Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3D

Orthogroup ID

OG0003980

Physical Location & Seq

Genomic Coordinates Forward (+)

20948116 .. 20955534

Gene Structure 7419 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3DG223000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 858 bp

ATGTCGTCCTCCTCCTCCTCCTCATCATCAGAACCCCCGCCGCCTTCTTCAGAAATCCGAATCCGATCGGTATGGGCCGATAACCTCGACGACGAGTTCGACAAGATCCGATCCGTGATCGACGAATTCCCGATGATCTCCATGGACACGGAGTTTCCCGGCGTCGTTTTCCGGCCCAACGCCGAGGATCCTAATTTCCGGCACCTGGATCGCCCCGACGCGAACTACCTCGTTCTCAAGGCGAACGTGGACCGGCTGAATCTGATCCAGGTCGGGCTGACTCTCTCGGACCGCGTCGGGAATTTGCCGGATTTAGGATCGGAGAACAAGTATATTTGGGAATTCAATTTCAGAGACTTCGACGTGGGGCGTGACCCCCACGCGCACGACTCCATCGAGTTGCTGCGGCGGCAGGGTATCGATTTCGAGCGCAACCGGGACAGAGGGATCGACTCGTACAAATTCGCCCAGCTGATGATGTCATCGGGCCTCGTGTGCAACGAGGACGTGACGTGGATCACGTTTCACAGCGCGTACGATTTCGGATACCTGGTCAAGCTGTTGACGCAGCAAGCCTTGCCGGAGGAGCTGCCGGGATTCTTGAGCCGGGTGAAGGTGTTCTTTGGTTCCGGAGGGTACGACGTGAAGCACCTGACCAAGTTCTGTGCTCATCTCTATGGTGGATTGGACCGGGTTTGCCAGGCCTTAAATGTGGGCCGGGCTATCGGAAAAAGCCACCAGGCCGGGTCGGATAGCCTCCTGACTTTGCATGCGTACCAGAGGATCAAAGAGCTCTTCTTTAGCAAAGATGGAATAGAGCAGTACGCTGGCGTTTTGTATGGTCTAGAGGTTTCTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000175 GO:0000288 GO:0000289 GO:0000291 GO:0000932 GO:0000956 GO:0002213 GO:0003674 GO:0003824 GO:0004518 GO:0004527 GO:0004532 GO:0004535 GO:0004540 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0006139 GO:0006401 GO:0006402 GO:0006417 GO:0006725 GO:0006807 GO:0006950 GO:0006952 GO:0008150 GO:0008152 GO:0008408 GO:0009056 GO:0009057 GO:0009605 GO:0009607 GO:0009611 GO:0009617 GO:0009889 GO:0009890 GO:0009892 GO:0009987 GO:0010468 GO:0010556 GO:0010558 GO:0010605 GO:0010608 GO:0010629 GO:0016070 GO:0016071 GO:0016787 GO:0016788 GO:0016796 GO:0016896 GO:0017148 GO:0019222 GO:0019439 GO:0030014 GO:0030015 GO:0031323 GO:0031324 GO:0031326 GO:0031327 GO:0032268 GO:0032269 GO:0032991 GO:0034248 GO:0034249 GO:0034641 GO:0034655 GO:0035770 GO:0036464 GO:0042742 GO:0043170 GO:0043207 GO:0043226 GO:0043228 GO:0043229 GO:0043232 GO:0043928 GO:0044237 GO:0044238 GO:0044248 GO:0044260 GO:0044265 GO:0044270 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0046700 GO:0048519 GO:0048523 GO:0050789 GO:0050794 GO:0050896 GO:0051171 GO:0051172 GO:0051246 GO:0051248 GO:0051704 GO:0051707 GO:0060255 GO:0065007 GO:0071704 GO:0080090 GO:0090304 GO:0090305 GO:0090501 GO:0090503 GO:0098542 GO:0140098 GO:1901360 GO:1901361 GO:1901575 GO:1990904 GO:2000112 GO:2000113

