AG045100 Rh2AG048900 Rh2BG047800 Rh2CG016000 Rh2CG016100 Rh2CG045000 Rh2CG049900 Rh5BG561000 Rh5CG583600
rosa_wichuraiana	Rw2G001320

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	701
AciI	CCGC	4 cut(s)	18, 131, 494, 567
AclI	AACGTT	1 cut(s)	199
AclWI	GGATC	3 cut(s)	18, 392, 713
AcoI	YGGCCR	1 cut(s)	824
AcsI	RAATTY	3 cut(s)	134, 735, 787
AcuI	CTGAAG	2 cut(s)	230, 855
AfaI	GTAC	6 cut(s)	452, 466, 546, 764, 776, 1025
AfiI	CCNNNNNNNGG	2 cut(s)	647, 701
AflIII	ACRYGT	1 cut(s)	330
AgsI	TTSAA	6 cut(s)	44, 104, 295, 523, 986, 1045
AjiI	CACGTC	1 cut(s)	333
AluBI	AGCT	7 cut(s)	107, 242, 325, 339, 344, 725, 989
AluI	AGCT	7 cut(s)	107, 242, 325, 339, 344, 725, 989
Alw21I	GWGCWC	1 cut(s)	341
AlwI	GGATC	3 cut(s)	18, 392, 713
AoxI	GGCC	2 cut(s)	703, 824
ApeKI	GCWGC	1 cut(s)	752
ApoI	RAATTY	3 cut(s)	134, 735, 787
AspLEI	GCGC	3 cut(s)	208, 365, 844
BaeGI	GKGCMC	1 cut(s)	1008
BanII	GRGCYC	1 cut(s)	341
BauI	CACGAG	2 cut(s)	59, 150
Bbv12I	GWGCWC	1 cut(s)	341
BbvI	GCAGC	1 cut(s)	739
BccI	CCATC	4 cut(s)	182, 266, 473, 497
BciVI	GTATCC	1 cut(s)	936
BfaI	CTAG	1 cut(s)	402
BfmI	CTRYAG	1 cut(s)	366
BfuI	GTATCC	1 cut(s)	936
BisI	GCNGC	1 cut(s)	753
BlpI	GCTNAGC	2 cut(s)	321, 340
BlsI	GCNGC	1 cut(s)	754
BmcAI	AGTACT	1 cut(s)	1025
BmgBI	CACGTC	1 cut(s)	333
BmiI	GGNNCC	2 cut(s)	486, 535
BmsI	GCATC	3 cut(s)	37, 118, 738
BplI	GAGNNNNNCTC	2 cut(s)	328, 360
Bpu1102I	GCTNAGC	2 cut(s)	321, 340
BpuEI	CTTGAG	2 cut(s)	95, 959
BsaXI	ACNNNNNCTCC	2 cut(s)	643, 673
Bsc4I	CCNNNNNNNGG	2 cut(s)	647, 701
Bse1I	ACTGG	4 cut(s)	286, 552, 631, 695
Bse3DI	GCAATG	1 cut(s)	932
BseGI	GGATG	4 cut(s)	26, 258, 481, 489
BseLI	CCNNNNNNNGG	2 cut(s)	647, 701
BseMI	GCAATG	1 cut(s)	932
BseMII	CTCAG	1 cut(s)	354
BseNI	ACTGG	4 cut(s)	286, 552, 631, 695
BseRI	GAGGAG	3 cut(s)	107, 890, 956
BseSI	GKGCMC	1 cut(s)	1008
BseXI	GCAGC	1 cut(s)	739
BseYI	CCCAGC	1 cut(s)	755
BshFI	GGCC	2 cut(s)	705, 826
BsiHKAI	GWGCWC	1 cut(s)	341
BsiSI	CCGG	1 cut(s)	641
BsiWI	CGTACG	1 cut(s)	774
BslI	CCNNNNNNNGG	2 cut(s)	647, 701
BsmI	GAATGC	2 cut(s)	505, 642
BsnI	GGCC	2 cut(s)	705, 826
Bsp1286I	GDGCHC	2 cut(s)	341, 1008
Bsp1407I	TGTACA	1 cut(s)	464
Bsp143I	GATC	6 cut(s)	10, 274, 380, 397, 435, 718
Bsp1720I	GCTNAGC	2 cut(s)	321, 340
BspACI	CCGC	4 cut(s)	18, 131, 494, 567
BspANI	GGCC	2 cut(s)	705, 826
BspCNI	CTCAG	1 cut(s)	353
BspLI	GGNNCC	2 cut(s)	486, 535
BspPI	GGATC	3 cut(s)	18, 392, 713
BsrDI	GCAATG	1 cut(s)	932
BsrGI	TGTACA	1 cut(s)	464
BsrI	ACTGG	4 cut(s)	286, 552, 631, 695
BssMI	GATC	6 cut(s)	10, 274, 380, 397, 435, 718
BssSI	CACGAG	2 cut(s)	59, 150
Bst2BI	CACGAG	2 cut(s)	59, 150
