Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr3A

Orthogroup ID

OG0003980

Physical Location & Seq

Genomic Coordinates Forward (+)

19371011 .. 19378522

Gene Structure 7512 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh3AG197500.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 861 bp

ATGTCGTCGTCGTCGTCCTCCTCCTCTTCATCAGAACCCCCGCCGCCTTCTTCAGAAATCCGAATCCGATCGGTATGGGCCGATAACCTCGACGACGAGTTCGACAAGATCCGATCCGTGATCGACGAATTCCCGATGATCTCCATGGACACGGAGTTTCCCGGCGTCGTTTTCCGGCCCAACGCCGAGGATCCTAATTTCCGGCACCTGGATCGCCCCGACGCGAACTACCTCGTTCTCAAGGCGAACGTGGACCGGCTGAATCTGATCCAGGTCGGGCTGACTCTCTCGGACCGCGTCGGGAATTTGCCGGATTTAGGATCGGAGAACAAGTATATTTGGGAATTCAATTTCAGAGACTTCGACGTGGGGCGTGACCCCCACGCGCACGACTCCATCGAGTTGCTGCGGCGGCAGGGTATCGATTTCGAGCGCAACCGGGACAGAGGGATCGACTCGTACAAATTCGCCCAGCTGATGATGTCATCGGGCCTCGTGTGCAACGAGGACGTGACGTGGATCACGTTTCACAGCGCGTACGATTTCGGATACCTGGTCAAGCTGTTGACGCAGCAAGCCTTGCCGGAGGAGCTGCCGGGATTCTTGAGCCGGGTGAAGGTGTTCTTTGGTTCCGGAGGGTACGACGTGAAGCACCTGACCAAGTTCTGTGCTCATCTCTATGGTGGATTGGACCGGGTTTGCCAGGCCTTAAATGTGGGCCGGGCCATCGGAAAAAGCCACCAGGCCGGGTCGGATAGCCTCCTGACTTTGCATGCGTACCAGAGGATCAAAGAGCTCTTCTTTAGCAAAGATGGAATAGAGCAGTACGCTGGCGTTTTGTATGGTCTAGAGGTTTCTTGA

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

286

Amino Acids

32.31

Weight (kDa)

5.19

Isoelectric Point (pI)