KEGG Pathways

Metabolic & Signaling

ko03018 map03018

Pfam Domains

Protein Families

CAF1

Protein Analysis

285

Amino Acids

32.23

Weight (kDa)

5.19

Isoelectric Point (pI)

39.89

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CAF1	PF04857	24 - 150	2e-10	CAF1 family ribonuclease

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

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Publication-ready

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Orthologous Genes (Group: OG0003980)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G44260 AT5G22250
fragaria_vesca	FvH4_3g25960 FvH4_6g19860
malus_domestica	MD03G1152000.v1.1 MD03G1152100.v1.1 MD11G1172400.v1.1 MD12G1034100.v1.1
prunus_persica	Prupe.6G139200_v2.0.a1 Prupe.6G139300_v2.0.a1 Prupe.6G139800_v2.0.a1 Prupe.7G098700_v2.0.a1
pyrus_communis	pycom03g10580 pycom05g09910 pycom11g14510 pycom12g03160 pycom14g03120
rosa_chinensis	RchiOBHm_Chr3g0475261 RchiOBHm_Chr5g0047241
rosa_laevigata	RLG00000023855 RLG00000034481
rosa_roxburghii	Rroxscaffold_1G00034130 Rroxscaffold_6G00406420
rosa_rugosa	Rorug03G0147600 Rorug05G0235200
rosa_samantha	Rh3AG197500 Rh3BG227800 Rh3DG223000 Rh5AG314100 Rh5CG349900 Rh5DG333600
rosa_wichuraiana	Rw3G017960 Rw5G029350

