Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0003318

Physical Location & Seq

Genomic Coordinates Forward (+)

25849420 .. 25855991

Gene Structure 6572 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG244500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1380 bp

ATGATGTCACTTAAAAAATTTCTTCTCTCAATATTCATCATCATCATCATCAATATCATCTCTTCAATTTCATGTGACAGAAGTACTAATTTGCAAGAGAACACACTTGAGGATTTTGTTGATGAAGCATCAGGTACTGGATATGATTCCCAAGCGTATCCTTCATACTGGAGCATGATTGATGACAGCAAGGACTTGATCGAGCAAAGTACTGATGATGTCCTCACTTTGAAGAGCTCTGATCAAGTGGCAGTTACCACAGTCAGTGTTCATGATTTTGGAGCTAAGGGTGATGGAGAAACTGATGACACAGAGGCGTTTGTGAAGGCATGGAAGGTAGCTTGTTCGTCTAAGAATGCAGCTGTTTTGGTGGTGCCTCAGAAGATCTATTGGCTTAAACCGATTAGATTTTCAGGTCCTTGCTTATCTCAATTGATGGTGCAGATTGTTGGTACCTTAGAAGCGTCGGATGATCGATCTGACTTCCGCCAAGATGGTAAACACTGGCTTATTTTTGATAGTGTTCGGAAGTTACTGCTTGATGGTGGTGGAACCATCAATGGCAATGGCAAGGAATGGTGGCAGAACTCATGCAAAATCAATAAATCTAAGCCATGCCAGGATGCACCAACGGCACTTGCGTTCTATAAATGTAAGGATTTGATAGTGAAGAATCTAAAGATACAAGATGCTCAGCAAATTCATTTGTCTTTCCAGAAGTGCATGAACGTTCTAGCTTCCAATCTCTCAATTACTGCACCAGAGAAAAGCCCCAACACCGATGGAATTCATGTTACAAATACTCAAGACATACTCATCACAACCTCTATTATATCCACTGGTGATGATTGTATTTCAATTGTAAGTGGATCCGAAAAGGTGCAAGCAATGAACATAACCTGCGGACCTGGACATGGAATCAGTATCGGAAGCTTGGGATCTGGAAAATCAGAAGCTTATGTTTCTGAAGTTGCTCTATATGGAGCTAAACTAATTGGAACCACAAATGGAGTCAGGATCAAGACTTGGCAGGGAGGATCTGGTAGTGCAAACAACATCACATTTGAGAACATTGAAATGCTTGATGTTACCAACCCCATCCTAATAGATCAATACTATTGTGACAGCAAGAAGCCATGTAAAGAACAGAAATCGGCAGTTCAAGTGCAAAATGTATTGTACAAGAACATCAAAGGAACAAGTGCCTCAGACGTTGCTATTAAGTTTGATTGCAGCAAGAACTTTCCTTGTCAGGGTATTGTGTTGCAAGACATTAAACTTGAGCATGGAGGAGGGAAAACAGCTAAAGCATTATGCAACAATATTAATTTCACTAGCATAGGAGTTGTTTCCCCTCTCTGTTATCAAGCGAAACTATGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0003006 GO:0003674 GO:0003824 GO:0004553 GO:0004650 GO:0005575 GO:0005576 GO:0005618 GO:0005623 GO:0007275 GO:0008150 GO:0009664 GO:0009791 GO:0009827 GO:0009830 GO:0009838 GO:0009900 GO:0009901 GO:0009908 GO:0009987 GO:0010047 GO:0010227 GO:0016043 GO:0016787 GO:0016798 GO:0022411 GO:0022414 GO:0030312 GO:0032501 GO:0032502 GO:0032504 GO:0042545 GO:0044277 GO:0044464 GO:0045229 GO:0048367 GO:0048437 GO:0048438 GO:0048443 GO:0048466 GO:0048608 GO:0048609 GO:0048653 GO:0048731 GO:0048827 GO:0048856 GO:0061458 GO:0071554 GO:0071555 GO:0071669 GO:0071840 GO:0071944 GO:0090567 GO:0099402

KEGG Pathways

Metabolic & Signaling

ko00040 ko01100 map00040 map01100

Pfam Domains

Protein Families

Glyco_hydro_28

Protein Analysis

459

Amino Acids

49.91

Weight (kDa)