40.46

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CAF1	PF04857	25 - 151	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)	204
AccII	CGCG	4 cut(s)	224, 297, 386, 536
AccIII	TCCGGA	1 cut(s)	632
AciI	CCGC	5 cut(s)	41, 44, 295, 409, 412
AcsI	RAATTY	4 cut(s)	128, 304, 344, 464
AcuI	CTGAAG	1 cut(s)	36
AcyI	GRCGYC	1 cut(s)	165
AfaI	GTAC	5 cut(s)	461, 539, 641, 779, 827
AfiI	CCNNNNNNNGG	3 cut(s)	208, 317, 616
AgsI	TTSAA	1 cut(s)	349
AjiI	CACGTC	4 cut(s)	367, 511, 516, 646
AjnI	CCWGG	5 cut(s)	207, 270, 552, 702, 741
AluBI	AGCT	4 cut(s)	475, 562, 592, 796
AluI	AGCT	4 cut(s)	475, 562, 592, 796
Alw21I	GWGCWC	2 cut(s)	673, 798
Alw26I	GTCTC	1 cut(s)	351
Aor13HI	TCCGGA	1 cut(s)	632
AoxI	GGCC	7 cut(s)	78, 176, 490, 705, 718, 723, 744
ApeKI	GCWGC	3 cut(s)	406, 571, 592
ApoI	RAATTY	4 cut(s)	128, 304, 344, 464
ArsI	GACNNNNNNTTYG	2 cut(s)	83, 115
Asp700I	GAANNNNTTC	1 cut(s)	620
AspLEI	GCGC	3 cut(s)	388, 435, 536
AspS9I	GGNCC	8 cut(s)	78, 177, 253, 292, 490, 691, 718, 723
AsuC2I	CCSGG	7 cut(s)	162, 440, 597, 611, 695, 722, 748
AsuHPI	GGTGA	1 cut(s)	625
AvaII	GGWCC	3 cut(s)	253, 292, 691
BamHI	GGATCC	1 cut(s)	190
BanI	GGYRCC	1 cut(s)	204
BanII	GRGCYC	1 cut(s)	798
BauI	CACGAG	1 cut(s)	494
Bbv12I	GWGCWC	2 cut(s)	673, 798
BbvI	GCAGC	3 cut(s)	393, 579, 583
BccI	CCATC	3 cut(s)	404, 734, 806
BcgI	CGANNNNNNTGC	2 cut(s)	194, 228
BciT130I	CCWGG	5 cut(s)	209, 272, 554, 704, 743
BciVI	GTATCC	1 cut(s)	542
BcnI	CCSGG	7 cut(s)	162, 440, 597, 611, 695, 722, 748
BcoDI	GTCTC	1 cut(s)	351
BfaI	CTAG	1 cut(s)	848
BfuI	GTATCC	1 cut(s)	542
BisI	GCNGC	6 cut(s)	44, 407, 410, 413, 572, 593
BlsI	GCNGC	6 cut(s)	45, 408, 411, 414, 573, 594
Bme18I	GGWCC	3 cut(s)	253, 292, 691
BmgBI	CACGTC	4 cut(s)	367, 511, 516, 646
BmgT120I	GGNCC	8 cut(s)	78, 177, 253, 292, 490, 691, 718, 723
BmiI	GGNNCC	3 cut(s)	192, 206, 631
BpuEI	CTTGAG	2 cut(s)	224, 625
BpuMI	CCSGG	7 cut(s)	162, 440, 597, 611, 695, 722, 748
Bsa29I	ATCGAT	1 cut(s)	423
BsaHI	GRCGYC	1 cut(s)	165
BsaJI	CCNNGG	2 cut(s)	144, 186
BsaWI	WCCGGW	1 cut(s)	632
BsaXI	ACNNNNNCTCC	2 cut(s)	317, 347
Bsc4I	CCNNNNNNNGG	3 cut(s)	208, 317, 616
Bse118I	RCCGGY	1 cut(s)	255
BseAI	TCCGGA	1 cut(s)	632
BseBI	CCWGG	5 cut(s)	209, 272, 554, 704, 743
BseCI	ATCGAT	1 cut(s)	423
BseDI	CCNNGG	2 cut(s)	144, 186
BseLI	CCNNNNNNNGG	3 cut(s)	208, 317, 616
BseRI	GAGGAG	3 cut(s)	10, 13, 602
BseXI	GCAGC	3 cut(s)	393, 579, 583
BseYI	CCCAGC	1 cut(s)	471
