Basic Information

Type: gene

Biological Identity

Species

rosa_laevigata

Chromosome

Chr3

Orthogroup ID

OG0014895

Physical Location & Seq

Genomic Coordinates Reverse (-)

9147063 .. 9148480

Gene Structure 1418 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

RLM00000011401

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1050 bp

ATGGACGATACGCGGTCGTTTCGTGTGAGCTTCATCCATTCACTTGCAGTTATCGGGCCCCCGTCCCTCACAGTCGTTAAGAACCCACCCTCCAGTAAAGACCCCCAAATCACTGTTCCCAACTCCCAGATCCGTTATTCTCAATTCTCAAACTCACACATCCAAGATCCGAGAACTGCAGCGACTCAATCTGGAAGATCTTCACTTCAGGTTCGGAGATTGGAAATGTCAATTTTGCCCAAAGGGGATTCGATTCAAATCCGGGAGGTGTGGAATGATAATCTTGAGGAAGAGTTTCATATAATCCGTGGTATTGTTGACAAGTATAACTATGTTGCTATGGATACCGAGTTCCCTGGGGTGGTTCTACGCCCCGTGGGTGCCTTTAAGAACATTAGTGATTACAACTATCAGACCCTGAAAGACAATGTTGATATGCTGAAATTGATTCAGTTGGGCCTCACTTTCTCGGATGAGAATGGGAACCTGCCTACTTGTGGAACCGAAAAGTTTTTCATTTGGCAGTTCAATTTCCGCGAGTTCAATGTCACCGAGGACATCTTTGCCAGCGATTCCATTGAGTTGTTGCGTCAATGTGGGATTGACTTCAAGAAGAACAGCGAGAAGGGTATTGATGTGAATCGGTTTGCTGAGCTTTTGATGTCTTCAGGGATTGTGTTGAATGATGCTGTGCATTGGGTCACCTTCCATAGCGGGTATGATTTTGGATACCTGCTCAAGTTATTGACTTGTAGGAGTTTGCCTGACACGCAAGCCGGTTTCTTTGATTTGATCAAGATATACTTCCCAATGGTGTATGATATCAAGCATTTGATGAAGTTTTGCAACAGCCTCCATGGTGGGTTGAACAAGCTTGCAGAACTGTTGGATGTGGAAAGAGTTGGTGTGTGCCATCAAGCAGGCTCGGACAGTTTGCTTACAGCTTGCACCTTTAGGAAATTGAGGGATACCTTCTTCAGTGGCTCTACTGAGAAATATGCAGGTGTTTTGTATGGTCTGGGTGTCGAAAATGGACAGAGTACTAATTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000175 GO:0000288 GO:0000291 GO:0000932 GO:0000956 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:0008150 GO:0008152 GO:0008408 GO:0009056 GO:0009057 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:0043170 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:0051171 GO:0051172 GO:0051246 GO:0051248 GO:0060255 GO:0065007 GO:0071704 GO:0080090 GO:0090304 GO:0090305 GO:0090501 GO:0090503 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

350

Amino Acids

39.45

Weight (kDa)

5.79

Isoelectric Point (pI)

39.08

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
CAF1	PF04857	90 - 211	2.4e-13	CAF1 family ribonuclease

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

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Orthologous Genes (Group: OG0014895)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G10960
fragaria_vesca	FvH4_2g40930
malus_domestica	MD08G1058500.v1.1 MD15G1038000.v1.1
prunus_persica	Prupe.1G391900_v2.0.a1
pyrus_communis	pycom08g04840 pycom15g03520
rosa_chinensis	RchiOBHm_Chr6g0299631
rosa_laevigata	RLG00000011401
rosa_roxburghii	Rroxscaffold_7G00168490
rosa_rugosa	Rorug06G0291200
rosa_samantha	Rh6AG402000 Rh6BG410400 Rh6CG416100 Rh6DG403300
rosa_wichuraiana	Rw6G035180