5.77

Isoelectric Point (pI)

30.64

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Pect-lyase_RHGA_epim	PF12708	88 - 127	1e-05	Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28	PF00295	115 - 443	2e-104	Glycosyl hydrolases family 28

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0003318)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G41850
fragaria_vesca	FvH4_2g20930 FvH4_2g20930 FvH4_6g23580
malus_domestica	MD05G1192600.v1.1 MD10G1179100.v1.1 MD12G1077400.v1.1 MD12G1077600.v1.1
prunus_persica	Prupe.7G063900_v2.0.a1 Prupe.8G218900_v2.0.a1
pyrus_communis	pycom05g17960 pycom10g15530 pycom12g06230
rosa_chinensis	RchiOBHm_Chr3g0481691 RchiOBHm_Chr6g0287311
rosa_laevigata	RLG00000012502 RLG00000023383
rosa_multiflora	Rmu_sc0007029.1_g000032 Rmu_ssc0000267.1_g000001
rosa_roxburghii	Rroxscaffold_6G00399870 Rroxscaffold_6G00400230 Rroxscaffold_7G00181550
rosa_rugosa	Rorug03G0193400 Rorug06G0186800 Rorug06G0186900
rosa_samantha	Rh3AG244500 Rh3BG279600 Rh3CG274700 Rh3DG271500 Rh6AG298300 Rh6BG303700 Rh6CG306100 Rh6CG312000 Rh6DG295600
rosa_wichuraiana	Rw3G021820 Rw6G025780