Bsh1236I	CGCG	4 cut(s)	224, 297, 386, 536
Bsh1285I	CGRYCG	1 cut(s)	71
BshFI	GGCC	7 cut(s)	80, 178, 492, 707, 720, 725, 746
BshNI	GGYRCC	1 cut(s)	204
BshVI	ATCGAT	1 cut(s)	423
BsiEI	CGRYCG	1 cut(s)	71
BsiHKAI	GWGCWC	2 cut(s)	673, 798
BsiWI	CGTACG	1 cut(s)	537
BslFI	GGGAC	1 cut(s)	455
BslI	CCNNNNNNNGG	3 cut(s)	208, 317, 616
BsmAI	GTCTC	1 cut(s)	351
BsmFI	GGGAC	1 cut(s)	455
BsnI	GGCC	7 cut(s)	80, 178, 492, 707, 720, 725, 746
Bsp1286I	GDGCHC	2 cut(s)	673, 798
Bsp13I	TCCGGA	1 cut(s)	632
Bsp19I	CCATGG	1 cut(s)	144
BspACI	CCGC	5 cut(s)	41, 44, 295, 409, 412
BspANI	GGCC	7 cut(s)	80, 178, 492, 707, 720, 725, 746
BspDI	ATCGAT	1 cut(s)	423
BspEI	TCCGGA	1 cut(s)	632
BspFNI	CGCG	4 cut(s)	224, 297, 386, 536
BspLI	GGNNCC	3 cut(s)	192, 206, 631
BspQI	GCTCTTC	1 cut(s)	803
BspT107I	GGYRCC	1 cut(s)	204
BsrFI	RCCGGY	1 cut(s)	255
BssAI	RCCGGY	1 cut(s)	255
BssECI	CCNNGG	2 cut(s)	144, 186
BssNI	GRCGYC	1 cut(s)	165
BssSI	CACGAG	1 cut(s)	494
BssT1I	CCWWGG	1 cut(s)	144
Bst2BI	CACGAG	1 cut(s)	494
Bst2UI	CCWGG	5 cut(s)	209, 272, 554, 704, 743
Bst6I	CTCTTC	2 cut(s)	31, 803
BstACI	GRCGYC	1 cut(s)	165
BstAPI	GCANNNNNTGC	1 cut(s)	580
BstC8I	GCNNGC	3 cut(s)	576, 774, 832
BstDSI	CCRYGG	1 cut(s)	144
BstFNI	CGCG	4 cut(s)	224, 297, 386, 536
BstHHI	GCGC	3 cut(s)	388, 435, 536
BstMAI	GTCTC	1 cut(s)	351
BstMCI	CGRYCG	1 cut(s)	71
BstMWI	GCNNNNNNNGC	5 cut(s)	412, 498, 568, 580, 589
BstNI	CCWGG	5 cut(s)	209, 272, 554, 704, 743
BstNSI	RCATGY	1 cut(s)	776
BstUI	CGCG	4 cut(s)	224, 297, 386, 536
BstV1I	GCAGC	3 cut(s)	393, 579, 583
BstX2I	RGATCY	2 cut(s)	108, 190
BstYI	RGATCY	2 cut(s)	108, 190
Bsu15I	ATCGAT	1 cut(s)	423
BsuI	GTATCC	1 cut(s)	542
BsuRI	GGCC	7 cut(s)	80, 178, 492, 707, 720, 725, 746
BsuTUI	ATCGAT	1 cut(s)	423
BtgI	CCRYGG	1 cut(s)	144
BtrI	CACGTC	4 cut(s)	367, 511, 516, 646
Cac8I	GCNNGC	3 cut(s)	576, 774, 832
CfoI	GCGC	3 cut(s)	388, 435, 536
Cfr10I	RCCGGY	1 cut(s)	255
Cfr13I	GGNCC	8 cut(s)	78, 177, 253, 292, 490, 691, 718, 723
ClaI	ATCGAT	1 cut(s)	423
CpoI	CGGWCCG	1 cut(s)	292
CseI	GACGC	4 cut(s)	154, 230, 286, 577
CsiI	ACCWGGT	1 cut(s)	552
Csp6I	GTAC	5 cut(s)	460, 538, 640, 778, 826
CspI	CGGWCCG	1 cut(s)	292
CviAII	CATG	2 cut(s)	145, 773
CviQI	GTAC	5 cut(s)	460, 538, 640, 778, 826
Eam1104I	CTCTTC	2 cut(s)	31, 803
EarI	CTCTTC	2 cut(s)	31, 803
Ecl136II	GAGCTC	1 cut(s)	796
Eco130I	CCWWGG	1 cut(s)	144
Eco147I	AGGCCT	1 cut(s)	707
Eco24I	GRGCYC	1 cut(s)	798