Bst4CI	ACNGT	1 cut(s)	716
Bst6I	CTCTTC	1 cut(s)	962
BstAUI	TGTACA	1 cut(s)	464
BstC8I	GCNNGC	1 cut(s)	727
BstDEI	CTNAG	2 cut(s)	321, 340
BstF5I	GGATG	4 cut(s)	26, 258, 481, 489
BstHHI	GCGC	3 cut(s)	208, 365, 844
BstKTI	GATC	6 cut(s)	13, 277, 383, 400, 438, 721
BstMBI	GATC	6 cut(s)	10, 274, 380, 397, 435, 718
BstMWI	GCNNNNNNNGC	1 cut(s)	502
BstNSI	RCATGY	1 cut(s)	842
BstSFI	CTRYAG	1 cut(s)	366
BstSLI	GKGCMC	1 cut(s)	1008
BstV1I	GCAGC	1 cut(s)	739
BstX2I	RGATCY	1 cut(s)	397
BstYI	RGATCY	1 cut(s)	397
BsuI	GTATCC	1 cut(s)	936
BsuRI	GGCC	2 cut(s)	705, 826
BtgZI	GCGATG	1 cut(s)	201
BtrI	CACGTC	1 cut(s)	333
BtsCI	GGATG	4 cut(s)	26, 258, 481, 489
BtsIMutI	CAGTG	2 cut(s)	624, 702
Cac8I	GCNNGC	1 cut(s)	727
CfoI	GCGC	3 cut(s)	208, 365, 844
Csp6I	GTAC	6 cut(s)	451, 465, 545, 763, 775, 1024
CviAII	CATG	3 cut(s)	583, 612, 839
CviQI	GTAC	6 cut(s)	451, 465, 545, 763, 775, 1024
DdeI	CTNAG	2 cut(s)	321, 340
DpnI	GATC	6 cut(s)	12, 276, 382, 399, 437, 720
DpnII	GATC	6 cut(s)	10, 274, 380, 397, 435, 718
DraI	TTTAAA	1 cut(s)	232
EaeI	YGGCCR	1 cut(s)	824
Eam1104I	CTCTTC	1 cut(s)	962
EarI	CTCTTC	1 cut(s)	962
Ecl136II	GAGCTC	1 cut(s)	339
Eco24I	GRGCYC	1 cut(s)	341
Eco53kI	GAGCTC	1 cut(s)	339
Eco57I	CTGAAG	2 cut(s)	230, 855
EcoICRI	GAGCTC	1 cut(s)	339
EcoT22I	ATGCAT	1 cut(s)	507
EcoT38I	GRGCYC	1 cut(s)	341
FaeI	CATG	3 cut(s)	586, 615, 842
FalI	AAGNNNNNCTT	2 cut(s)	1037, 1069
FatI	CATG	3 cut(s)	582, 611, 838
FauI	CCCGC	1 cut(s)	501
FauNDI	CATATG	1 cut(s)	356
Fnu4HI	GCNGC	1 cut(s)	753
FokI	GGATG	4 cut(s)	13, 245, 476, 488
FriOI	GRGCYC	1 cut(s)	341
Fsp4HI	GCNGC	1 cut(s)	753
FspBI	CTAG	1 cut(s)	402
GlaI	GCGC	3 cut(s)	207, 364, 843
GluI	GCNGC	1 cut(s)	753
GsaI	CCCAGC	1 cut(s)	759
HaeIII	GGCC	2 cut(s)	705, 826
HapII	CCGG	1 cut(s)	641
HhaI	GCGC	3 cut(s)	208, 365, 844
Hin1II	CATG	3 cut(s)	586, 615, 842
Hin6I	GCGC	3 cut(s)	206, 363, 842
HinP1I	GCGC	3 cut(s)	206, 363, 842
HindIII	AAGCTT	1 cut(s)	987
HinfI	GANTC	2 cut(s)	526, 691
HpaII	CCGG	1 cut(s)	641
Hpy166II	GTNNAC	3 cut(s)	465, 467, 892
Hpy188I	TCNGA	5 cut(s)	15, 511, 679, 874, 930
Hpy188III	TCNNGA	5 cut(s)	59, 112, 150, 347, 439
Hpy8I	GTNNAC	3 cut(s)	465, 467, 892
Hpy99I	CGWCG	1 cut(s)	337
HpyAV	CCTTC	2 cut(s)	205, 301
HpyCH4III	ACNGT	1 cut(s)	716
HpyCH4IV	ACGT	4 cut(s)	199, 332, 600, 669
HpyCH4V	TGCA	5 cut(s)	375, 505, 586, 858, 949
HpyF10VI	GCNNNNNNNGC	1 cut(s)	502
HpyF3I	CTNAG	2 cut(s)	321, 340
HpySE526I	ACGT	4 cut(s)	199, 332, 600, 669
Hsp92II	CATG	3 cut(s)	586, 615, 842
HspAI	GCGC	3 cut(s)	206, 363, 842
Kzo9I	GATC	6 cut(s)	10, 274, 380, 397, 435, 718