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	201
AccII	CGCG	4 cut(s)	221, 294, 383, 533
AccIII	TCCGGA	1 cut(s)	629
AciI	CCGC	5 cut(s)	38, 41, 292, 406, 409
AcsI	RAATTY	4 cut(s)	125, 301, 341, 461
AcuI	CTGAAG	1 cut(s)	33
AcyI	GRCGYC	1 cut(s)	162
AfaI	GTAC	5 cut(s)	458, 536, 638, 776, 824
AfiI	CCNNNNNNNGG	3 cut(s)	205, 314, 613
AgsI	TTSAA	1 cut(s)	346
AjiI	CACGTC	4 cut(s)	364, 508, 513, 643
AjnI	CCWGG	5 cut(s)	204, 267, 549, 699, 738
AluBI	AGCT	4 cut(s)	472, 559, 589, 793
AluI	AGCT	4 cut(s)	472, 559, 589, 793
Alw21I	GWGCWC	2 cut(s)	670, 795
Alw26I	GTCTC	1 cut(s)	348
Aor13HI	TCCGGA	1 cut(s)	629
AoxI	GGCC	6 cut(s)	75, 173, 487, 702, 715, 741
ApeKI	GCWGC	3 cut(s)	403, 568, 589
ApoI	RAATTY	4 cut(s)	125, 301, 341, 461
ArsI	GACNNNNNNTTYG	2 cut(s)	80, 112
Asp700I	GAANNNNTTC	1 cut(s)	617
AspLEI	GCGC	3 cut(s)	385, 432, 533
AspS9I	GGNCC	7 cut(s)	75, 174, 250, 289, 487, 688, 715
AsuC2I	CCSGG	7 cut(s)	159, 437, 594, 608, 692, 719, 745
AsuHPI	GGTGA	1 cut(s)	622
AvaII	GGWCC	3 cut(s)	250, 289, 688
BamHI	GGATCC	1 cut(s)	187
BanI	GGYRCC	1 cut(s)	201
BanII	GRGCYC	1 cut(s)	795
BauI	CACGAG	1 cut(s)	491
Bbv12I	GWGCWC	2 cut(s)	670, 795
BbvI	GCAGC	3 cut(s)	390, 576, 580
BccI	CCATC	2 cut(s)	401, 803
BcgI	CGANNNNNNTGC	2 cut(s)	191, 225
BciT130I	CCWGG	5 cut(s)	206, 269, 551, 701, 740
BciVI	GTATCC	1 cut(s)	539
BcnI	CCSGG	7 cut(s)	159, 437, 594, 608, 692, 719, 745
BcoDI	GTCTC	1 cut(s)	348
BfaI	CTAG	1 cut(s)	845
BfuI	GTATCC	1 cut(s)	539
BisI	GCNGC	6 cut(s)	41, 404, 407, 410, 569, 590
BlsI	GCNGC	6 cut(s)	42, 405, 408, 411, 570, 591
Bme18I	GGWCC	3 cut(s)	250, 289, 688
BmgBI	CACGTC	4 cut(s)	364, 508, 513, 643
BmgT120I	GGNCC	7 cut(s)	75, 174, 250, 289, 487, 688, 715
BmiI	GGNNCC	3 cut(s)	189, 203, 628
BpuEI	CTTGAG	2 cut(s)	221, 622
BpuMI	CCSGG	7 cut(s)	159, 437, 594, 608, 692, 719, 745
Bsa29I	ATCGAT	1 cut(s)	420
BsaHI	GRCGYC	1 cut(s)	162
BsaJI	CCNNGG	2 cut(s)	141, 183
BsaWI	WCCGGW	1 cut(s)	629
BsaXI	ACNNNNNCTCC	2 cut(s)	314, 344
Bsc4I	CCNNNNNNNGG	3 cut(s)	205, 314, 613
Bse118I	RCCGGY	1 cut(s)	252
BseAI	TCCGGA	1 cut(s)	629
BseBI	CCWGG	5 cut(s)	206, 269, 551, 701, 740
BseCI	ATCGAT	1 cut(s)	420
BseDI	CCNNGG	2 cut(s)	141, 183
BseLI	CCNNNNNNNGG	3 cut(s)	205, 314, 613
BseRI	GAGGAG	4 cut(s)	4, 7, 10, 599
BseXI	GCAGC	3 cut(s)	390, 576, 580
BseYI	CCCAGC	1 cut(s)	468
Bsh1236I	CGCG	4 cut(s)	221, 294, 383, 533
Bsh1285I	CGRYCG	1 cut(s)	68