Eco47I	GGWCC	3 cut(s)	253, 292, 691
Eco53kI	GAGCTC	1 cut(s)	796
Eco57I	CTGAAG	1 cut(s)	36
EcoICRI	GAGCTC	1 cut(s)	796
EcoRI	GAATTC	2 cut(s)	128, 344
EcoRII	CCWGG	5 cut(s)	207, 270, 552, 702, 741
EcoT14I	CCWWGG	1 cut(s)	144
EcoT38I	GRGCYC	1 cut(s)	798
ErhI	CCWWGG	1 cut(s)	144
FaeI	CATG	2 cut(s)	148, 776
FaiI	YATR	6 cut(s)	76, 146, 336, 681, 774, 843
FalI	AAGNNNNNCTT	2 cut(s)	608, 640
FaqI	GGGAC	1 cut(s)	455
FatI	CATG	2 cut(s)	144, 772
FauI	CCCGC	1 cut(s)	48
Fnu4HI	GCNGC	6 cut(s)	44, 407, 410, 413, 572, 593
FriOI	GRGCYC	1 cut(s)	798
Fsp4HI	GCNGC	6 cut(s)	44, 407, 410, 413, 572, 593
FspBI	CTAG	1 cut(s)	848
GlaI	GCGC	3 cut(s)	387, 434, 535
GluI	GCNGC	6 cut(s)	44, 407, 410, 413, 572, 593
GsaI	CCCAGC	1 cut(s)	475
HaeIII	GGCC	7 cut(s)	80, 178, 492, 707, 720, 725, 746
HgaI	GACGC	4 cut(s)	154, 230, 286, 577
HhaI	GCGC	3 cut(s)	388, 435, 536
Hin1I	GRCGYC	1 cut(s)	165
Hin1II	CATG	2 cut(s)	148, 776
Hin6I	GCGC	3 cut(s)	386, 433, 534
HinP1I	GCGC	3 cut(s)	386, 433, 534
HincII	GTYRAC	1 cut(s)	567
HindII	GTYRAC	1 cut(s)	567
HinfI	GANTC	6 cut(s)	63, 262, 283, 392, 455, 600
HphI	GGTGA	1 cut(s)	625
Hpy166II	GTNNAC	2 cut(s)	253, 567
Hpy188III	TCNNGA	7 cut(s)	133, 301, 604, 633, 763, 848, 858
Hpy8I	GTNNAC	2 cut(s)	253, 567
HpyAV	CCTTC	2 cut(s)	57, 610
HpyCH4IV	ACGT	6 cut(s)	249, 366, 510, 515, 524, 645
HpyCH4V	TGCA	2 cut(s)	501, 772
HpyF10VI	GCNNNNNNNGC	5 cut(s)	412, 498, 568, 580, 589
HpySE526I	ACGT	6 cut(s)	249, 366, 510, 515, 524, 645
Hsp92I	GRCGYC	1 cut(s)	165
Hsp92II	CATG	2 cut(s)	148, 776
HspAI	GCGC	3 cut(s)	386, 433, 534
Kpn2I	TCCGGA	1 cut(s)	632
LguI	GCTCTTC	1 cut(s)	803
LmnI	GCTCC	1 cut(s)	589
Lsp1109I	GCAGC	3 cut(s)	393, 579, 583
MabI	ACCWGGT	1 cut(s)	552
MaeI	CTAG	1 cut(s)	848
MaeII	ACGT	6 cut(s)	249, 366, 510, 515, 524, 645
MaeIII	GTNAC	2 cut(s)	374, 511
MboII	GAAGA	3 cut(s)	18, 42, 790
MflI	RGATCY	2 cut(s)	108, 190
MhlI	GDGCHC	2 cut(s)	673, 798
MluCI	AATT	6 cut(s)	128, 196, 304, 344, 349, 464
MlyI	GAGTC	3 cut(s)	277, 386, 449
MmeI	TCCRAC	1 cut(s)	732
MroI	TCCGGA	1 cut(s)	632
MroXI	GAANNNNTTC	1 cut(s)	620
MseI	TTAA	1 cut(s)	710
MslI	CAYNNNNRTG	1 cut(s)	678
MspA1I	CMGCKG	1 cut(s)	475
MvaI	CCWGG	5 cut(s)	209, 272, 554, 704, 743
MvnI	CGCG	4 cut(s)	224, 297, 386, 536
MwoI	GCNNNNNNNGC	5 cut(s)	412, 498, 568, 580, 589
NciI	CCSGG	7 cut(s)	162, 440, 597, 611, 695, 722, 748
NcoI	CCATGG	1 cut(s)	144
NlaIII	CATG	2 cut(s)	148, 776