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	908
Acc65I	GGTACC	1 cut(s)	452
AccB1I	GGYRCC	2 cut(s)	373, 452
AciI	CCGC	2 cut(s)	487, 903
AclI	AACGTT	1 cut(s)	729
AclWI	GGATC	5 cut(s)	864, 877, 946, 1025, 1045
AcsI	RAATTY	3 cut(s)	17, 699, 786
AcuI	CTGAAG	1 cut(s)	987
AfaI	GTAC	5 cut(s)	85, 136, 211, 454, 1181
AfiI	CCNNNNNNNGG	2 cut(s)	914, 1253
AgsI	TTSAA	5 cut(s)	66, 232, 858, 1076, 1163
AjnI	CCWGG	2 cut(s)	618, 907
AluBI	AGCT	9 cut(s)	237, 284, 341, 362, 737, 933, 956, 986, 1304
AluI	AGCT	9 cut(s)	237, 284, 341, 362, 737, 933, 956, 986, 1304
Alw21I	GWGCWC	1 cut(s)	239
AlwI	GGATC	5 cut(s)	864, 877, 946, 1025, 1045
AlwNI	CAGNNNCTG	1 cut(s)	137
ApeKI	GCWGC	2 cut(s)	359, 1233
ApoI	RAATTY	3 cut(s)	17, 699, 786
AseI	ATTAAT	1 cut(s)	1326
Asp718I	GGTACC	1 cut(s)	452
AspS9I	GGNCC	2 cut(s)	416, 905
AsuHPI	GGTGA	2 cut(s)	302, 854
AvaII	GGWCC	2 cut(s)	416, 905
BamHI	GGATCC	1 cut(s)	869
BanI	GGYRCC	2 cut(s)	373, 452
BanII	GRGCYC	1 cut(s)	239
Bbv12I	GWGCWC	1 cut(s)	239
BbvI	GCAGC	2 cut(s)	371, 1245
BccI	CCATC	7 cut(s)	287, 430, 488, 536, 563, 776, 1106
BceAI	ACGGC	1 cut(s)	648
BciT130I	CCWGG	2 cut(s)	620, 909
BciVI	GTATCC	1 cut(s)	168
BclI	TGATCA	1 cut(s)	241
BfaI	CTAG	2 cut(s)	734, 1335
BfuAI	ACCTGC	1 cut(s)	908
BfuI	GTATCC	1 cut(s)	168
BglII	AGATCT	1 cut(s)	384
BisI	GCNGC	2 cut(s)	360, 1234
BlpI	GCTNAGC	1 cut(s)	693
BlsI	GCNGC	2 cut(s)	361, 1235
BmcAI	AGTACT	2 cut(s)	85, 211
Bme1390I	CCNGG	2 cut(s)	620, 909
Bme18I	GGWCC	2 cut(s)	416, 905
BmgT120I	GGNCC	2 cut(s)	416, 905
BmiI	GGNNCC	5 cut(s)	375, 454, 553, 871, 1000
BmrFI	CCNGG	2 cut(s)	620, 909
BmsI	GCATC	3 cut(s)	137, 613, 679
BpmI	CTGGAG	1 cut(s)	190
Bpu10I	CCTNAGC	1 cut(s)	285
Bpu1102I	GCTNAGC	1 cut(s)	693
BpuEI	CTTGAG	3 cut(s)	128, 789, 1301
Bsa29I	ATCGAT	1 cut(s)	475
Bsc4I	CCNNNNNNNGG	2 cut(s)	914, 1253
Bse1I	ACTGG	4 cut(s)	142, 173, 509, 844
Bse3DI	GCAATG	2 cut(s)	571, 894
BseBI	CCWGG	2 cut(s)	620, 909
BseCI	ATCGAT	1 cut(s)	475
BseGI	GGATG	3 cut(s)	475, 628, 1098
BseLI	CCNNNNNNNGG	2 cut(s)	914, 1253
BseMI	GCAATG	2 cut(s)	571, 894
BseMII	CTCAG	3 cut(s)	392, 707, 1221
BseNI	ACTGG	4 cut(s)	142, 173, 509, 844
BseRI	GAGGAG	1 cut(s)	1305
BseXI	GCAGC	2 cut(s)	371, 1245
BsgI	GTGCAG	2 cut(s)	461, 741
BshNI	GGYRCC	2 cut(s)	373, 452
BshVI	ATCGAT	1 cut(s)	475
BsiHKAI	GWGCWC	1 cut(s)	239
BslI	CCNNNNNNNGG	2 cut(s)	914, 1253
BsmI	GAATGC	1 cut(s)	361
Bsp1286I	GDGCHC	1 cut(s)	239
Bsp1407I	TGTACA	1 cut(s)	1179
Bsp1720I	GCTNAGC	1 cut(s)	693
BspACI	CCGC	2 cut(s)	487, 903
BspCNI	CTCAG	3 cut(s)	391, 706, 1220
BspDI	ATCGAT	1 cut(s)	475
BspHI	TCATGA	1 cut(s)	271