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AarI	CACCTGC	1 cut(s)	992
Acc36I	ACCTGC	3 cut(s)	495, 741, 992
AccB1I	GGYRCC	1 cut(s)	380
AccII	CGCG	2 cut(s)	13, 537
AciI	CCGC	3 cut(s)	13, 535, 714
AclWI	GGATC	2 cut(s)	124, 161
AcuI	CTGAAG	3 cut(s)	191, 651, 961
AfaI	GTAC	1 cut(s)	1042
AfiI	CCNNNNNNNGG	2 cut(s)	361, 497
AgsI	TTSAA	6 cut(s)	257, 529, 544, 610, 682, 868
AjnI	CCWGG	1 cut(s)	355
AjuI	GAANNNNNNNTTGG	2 cut(s)	99, 131
AloI	GAACNNNNNNTCC	4 cut(s)	74, 106, 335, 367
AluBI	AGCT	4 cut(s)	30, 655, 874, 944
AluI	AGCT	4 cut(s)	30, 655, 874, 944
AlwI	GGATC	2 cut(s)	124, 161
AlwNI	CAGNNNCTG	1 cut(s)	418
AoxI	GGCC	2 cut(s)	56, 457
ApaI	GGGCCC	1 cut(s)	60
ApeKI	GCWGC	1 cut(s)	179
Asp700I	GAANNNNTTC	2 cut(s)	199, 294
AspS9I	GGNCC	3 cut(s)	56, 57, 457
AsuC2I	CCSGG	1 cut(s)	263
AsuHPI	GGTGA	2 cut(s)	541, 694
BaeGI	GKGCMC	1 cut(s)	60
BanI	GGYRCC	1 cut(s)	380
BanII	GRGCYC	1 cut(s)	60
BbsI	GAAGAC	1 cut(s)	657
BbvI	GCAGC	1 cut(s)	191
BccI	CCATC	1 cut(s)	921
BciT130I	CCWGG	1 cut(s)	357
BciVI	GTATCC	3 cut(s)	337, 722, 961
BclI	TGATCA	1 cut(s)	792
BcnI	CCSGG	1 cut(s)	263
BfmI	CTRYAG	1 cut(s)	177
BfuAI	ACCTGC	3 cut(s)	495, 741, 992
BfuI	GTATCC	3 cut(s)	337, 722, 961
BglII	AGATCT	1 cut(s)	197
BisI	GCNGC	1 cut(s)	180
BlpI	GCTNAGC	1 cut(s)	651
BlsI	GCNGC	1 cut(s)	181
BmcAI	AGTACT	1 cut(s)	1042
Bme1390I	CCNGG	2 cut(s)	263, 357
BmgT120I	GGNCC	3 cut(s)	56, 57, 457
BmiI	GGNNCC	5 cut(s)	58, 59, 382, 485, 502
BmrFI	CCNGG	2 cut(s)	263, 357
BmsI	GCATC	1 cut(s)	676
BpiI	GAAGAC	1 cut(s)	657
BpmI	CTGGAG	1 cut(s)	76
Bpu1102I	GCTNAGC	1 cut(s)	651
BpuEI	CTTGAG	2 cut(s)	305, 722
BpuMI	CCSGG	1 cut(s)	263
BsaBI	GATNNNNATC	2 cut(s)	257, 639
BsaJI	CCNNGG	6 cut(s)	307, 355, 356, 375, 552, 856
BsaXI	ACNNNNNCTCC	2 cut(s)	74, 104
Bsc4I	CCNNNNNNNGG	2 cut(s)	361, 497
Bse118I	RCCGGY	1 cut(s)	776
Bse1I	ACTGG	1 cut(s)	93
Bse8I	GATNNNNATC	2 cut(s)	257, 639
BseBI	CCWGG	1 cut(s)	357
BseDI	CCNNGG	6 cut(s)	307, 355, 356, 375, 552, 856
BseGI	GGATG	4 cut(s)	33, 159, 478, 895
BseJI	GATNNNNATC	2 cut(s)	257, 639
BseLI	CCNNNNNNNGG	2 cut(s)	361, 497