BshFI	GGCC	6 cut(s)	77, 175, 489, 704, 717, 743
BshNI	GGYRCC	1 cut(s)	201
BshVI	ATCGAT	1 cut(s)	420
BsiEI	CGRYCG	1 cut(s)	68
BsiHKAI	GWGCWC	2 cut(s)	670, 795
BsiWI	CGTACG	1 cut(s)	534
BslFI	GGGAC	1 cut(s)	452
BslI	CCNNNNNNNGG	3 cut(s)	205, 314, 613
BsmAI	GTCTC	1 cut(s)	348
BsmFI	GGGAC	1 cut(s)	452
BsnI	GGCC	6 cut(s)	77, 175, 489, 704, 717, 743
Bsp1286I	GDGCHC	2 cut(s)	670, 795
Bsp13I	TCCGGA	1 cut(s)	629
Bsp19I	CCATGG	1 cut(s)	141
BspACI	CCGC	5 cut(s)	38, 41, 292, 406, 409
BspANI	GGCC	6 cut(s)	77, 175, 489, 704, 717, 743
BspDI	ATCGAT	1 cut(s)	420
BspEI	TCCGGA	1 cut(s)	629
BspFNI	CGCG	4 cut(s)	221, 294, 383, 533
BspLI	GGNNCC	3 cut(s)	189, 203, 628
BspQI	GCTCTTC	1 cut(s)	800
BspT107I	GGYRCC	1 cut(s)	201
BsrFI	RCCGGY	1 cut(s)	252
BssAI	RCCGGY	1 cut(s)	252
BssECI	CCNNGG	2 cut(s)	141, 183
BssNI	GRCGYC	1 cut(s)	162
BssSI	CACGAG	1 cut(s)	491
BssT1I	CCWWGG	1 cut(s)	141
Bst2BI	CACGAG	1 cut(s)	491
Bst2UI	CCWGG	5 cut(s)	206, 269, 551, 701, 740
Bst6I	CTCTTC	1 cut(s)	800
BstACI	GRCGYC	1 cut(s)	162
BstAPI	GCANNNNNTGC	1 cut(s)	577
BstC8I	GCNNGC	3 cut(s)	573, 771, 829
BstDSI	CCRYGG	1 cut(s)	141
BstFNI	CGCG	4 cut(s)	221, 294, 383, 533
BstHHI	GCGC	3 cut(s)	385, 432, 533
BstMAI	GTCTC	1 cut(s)	348
BstMCI	CGRYCG	1 cut(s)	68
BstMWI	GCNNNNNNNGC	5 cut(s)	409, 495, 565, 577, 586
BstNI	CCWGG	5 cut(s)	206, 269, 551, 701, 740
BstNSI	RCATGY	1 cut(s)	773
BstUI	CGCG	4 cut(s)	221, 294, 383, 533
BstV1I	GCAGC	3 cut(s)	390, 576, 580
BstX2I	RGATCY	2 cut(s)	105, 187
BstYI	RGATCY	2 cut(s)	105, 187
Bsu15I	ATCGAT	1 cut(s)	420
BsuI	GTATCC	1 cut(s)	539
BsuRI	GGCC	6 cut(s)	77, 175, 489, 704, 717, 743
BsuTUI	ATCGAT	1 cut(s)	420
BtgI	CCRYGG	1 cut(s)	141
BtrI	CACGTC	4 cut(s)	364, 508, 513, 643
Cac8I	GCNNGC	3 cut(s)	573, 771, 829
CfoI	GCGC	3 cut(s)	385, 432, 533
Cfr10I	RCCGGY	1 cut(s)	252
Cfr13I	GGNCC	7 cut(s)	75, 174, 250, 289, 487, 688, 715
ClaI	ATCGAT	1 cut(s)	420
CpoI	CGGWCCG	1 cut(s)	289
CseI	GACGC	4 cut(s)	151, 227, 283, 574
CsiI	ACCWGGT	1 cut(s)	549
Csp6I	GTAC	5 cut(s)	457, 535, 637, 775, 823
CspI	CGGWCCG	1 cut(s)	289
CviAII	CATG	2 cut(s)	142, 770
CviQI	GTAC	5 cut(s)	457, 535, 637, 775, 823
Eam1104I	CTCTTC	1 cut(s)	800
EarI	CTCTTC	1 cut(s)	800
Ecl136II	GAGCTC	1 cut(s)	793
Eco130I	CCWWGG	1 cut(s)	141
Eco147I	AGGCCT	1 cut(s)	704
Eco24I	GRGCYC	1 cut(s)	795
Eco47I	GGWCC	3 cut(s)	250, 289, 688
Eco53kI	GAGCTC	1 cut(s)	793