NlaIV	GGNNCC	3 cut(s)	192, 206, 631
NmeAIII	GCCGAG	1 cut(s)	211
NmuCI	GTSAC	2 cut(s)	374, 511
NspI	RCATGY	1 cut(s)	776
PaeI	GCATGC	1 cut(s)	776
PceI	AGGCCT	1 cut(s)	707
PciSI	GCTCTTC	1 cut(s)	803
PcsI	WCGNNNNNNNCGW	5 cut(s)	11, 99, 396, 501, 521
PdmI	GAANNNNTTC	1 cut(s)	620
PfeI	GAWTC	3 cut(s)	63, 262, 600
Pfl23II	CGTACG	1 cut(s)	537
PflFI	GACNNNGTC	1 cut(s)	296
PkrI	GCNGC	6 cut(s)	45, 408, 411, 414, 573, 594
Ple19I	CGATCG	1 cut(s)	71
PleI	GAGTC	3 cut(s)	277, 386, 449
PpsI	GAGTC	3 cut(s)	277, 386, 449
Psp124BI	GAGCTC	1 cut(s)	798
Psp6I	CCWGG	5 cut(s)	207, 270, 552, 702, 741
PspFI	CCCAGC	1 cut(s)	471
PspGI	CCWGG	5 cut(s)	207, 270, 552, 702, 741
PspLI	CGTACG	1 cut(s)	537
PspN4I	GGNNCC	3 cut(s)	192, 206, 631
PspPI	GGNCC	8 cut(s)	78, 177, 253, 292, 490, 691, 718, 723
PsuI	RGATCY	2 cut(s)	108, 190
PsyI	GACNNNGTC	1 cut(s)	296
PvuI	CGATCG	1 cut(s)	71
PvuII	CAGCTG	1 cut(s)	475
RsaI	GTAC	5 cut(s)	461, 539, 641, 779, 827
RsaNI	GTAC	5 cut(s)	460, 538, 640, 778, 826
RseI	CAYNNNNRTG	1 cut(s)	678
Rsr2I	CGGWCCG	1 cut(s)	292
RsrII	CGGWCCG	1 cut(s)	292
SacI	GAGCTC	1 cut(s)	798
SapI	GCTCTTC	1 cut(s)	803
SaqAI	TTAA	1 cut(s)	710
SatI	GCNGC	6 cut(s)	44, 407, 410, 413, 572, 593
Sau96I	GGNCC	8 cut(s)	78, 177, 253, 292, 490, 691, 718, 723
SchI	GAGTC	3 cut(s)	277, 386, 449
SduI	GDGCHC	2 cut(s)	673, 798
SexAI	ACCWGGT	1 cut(s)	552
SinI	GGWCC	3 cut(s)	253, 292, 691
SmiMI	CAYNNNNRTG	1 cut(s)	678
SmlI	CTYRAG	2 cut(s)	239, 604
SmoI	CTYRAG	2 cut(s)	239, 604
SphI	GCATGC	1 cut(s)	776
Sse9I	AATT	6 cut(s)	128, 196, 304, 344, 349, 464
SseBI	AGGCCT	1 cut(s)	707
SsiI	CCGC	5 cut(s)	41, 44, 295, 409, 412
SspMI	CTAG	1 cut(s)	848
SstI	GAGCTC	1 cut(s)	798
StuI	AGGCCT	1 cut(s)	707
StyI	CCWWGG	1 cut(s)	144
TaiI	ACGT	6 cut(s)	252, 369, 513, 518, 527, 648
TaqI	TCGA	8 cut(s)	90, 102, 123, 363, 399, 423, 429, 453
TasI	AATT	6 cut(s)	128, 196, 304, 344, 349, 464
TauI	GCSGC	3 cut(s)	46, 412, 415
TfiI	GAWTC	3 cut(s)	63, 262, 600
Tru1I	TTAA	1 cut(s)	710
Tru9I	TTAA	1 cut(s)	710
TseFI	GTSAC	2 cut(s)	374, 511
TseI	GCWGC	3 cut(s)	406, 571, 592
Tsp45I	GTSAC	2 cut(s)	374, 511
TspDTI	ATGAA	1 cut(s)	18
TspGWI	ACGGA	2 cut(s)	106, 167
Tth111I	GACNNNGTC	1 cut(s)	296
VpaK11BI	GGWCC	3 cut(s)	253, 292, 691
XapI	RAATTY	4 cut(s)	128, 304, 344, 464
XbaI	TCTAGA	1 cut(s)	847
XceI	RCATGY	1 cut(s)	776
XmnI	GAANNNNTTC	1 cut(s)	620
XspI	CTAG	1 cut(s)	848

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