BseMII	CTCAG	2 cut(s)	642, 981
BseNI	ACTGG	1 cut(s)	93
BseSI	GKGCMC	1 cut(s)	60
BseXI	GCAGC	1 cut(s)	191
Bsh1236I	CGCG	2 cut(s)	13, 537
Bsh1285I	CGRYCG	1 cut(s)	17
BshFI	GGCC	2 cut(s)	58, 459
BshNI	GGYRCC	1 cut(s)	380
BsiEI	CGRYCG	1 cut(s)	17
BsiSI	CCGG	2 cut(s)	262, 777
BslFI	GGGAC	1 cut(s)	49
BslI	CCNNNNNNNGG	2 cut(s)	361, 497
BsmFI	GGGAC	1 cut(s)	49
BsnI	GGCC	2 cut(s)	58, 459
Bsp120I	GGGCCC	1 cut(s)	56
Bsp1286I	GDGCHC	1 cut(s)	60
Bsp143I	GATC	4 cut(s)	129, 166, 197, 792
Bsp1720I	GCTNAGC	1 cut(s)	651
Bsp19I	CCATGG	1 cut(s)	856
BspACI	CCGC	3 cut(s)	13, 535, 714
BspANI	GGCC	2 cut(s)	58, 459
BspCNI	CTCAG	2 cut(s)	643, 982
BspFNI	CGCG	2 cut(s)	13, 537
BspLI	GGNNCC	5 cut(s)	58, 59, 382, 485, 502
BspMAI	CTGCAG	1 cut(s)	181
BspMI	ACCTGC	3 cut(s)	495, 741, 992
BspPI	GGATC	2 cut(s)	124, 161
BspT107I	GGYRCC	1 cut(s)	380
BsrFI	RCCGGY	1 cut(s)	776
BsrI	ACTGG	1 cut(s)	93
BssAI	RCCGGY	1 cut(s)	776
BssECI	CCNNGG	6 cut(s)	307, 355, 356, 375, 552, 856
BssMI	GATC	4 cut(s)	129, 166, 197, 792
BssT1I	CCWWGG	1 cut(s)	856
Bst2UI	CCWGG	1 cut(s)	357
Bst4CI	ACNGT	4 cut(s)	73, 115, 885, 932
Bst6I	CTCTTC	1 cut(s)	285
BstC8I	GCNNGC	5 cut(s)	568, 774, 876, 922, 946
BstDEI	CTNAG	2 cut(s)	651, 990
BstDSI	CCRYGG	3 cut(s)	307, 375, 856
BstEII	GGTNACC	1 cut(s)	700
BstF5I	GGATG	4 cut(s)	33, 159, 478, 895
BstFNI	CGCG	2 cut(s)	13, 537
BstKTI	GATC	4 cut(s)	132, 169, 200, 795
BstMBI	GATC	4 cut(s)	129, 166, 197, 792
BstMCI	CGRYCG	1 cut(s)	17
BstMWI	GCNNNNNNNGC	1 cut(s)	769
BstNI	CCWGG	1 cut(s)	357
BstPI	GGTNACC	1 cut(s)	700
BstSCI	CCNGG	2 cut(s)	261, 355
BstSFI	CTRYAG	1 cut(s)	177
BstSLI	GKGCMC	1 cut(s)	60
BstUI	CGCG	2 cut(s)	13, 537
BstV1I	GCAGC	1 cut(s)	191
BstV2I	GAAGAC	1 cut(s)	657
BstX2I	RGATCY	3 cut(s)	129, 166, 197
BstYI	RGATCY	3 cut(s)	129, 166, 197
BsuI	GTATCC	3 cut(s)	337, 722, 961
BsuRI	GGCC	2 cut(s)	58, 459
BtgI	CCRYGG	3 cut(s)	307, 375, 856
BtsCI	GGATG	4 cut(s)	33, 159, 478, 895
BtsIMutI	CAGTG	2 cut(s)	111, 985
BveI	ACCTGC	3 cut(s)	495, 741, 992
Cac8I	GCNNGC	5 cut(s)	568, 774, 876, 922, 946
CaiI	CAGNNNCTG	1 cut(s)	418
Cfr10I	RCCGGY	1 cut(s)	776