Eco57I	CTGAAG	1 cut(s)	33
EcoICRI	GAGCTC	1 cut(s)	793
EcoRI	GAATTC	2 cut(s)	125, 341
EcoRII	CCWGG	5 cut(s)	204, 267, 549, 699, 738
EcoT14I	CCWWGG	1 cut(s)	141
EcoT38I	GRGCYC	1 cut(s)	795
ErhI	CCWWGG	1 cut(s)	141
FaeI	CATG	2 cut(s)	145, 773
FaiI	YATR	6 cut(s)	73, 143, 333, 678, 771, 840
FalI	AAGNNNNNCTT	2 cut(s)	605, 637
FaqI	GGGAC	1 cut(s)	452
FatI	CATG	2 cut(s)	141, 769
FauI	CCCGC	1 cut(s)	45
Fnu4HI	GCNGC	6 cut(s)	41, 404, 407, 410, 569, 590
FriOI	GRGCYC	1 cut(s)	795
Fsp4HI	GCNGC	6 cut(s)	41, 404, 407, 410, 569, 590
FspBI	CTAG	1 cut(s)	845
GlaI	GCGC	3 cut(s)	384, 431, 532
GluI	GCNGC	6 cut(s)	41, 404, 407, 410, 569, 590
GsaI	CCCAGC	1 cut(s)	472
HaeIII	GGCC	6 cut(s)	77, 175, 489, 704, 717, 743
HgaI	GACGC	4 cut(s)	151, 227, 283, 574
HhaI	GCGC	3 cut(s)	385, 432, 533
Hin1I	GRCGYC	1 cut(s)	162
Hin1II	CATG	2 cut(s)	145, 773
Hin6I	GCGC	3 cut(s)	383, 430, 531
HinP1I	GCGC	3 cut(s)	383, 430, 531
HincII	GTYRAC	1 cut(s)	564
HindII	GTYRAC	1 cut(s)	564
HinfI	GANTC	6 cut(s)	60, 259, 280, 389, 452, 597
HphI	GGTGA	1 cut(s)	622
Hpy166II	GTNNAC	2 cut(s)	250, 564
Hpy188III	TCNNGA	7 cut(s)	130, 298, 601, 630, 760, 845, 855
Hpy8I	GTNNAC	2 cut(s)	250, 564
Hpy99I	CGWCG	8 cut(s)	92, 95, 125, 167, 221, 299, 365, 644
HpyAV	CCTTC	2 cut(s)	54, 607
HpyCH4IV	ACGT	6 cut(s)	246, 363, 507, 512, 521, 642
HpyCH4V	TGCA	2 cut(s)	498, 769
HpyF10VI	GCNNNNNNNGC	5 cut(s)	409, 495, 565, 577, 586
HpySE526I	ACGT	6 cut(s)	246, 363, 507, 512, 521, 642
Hsp92I	GRCGYC	1 cut(s)	162
Hsp92II	CATG	2 cut(s)	145, 773
HspAI	GCGC	3 cut(s)	383, 430, 531
Kpn2I	TCCGGA	1 cut(s)	629
LguI	GCTCTTC	1 cut(s)	800
LmnI	GCTCC	1 cut(s)	586
Lsp1109I	GCAGC	3 cut(s)	390, 576, 580
MabI	ACCWGGT	1 cut(s)	549
MaeI	CTAG	1 cut(s)	845
MaeII	ACGT	6 cut(s)	246, 363, 507, 512, 521, 642
MaeIII	GTNAC	2 cut(s)	371, 508
MboII	GAAGA	2 cut(s)	39, 787
MflI	RGATCY	2 cut(s)	105, 187
MhlI	GDGCHC	2 cut(s)	670, 795
MluCI	AATT	6 cut(s)	125, 193, 301, 341, 346, 461
MlyI	GAGTC	3 cut(s)	274, 383, 446
MmeI	TCCRAC	1 cut(s)	729
MroI	TCCGGA	1 cut(s)	629
MroXI	GAANNNNTTC	1 cut(s)	617
MseI	TTAA	1 cut(s)	707
MslI	CAYNNNNRTG	1 cut(s)	675
MspA1I	CMGCKG	1 cut(s)	472
MvaI	CCWGG	5 cut(s)	206, 269, 551, 701, 740
MvnI	CGCG	4 cut(s)	221, 294, 383, 533
MwoI	GCNNNNNNNGC	5 cut(s)	409, 495, 565, 577, 586
NciI	CCSGG	7 cut(s)	159, 437, 594, 608, 692, 719, 745
NcoI	CCATGG	1 cut(s)	141
NlaIII	CATG	2 cut(s)	145, 773