BspLI	GGNNCC	5 cut(s)	375, 454, 553, 871, 1000
BspMI	ACCTGC	1 cut(s)	908
BspPI	GGATC	5 cut(s)	864, 877, 946, 1025, 1045
BspQI	GCTCTTC	1 cut(s)	227
BspT107I	GGYRCC	2 cut(s)	373, 452
BsrDI	GCAATG	2 cut(s)	571, 894
BsrGI	TGTACA	1 cut(s)	1179
BsrI	ACTGG	4 cut(s)	142, 173, 509, 844
Bst2UI	CCWGG	2 cut(s)	620, 909
Bst4CI	ACNGT	1 cut(s)	262
Bst6I	CTCTTC	2 cut(s)	67, 227
BstAUI	TGTACA	1 cut(s)	1179
BstC8I	GCNNGC	1 cut(s)	885
BstDEI	CTNAG	7 cut(s)	285, 351, 378, 457, 609, 693, 1207
BstF5I	GGATG	3 cut(s)	475, 628, 1098
BstMWI	GCNNNNNNNGC	1 cut(s)	632
BstNI	CCWGG	2 cut(s)	620, 909
BstSCI	CCNGG	2 cut(s)	618, 907
BstV1I	GCAGC	2 cut(s)	371, 1245
BstX2I	RGATCY	4 cut(s)	384, 869, 938, 1037
BstYI	RGATCY	4 cut(s)	384, 869, 938, 1037
Bsu15I	ATCGAT	1 cut(s)	475
BsuI	GTATCC	1 cut(s)	168
BsuTUI	ATCGAT	1 cut(s)	475
BtsCI	GGATG	3 cut(s)	475, 628, 1098
BtsIMutI	CAGTG	3 cut(s)	271, 502, 837
BveI	ACCTGC	1 cut(s)	908
Cac8I	GCNNGC	1 cut(s)	885
CaiI	CAGNNNCTG	1 cut(s)	137
CciI	TCATGA	1 cut(s)	271
Cfr13I	GGNCC	2 cut(s)	416, 905
ClaI	ATCGAT	1 cut(s)	475
CseI	GACGC	1 cut(s)	453
Csp6I	GTAC	5 cut(s)	84, 135, 210, 453, 1180
CviQI	GTAC	5 cut(s)	84, 135, 210, 453, 1180
DdeI	CTNAG	7 cut(s)	285, 351, 378, 457, 609, 693, 1207
Eam1104I	CTCTTC	2 cut(s)	67, 227
EarI	CTCTTC	2 cut(s)	67, 227
EciI	GGCGGA	1 cut(s)	476
Ecl136II	GAGCTC	1 cut(s)	237
Eco24I	GRGCYC	1 cut(s)	239
Eco47I	GGWCC	2 cut(s)	416, 905
Eco53kI	GAGCTC	1 cut(s)	237
Eco57I	CTGAAG	1 cut(s)	987
EcoICRI	GAGCTC	1 cut(s)	237
EcoO109I	RGGNCCY	1 cut(s)	416
EcoRI	GAATTC	1 cut(s)	786
EcoRII	CCWGG	2 cut(s)	618, 907
EcoT38I	GRGCYC	1 cut(s)	239
FbaI	TGATCA	1 cut(s)	241
Fnu4HI	GCNGC	2 cut(s)	360, 1234
FokI	GGATG	3 cut(s)	482, 635, 1085
FriOI	GRGCYC	1 cut(s)	239
Fsp4HI	GCNGC	2 cut(s)	360, 1234
FspBI	CTAG	2 cut(s)	734, 1335
GluI	GCNGC	2 cut(s)	360, 1234
GsuI	CTGGAG	1 cut(s)	190
HgaI	GACGC	1 cut(s)	453
HindIII	AAGCTT	2 cut(s)	931, 954
HinfI	GANTC	4 cut(s)	146, 673, 918, 1011
HphI	GGTGA	2 cut(s)	302, 854
Hpy166II	GTNNAC	1 cut(s)	500
Hpy188III	TCNNGA	6 cut(s)	272, 715, 806, 942, 1015, 1021
Hpy8I	GTNNAC	1 cut(s)	500
Hpy99I	CGWCG	1 cut(s)	469
HpyAV	CCTTC	3 cut(s)	171, 319, 328
HpyCH4III	ACNGT	1 cut(s)	262
HpyCH4IV	ACGT	2 cut(s)	729, 1212
HpyF10VI	GCNNNNNNNGC	1 cut(s)	632
HpyF3I	CTNAG	7 cut(s)	285, 351, 378, 457, 609, 693, 1207
HpySE526I	ACGT	2 cut(s)	729, 1212
KpnI	GGTACC	1 cut(s)	456
Ksp22I	TGATCA	1 cut(s)	241
LguI	GCTCTTC	1 cut(s)	227
LmnI	GCTCC	3 cut(s)	171, 281, 983
Lsp1109I	GCAGC	2 cut(s)	371, 1245
LweI	GCATC	3 cut(s)	137, 613, 679
MaeI	CTAG	2 cut(s)	734, 1335
MaeII	ACGT	2 cut(s)	729, 1212