LmnI	GCTCC	2 cut(s)	533, 651
Lsp1109I	GCAGC	1 cut(s)	739
LweI	GCATC	3 cut(s)	37, 118, 738
MaeI	CTAG	1 cut(s)	402
MaeII	ACGT	4 cut(s)	199, 332, 600, 669
MaeIII	GTNAC	1 cut(s)	830
MalI	GATC	6 cut(s)	12, 276, 382, 399, 437, 720
MboI	GATC	6 cut(s)	10, 274, 380, 397, 435, 718
MboII	GAAGA	7 cut(s)	56, 311, 535, 970, 973, 976, 979
MflI	RGATCY	1 cut(s)	397
MhlI	GDGCHC	2 cut(s)	341, 1008
MluCI	AATT	4 cut(s)	119, 134, 735, 787
MmeI	TCCRAC	4 cut(s)	186, 400, 657, 953
Mph1103I	ATGCAT	1 cut(s)	507
MseI	TTAA	7 cut(s)	231, 390, 573, 687, 846, 866, 1055
MspA1I	CMGCKG	1 cut(s)	725
MspI	CCGG	1 cut(s)	641
Mva1269I	GAATGC	2 cut(s)	505, 642
MwoI	GCNNNNNNNGC	1 cut(s)	502
NdeI	CATATG	1 cut(s)	356
NdeII	GATC	6 cut(s)	10, 274, 380, 397, 435, 718
NlaIII	CATG	3 cut(s)	586, 615, 842
NlaIV	GGNNCC	2 cut(s)	486, 535
NmeAIII	GCCGAG	1 cut(s)	852
NmuCI	GTSAC	1 cut(s)	830
NsiI	ATGCAT	1 cut(s)	507
NspI	RCATGY	1 cut(s)	842
PctI	GAATGC	2 cut(s)	505, 642
PfeI	GAWTC	2 cut(s)	526, 691
Pfl23II	CGTACG	1 cut(s)	774
PflMI	CCANNNNNTGG	1 cut(s)	701
PkrI	GCNGC	1 cut(s)	754
Psp124BI	GAGCTC	1 cut(s)	341
Psp1406I	AACGTT	1 cut(s)	199
PspFI	CCCAGC	1 cut(s)	755
PspLI	CGTACG	1 cut(s)	774
PspN4I	GGNNCC	2 cut(s)	486, 535
PsuI	RGATCY	1 cut(s)	397
PvuII	CAGCTG	1 cut(s)	725
RsaI	GTAC	6 cut(s)	452, 466, 546, 764, 776, 1025
RsaNI	GTAC	6 cut(s)	451, 465, 545, 763, 775, 1024
SacI	GAGCTC	1 cut(s)	341
SaqAI	TTAA	7 cut(s)	231, 390, 573, 687, 846, 866, 1055
SatI	GCNGC	1 cut(s)	753
Sau3AI	GATC	6 cut(s)	10, 274, 380, 397, 435, 718
ScaI	AGTACT	1 cut(s)	1025
SduI	GDGCHC	2 cut(s)	341, 1008
SfaNI	GCATC	3 cut(s)	37, 118, 738
SfcI	CTRYAG	1 cut(s)	366
SmlI	CTYRAG	2 cut(s)	110, 938
SmoI	CTYRAG	2 cut(s)	110, 938
Sse9I	AATT	4 cut(s)	119, 134, 735, 787
SsiI	CCGC	4 cut(s)	18, 131, 494, 567
SspMI	CTAG	1 cut(s)	402
SstI	GAGCTC	1 cut(s)	341
TaaI	ACNGT	1 cut(s)	716
TaiI	ACGT	4 cut(s)	202, 335, 603, 672
TaqI	TCGA	4 cut(s)	335, 434, 711, 732
TasI	AATT	4 cut(s)	119, 134, 735, 787
TatI	WGTACW	3 cut(s)	450, 464, 1023
TfiI	GAWTC	2 cut(s)	526, 691
Tru1I	TTAA	7 cut(s)	231, 390, 573, 687, 846, 866, 1055
Tru9I	TTAA	7 cut(s)	231, 390, 573, 687, 846, 866, 1055
TscAI	CASTG	2 cut(s)	631, 702
TseFI	GTSAC	1 cut(s)	830
TseI	GCWGC	1 cut(s)	752
Tsp45I	GTSAC	1 cut(s)	830
TspDTI	ATGAA	1 cut(s)	971
TspGWI	ACGGA	1 cut(s)	251
TspRI	CASTG	2 cut(s)	631, 702
Van91I	CCANNNNNTGG	1 cut(s)	701
XapI	RAATTY	3 cut(s)	134, 735, 787
XceI	RCATGY	1 cut(s)	842
XcmI	CCANNNNNNNNNTGG	1 cut(s)	544
XspI	CTAG	1 cut(s)	402
ZrmI	AGTACT	1 cut(s)	1025
Zsp2I	ATGCAT	1 cut(s)	507

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