NlaIV	GGNNCC	3 cut(s)	189, 203, 628
NmeAIII	GCCGAG	1 cut(s)	208
NmuCI	GTSAC	2 cut(s)	371, 508
NspI	RCATGY	1 cut(s)	773
PaeI	GCATGC	1 cut(s)	773
PceI	AGGCCT	1 cut(s)	704
PciSI	GCTCTTC	1 cut(s)	800
PcsI	WCGNNNNNNNCGW	4 cut(s)	96, 393, 498, 518
PdmI	GAANNNNTTC	1 cut(s)	617
PfeI	GAWTC	3 cut(s)	60, 259, 597
Pfl23II	CGTACG	1 cut(s)	534
PflFI	GACNNNGTC	1 cut(s)	293
PkrI	GCNGC	6 cut(s)	42, 405, 408, 411, 570, 591
Ple19I	CGATCG	1 cut(s)	68
PleI	GAGTC	3 cut(s)	274, 383, 446
PpsI	GAGTC	3 cut(s)	274, 383, 446
Psp124BI	GAGCTC	1 cut(s)	795
Psp6I	CCWGG	5 cut(s)	204, 267, 549, 699, 738
PspFI	CCCAGC	1 cut(s)	468
PspGI	CCWGG	5 cut(s)	204, 267, 549, 699, 738
PspLI	CGTACG	1 cut(s)	534
PspN4I	GGNNCC	3 cut(s)	189, 203, 628
PspPI	GGNCC	7 cut(s)	75, 174, 250, 289, 487, 688, 715
PsuI	RGATCY	2 cut(s)	105, 187
PsyI	GACNNNGTC	1 cut(s)	293
PvuI	CGATCG	1 cut(s)	68
PvuII	CAGCTG	1 cut(s)	472
RsaI	GTAC	5 cut(s)	458, 536, 638, 776, 824
RsaNI	GTAC	5 cut(s)	457, 535, 637, 775, 823
RseI	CAYNNNNRTG	1 cut(s)	675
Rsr2I	CGGWCCG	1 cut(s)	289
RsrII	CGGWCCG	1 cut(s)	289
SacI	GAGCTC	1 cut(s)	795
SapI	GCTCTTC	1 cut(s)	800
SaqAI	TTAA	1 cut(s)	707
SatI	GCNGC	6 cut(s)	41, 404, 407, 410, 569, 590
Sau96I	GGNCC	7 cut(s)	75, 174, 250, 289, 487, 688, 715
SchI	GAGTC	3 cut(s)	274, 383, 446
SduI	GDGCHC	2 cut(s)	670, 795
SexAI	ACCWGGT	1 cut(s)	549
SinI	GGWCC	3 cut(s)	250, 289, 688
SmiMI	CAYNNNNRTG	1 cut(s)	675
SmlI	CTYRAG	2 cut(s)	236, 601
SmoI	CTYRAG	2 cut(s)	236, 601
SphI	GCATGC	1 cut(s)	773
Sse9I	AATT	6 cut(s)	125, 193, 301, 341, 346, 461
SseBI	AGGCCT	1 cut(s)	704
SsiI	CCGC	5 cut(s)	38, 41, 292, 406, 409
SspMI	CTAG	1 cut(s)	845
SstI	GAGCTC	1 cut(s)	795
StuI	AGGCCT	1 cut(s)	704
StyI	CCWWGG	1 cut(s)	141
TaiI	ACGT	6 cut(s)	249, 366, 510, 515, 524, 645
TaqI	TCGA	8 cut(s)	87, 99, 120, 360, 396, 420, 426, 450
TasI	AATT	6 cut(s)	125, 193, 301, 341, 346, 461
TauI	GCSGC	3 cut(s)	43, 409, 412
TfiI	GAWTC	3 cut(s)	60, 259, 597
Tru1I	TTAA	1 cut(s)	707
Tru9I	TTAA	1 cut(s)	707
TseFI	GTSAC	2 cut(s)	371, 508
TseI	GCWGC	3 cut(s)	403, 568, 589
Tsp45I	GTSAC	2 cut(s)	371, 508
TspGWI	ACGGA	2 cut(s)	103, 164
Tth111I	GACNNNGTC	1 cut(s)	293
VpaK11BI	GGWCC	3 cut(s)	250, 289, 688
XapI	RAATTY	4 cut(s)	125, 301, 341, 461
XbaI	TCTAGA	1 cut(s)	844
XceI	RCATGY	1 cut(s)	773
XmnI	GAANNNNTTC	1 cut(s)	617
XspI	CTAG	1 cut(s)	845

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