MaeIII	GTNAC	7 cut(s)	6, 74, 253, 531, 793, 1087, 1121
MboII	GAAGA	5 cut(s)	14, 54, 244, 394, 682
MfeI	CAATTG	2 cut(s)	431, 858
MflI	RGATCY	4 cut(s)	384, 869, 938, 1037
MhlI	GDGCHC	1 cut(s)	239
MlyI	GAGTC	1 cut(s)	1020
MmeI	TCCRAC	1 cut(s)	447
MseI	TTAA	5 cut(s)	12, 396, 1221, 1275, 1326
MslI	CAYNNNNRTG	1 cut(s)	1076
MspA1I	CMGCKG	1 cut(s)	362
MspR9I	CCNGG	2 cut(s)	620, 909
MunI	CAATTG	2 cut(s)	431, 858
Mva1269I	GAATGC	1 cut(s)	361
MvaI	CCWGG	2 cut(s)	620, 909
MwoI	GCNNNNNNNGC	1 cut(s)	632
NlaIV	GGNNCC	5 cut(s)	375, 454, 553, 871, 1000
NmuCI	GTSAC	3 cut(s)	6, 74, 1121
PagI	TCATGA	1 cut(s)	271
PciSI	GCTCTTC	1 cut(s)	227
PcsI	WCGNNNNNNNCGW	1 cut(s)	638
PctI	GAATGC	1 cut(s)	361
PfeI	GAWTC	3 cut(s)	146, 673, 918
PkrI	GCNGC	2 cut(s)	361, 1235
PleI	GAGTC	1 cut(s)	1019
PpsI	GAGTC	1 cut(s)	1019
PpuMI	RGGWCCY	1 cut(s)	416
PshBI	ATTAAT	1 cut(s)	1326
Psp124BI	GAGCTC	1 cut(s)	239
Psp1406I	AACGTT	1 cut(s)	729
Psp5II	RGGWCCY	1 cut(s)	416
Psp6I	CCWGG	2 cut(s)	618, 907
PspGI	CCWGG	2 cut(s)	618, 907
PspN4I	GGNNCC	5 cut(s)	375, 454, 553, 871, 1000
PspPI	GGNCC	2 cut(s)	416, 905
PspPPI	RGGWCCY	1 cut(s)	416
PstNI	CAGNNNCTG	1 cut(s)	137
PsuI	RGATCY	4 cut(s)	384, 869, 938, 1037
PvuII	CAGCTG	1 cut(s)	362
RsaI	GTAC	5 cut(s)	85, 136, 211, 454, 1181
RsaNI	GTAC	5 cut(s)	84, 135, 210, 453, 1180
RseI	CAYNNNNRTG	1 cut(s)	1076
SacI	GAGCTC	1 cut(s)	239
SapI	GCTCTTC	1 cut(s)	227
SaqAI	TTAA	5 cut(s)	12, 396, 1221, 1275, 1326
SatI	GCNGC	2 cut(s)	360, 1234
Sau96I	GGNCC	2 cut(s)	416, 905
ScaI	AGTACT	2 cut(s)	85, 211
SchI	GAGTC	1 cut(s)	1020
ScrFI	CCNGG	2 cut(s)	620, 909
SduI	GDGCHC	1 cut(s)	239
SfaNI	GCATC	3 cut(s)	137, 613, 679
SinI	GGWCC	2 cut(s)	416, 905
SmiMI	CAYNNNNRTG	1 cut(s)	1076
SmlI	CTYRAG	3 cut(s)	107, 804, 1280
SmoI	CTYRAG	3 cut(s)	107, 804, 1280
SsiI	CCGC	2 cut(s)	487, 903
SspI	AATATT	2 cut(s)	33, 1324
SspMI	CTAG	2 cut(s)	734, 1335
SstI	GAGCTC	1 cut(s)	239
StyD4I	CCNGG	2 cut(s)	618, 907
TaaI	ACNGT	1 cut(s)	262
TaiI	ACGT	2 cut(s)	732, 1215
TaqI	TCGA	2 cut(s)	201, 475
TatI	WGTACW	3 cut(s)	83, 209, 1179
TfiI	GAWTC	3 cut(s)	146, 673, 918
Tru1I	TTAA	5 cut(s)	12, 396, 1221, 1275, 1326
Tru9I	TTAA	5 cut(s)	12, 396, 1221, 1275, 1326
TscAI	CASTG	3 cut(s)	271, 509, 844
TseFI	GTSAC	3 cut(s)	6, 74, 1121
TseI	GCWGC	2 cut(s)	359, 1233
Tsp45I	GTSAC	3 cut(s)	6, 74, 1121
TspDTI	ATGAA	9 cut(s)	25, 60, 138, 153, 260, 692, 740, 779, 905
TspRI	CASTG	3 cut(s)	271, 509, 844
VpaK11BI	GGWCC	2 cut(s)	416, 905
VspI	ATTAAT	1 cut(s)	1326
XapI	RAATTY	3 cut(s)	17, 699, 786
XspI	CTAG	2 cut(s)	734, 1335
ZrmI	AGTACT	2 cut(s)	85, 211

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