Cfr13I	GGNCC	3 cut(s)	56, 57, 457
CseI	GACGC	1 cut(s)	578
Csp6I	GTAC	1 cut(s)	1041
CviAII	CATG	1 cut(s)	857
CviQI	GTAC	1 cut(s)	1041
DdeI	CTNAG	2 cut(s)	651, 990
DpnI	GATC	4 cut(s)	131, 168, 199, 794
DpnII	GATC	4 cut(s)	129, 166, 197, 792
Eam1104I	CTCTTC	1 cut(s)	285
EarI	CTCTTC	1 cut(s)	285
Eco130I	CCWWGG	1 cut(s)	856
Eco24I	GRGCYC	1 cut(s)	60
Eco32I	GATATC	1 cut(s)	823
Eco57I	CTGAAG	3 cut(s)	191, 651, 961
Eco91I	GGTNACC	1 cut(s)	700
EcoO109I	RGGNCCY	1 cut(s)	57
EcoO65I	GGTNACC	1 cut(s)	700
EcoRII	CCWGG	1 cut(s)	355
EcoRV	GATATC	1 cut(s)	823
EcoT14I	CCWWGG	1 cut(s)	856
EcoT38I	GRGCYC	1 cut(s)	60
ErhI	CCWWGG	1 cut(s)	856
FaeI	CATG	1 cut(s)	860
FalI	AAGNNNNNCTT	2 cut(s)	788, 820
FaqI	GGGAC	1 cut(s)	49
FatI	CATG	1 cut(s)	856
FauI	CCCGC	1 cut(s)	707
FbaI	TGATCA	1 cut(s)	792
Fnu4HI	GCNGC	1 cut(s)	180
FokI	GGATG	4 cut(s)	20, 146, 485, 902
FriOI	GRGCYC	1 cut(s)	60
Fsp4HI	GCNGC	1 cut(s)	180
GluI	GCNGC	1 cut(s)	180
GsuI	CTGGAG	1 cut(s)	76
HaeIII	GGCC	2 cut(s)	58, 459
HapII	CCGG	2 cut(s)	262, 777
HgaI	GACGC	1 cut(s)	578
Hin1II	CATG	1 cut(s)	860
HincII	GTYRAC	1 cut(s)	319
HindII	GTYRAC	1 cut(s)	319
HindIII	AAGCTT	1 cut(s)	872
HinfI	GANTC	6 cut(s)	184, 248, 253, 448, 572, 640
HpaII	CCGG	2 cut(s)	262, 777
HphI	GGTGA	2 cut(s)	541, 694
Hpy166II	GTNNAC	1 cut(s)	319
Hpy188I	TCNGA	5 cut(s)	171, 216, 414, 472, 928
Hpy188III	TCNNGA	4 cut(s)	192, 284, 610, 796
Hpy8I	GTNNAC	1 cut(s)	319
HpyAV	CCTTC	3 cut(s)	619, 715, 982
HpyCH4III	ACNGT	4 cut(s)	73, 115, 885, 932
HpyCH4V	TGCA	7 cut(s)	47, 179, 694, 846, 878, 948, 1001
HpyF10VI	GCNNNNNNNGC	1 cut(s)	769
HpyF3I	CTNAG	2 cut(s)	651, 990
Hsp92II	CATG	1 cut(s)	860
Ksp22I	TGATCA	1 cut(s)	792
Kzo9I	GATC	4 cut(s)	129, 166, 197, 792
Lsp1109I	GCAGC	1 cut(s)	191
LweI	GCATC	1 cut(s)	676
MaeIII	GTNAC	2 cut(s)	547, 700
MalI	GATC	4 cut(s)	131, 168, 199, 794
MboI	GATC	4 cut(s)	129, 166, 197, 792
MboII	GAAGA	6 cut(s)	192, 207, 302, 625, 657, 967
MflI	RGATCY	3 cut(s)	129, 166, 197
MhlI	GDGCHC	1 cut(s)	60
MluCI	AATT	6 cut(s)	143, 231, 443, 529, 959, 1045
MlyI	GAGTC	1 cut(s)	178
MmeI	TCCRAC	1 cut(s)	867
MnlI	CCTC	8 cut(s)	77, 100, 259, 280, 470, 547, 863, 957
MroXI	GAANNNNTTC	2 cut(s)	199, 294
MseI	TTAA	2 cut(s)	78, 387
MspI	CCGG	2 cut(s)	262, 777
MspR9I	CCNGG	2 cut(s)	263, 357
MvaI	CCWGG	1 cut(s)	357
MvnI	CGCG	2 cut(s)	13, 537
MwoI	GCNNNNNNNGC	1 cut(s)	769
NciI	CCSGG	1 cut(s)	263
NcoI	CCATGG	1 cut(s)	856
NdeII	GATC	4 cut(s)	129, 166, 197, 792
NlaIII	CATG	1 cut(s)	860
NlaIV	GGNNCC	5 cut(s)	58, 59, 382, 485, 502
NmuCI	GTSAC	2 cut(s)	547, 700
PaqCI	CACCTGC	1 cut(s)	992
PasI	CCCWGGG	1 cut(s)	356
PdmI	GAANNNNTTC	2 cut(s)	199, 294
PfeI	GAWTC	5 cut(s)	248, 253, 448, 572, 640
PfoI	TCCNGGA	1 cut(s)	261
PkrI	GCNGC	1 cut(s)	181
PleI	GAGTC	1 cut(s)	178
PpsI	GAGTC	1 cut(s)	178
Psp6I	CCWGG	1 cut(s)	355
PspEI	GGTNACC	1 cut(s)	700
PspGI	CCWGG	1 cut(s)	355
PspN4I	GGNNCC	5 cut(s)	58, 59, 382, 485, 502
PspOMI	GGGCCC	1 cut(s)	56
PspPI	GGNCC	3 cut(s)	56, 57, 457
PstI	CTGCAG	1 cut(s)	181
PstNI	CAGNNNCTG	1 cut(s)	418
PsuI	RGATCY	3 cut(s)	129, 166, 197
RsaI	GTAC	1 cut(s)	1042
RsaNI	GTAC	1 cut(s)	1041
SaqAI	TTAA	2 cut(s)	78, 387
SatI	GCNGC	1 cut(s)	180
Sau3AI	GATC	4 cut(s)	129, 166, 197, 792
Sau96I	GGNCC	3 cut(s)	56, 57, 457
ScaI	AGTACT	1 cut(s)	1042
SchI	GAGTC	1 cut(s)	178
ScrFI	CCNGG	2 cut(s)	263, 357
SduI	GDGCHC	1 cut(s)	60
SfaNI	GCATC	1 cut(s)	676
SfcI	CTRYAG	1 cut(s)	177
SmlI	CTYRAG	2 cut(s)	284, 737
SmoI	CTYRAG	2 cut(s)	284, 737
Sse9I	AATT	6 cut(s)	143, 231, 443, 529, 959, 1045
SsiI	CCGC	3 cut(s)	13, 535, 714
StyD4I	CCNGG	2 cut(s)	261, 355
StyI	CCWWGG	1 cut(s)	856
TaaI	ACNGT	4 cut(s)	73, 115, 885, 932
TaqI	TCGA	2 cut(s)	251, 1026
TasI	AATT	6 cut(s)	143, 231, 443, 529, 959, 1045
TatI	WGTACW	1 cut(s)	1040
TfiI	GAWTC	5 cut(s)	248, 253, 448, 572, 640
Tru1I	TTAA	2 cut(s)	78, 387
Tru9I	TTAA	2 cut(s)	78, 387
TscAI	CASTG	2 cut(s)	118, 985
TseFI	GTSAC	2 cut(s)	547, 700
TseI	GCWGC	1 cut(s)	179
Tsp45I	GTSAC	2 cut(s)	547, 700
TspDTI	ATGAA	4 cut(s)	22, 287, 505, 851
TspGWI	ACGGA	2 cut(s)	122, 296
TspRI	CASTG	2 cut(s)	118, 985
XmnI	GAANNNNTTC	2 cut(s)	199, 294
ZrmI	AGTACT	1 cut(s)	1042

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