Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6C

Orthogroup ID

OG0005397

Physical Location & Seq

Genomic Coordinates Reverse (-)

10111926 .. 10115396

Gene Structure 3471 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6CG091800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 876 bp

ATGGCACAGGCAAAACCTGTGGAGAAACCCCAAGAATCCTCTGACATGGAAGTGAAAGATACAGGGAACACTACTTCCTTCAAATTCAATGCTCAGGCACCTGAATTTGTTCCCAGATCGCATACCCAGATGCCGATTTCGGGTTATTTCTATCCCTGCTTTCACTTTCTTGGTGACACTGCTTCCCCGAATTGGTTTTACATTGGGGACCAAGAATTACCTCCTTATTTGATCTCCAATCCCAATATTCCTATAACCAATCGATCCAAGAATGTGCTACCCGATGAGCTTCAGCAGAAAATCATCAAACAGGTGGAGTACCAGTTCAGTGACATGAGTCTGTTAGCAAATGAATCATTAGCAAAACACATGAGTAAAGATCCTGAAGGATATGTTCCGATATCTGTTGTTGCTTCTACGAAAAAGATGAAGTCACTTATTAGTAACAACCATATGCTTGCACAAGCAGTCCGGTCCTCTTCAAAGCTTGTTGTAAGTGATGATGGAAAGAAGGTTAAACGTAAGCACCCTTTCACTGAAAAAGACAAAGAAGAATTGCAGTCTCGTACTGTTGTGGCAGAGAACTTGCCAGAAGATCACTCTCATCAAAACCTAGAGAAGATATTTAGTGTGGTTGGGAGTGTGAAAACTATCCGAATATGCCATCCCCACGAATCCAATTCTTCCCGGTCCAAAGGTGATTTCATTATTAGCAACAAGCTCCATGCGCTGGTGGAGTACGAGACAACAGACATAGCAGATAAAGCGGTTGATAAGTTGAGTGATGAGAGGAACTGGAGAAAAGGACTCCGAGTAAGGACTTTGGTCAGACGCTCGGTATGTCTCAATGAAATATCAAAGCATTTGTTTCCTTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

La PAM2 RRM_1

Protein Analysis

291

Amino Acids

33.04

Weight (kDa)

8.77

Isoelectric Point (pI)

47.7

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
La	PF05383	101 - 158	2.1e-18	La domain
RRM_1	PF00076	194 - 261	1.3e-06	RNA recognition motif

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)

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Publication-ready

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Orthologous Genes (Group: OG0005397)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G19090 AT3G19090
fragaria_vesca	FvH4_2g06870 FvH4_2g06870
malus_domestica	MD05G1074900.v1.1 MD10G1089400.v1.1
prunus_persica	Prupe.8G116300_v2.0.a1 Prupe.8G116300_v2.0.a1 Prupe.8G116300_v2.0.a1
pyrus_communis	pycom05g06810 pycom10g07290
rosa_chinensis	RchiOBHm_Chr6g0259181
rosa_laevigata	RLG00000014551
rosa_multiflora	Rmu_co8316895.1_g000001 Rmu_sc0002723.1_g000050
rosa_roxburghii	Rroxscaffold_7G00206310 Rroxscaffold_7G00206480
rosa_rugosa	Rorug05G0585400 Rorug05G0585400
rosa_samantha	Rh1AG078000 Rh1DG082900 Rh2AG437600 Rh2BG446100 Rh2DG456300 Rh6AG102400 Rh6BG094700 Rh6CG091800 Rh6DG085800
rosa_wichuraiana	Rw6G008850

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	97
AccB7I	CCANNNNNTGG	1 cut(s)	730
AciI	CCGC	1 cut(s)	767
AclWI	GGATC	2 cut(s)	258, 374
AcsI	RAATTY	2 cut(s)	83, 104
AcuI	CTGAAG	2 cut(s)	275, 405
AfaI	GTAC	3 cut(s)	320, 568, 740
AfiI	CCNNNNNNNGG	3 cut(s)	140, 192, 730
AgsI	TTSAA	3 cut(s)	82, 88, 483
AjuI	GAANNNNNNNTTGG	2 cut(s)	686, 718
AloI	GAACNNNNNNTCC	4 cut(s)	59, 91, 308, 340
AluBI	AGCT	3 cut(s)	289, 487, 721
AluI	AGCT	3 cut(s)	289, 487, 721
Alw26I	GTCTC	3 cut(s)	567, 737, 848
AlwI	GGATC	2 cut(s)	258, 374
ApoI	RAATTY	2 cut(s)	83, 104
Asp700I	GAANNNNTTC	1 cut(s)	108
AspLEI	GCGC	1 cut(s)	730
AspS9I	GGNCC	3 cut(s)	208, 474, 690
AsuC2I	CCSGG	1 cut(s)	688
AsuHPI	GGTGA	2 cut(s)	185, 710
AvaII	GGWCC	3 cut(s)	208, 474, 690
BanI	GGYRCC	1 cut(s)	97
BccI	CCATC	2 cut(s)	497, 672
BcnI	CCSGG	1 cut(s)	688
BcoDI	GTCTC	3 cut(s)	567, 737, 848
BfaI	CTAG	1 cut(s)	614
Bme1390I	CCNGG	1 cut(s)	688
Bme18I	GGWCC	3 cut(s)	208, 474, 690
BmgT120I	GGNCC	3 cut(s)	208, 474, 690
BmiI	GGNNCC	2 cut(s)	99, 209
BmrFI	CCNGG	1 cut(s)	688
BmsI	GCATC	1 cut(s)	120
BoxI	GACNNNNGTC	2 cut(s)	336, 824
BpmI	CTGGAG	1 cut(s)	817
Bpu10I	CCTNAGC	1 cut(s)	93
BpuMI	CCSGG	1 cut(s)	688
Bsa29I	ATCGAT	1 cut(s)	262
BsaWI	WCCGGW	1 cut(s)	471
BsaXI	ACNNNNNCTCC	2 cut(s)	308, 338
Bsc4I	CCNNNNNNNGG	3 cut(s)	140, 192, 730
Bse1I	ACTGG	2 cut(s)	322, 800
BseCI	ATCGAT	1 cut(s)	262
BseGI	GGATG	1 cut(s)	664
BseLI	CCNNNNNNNGG	3 cut(s)	140, 192, 730
BseMII	CTCAG	1 cut(s)	107
BseNI	ACTGG	2 cut(s)	322, 800
BshNI	GGYRCC	1 cut(s)	97
BshVI	ATCGAT	1 cut(s)	262
BsiSI	CCGG	2 cut(s)	472, 688
BslFI	GGGAC	1 cut(s)	221
BslI	CCNNNNNNNGG	3 cut(s)	140, 192, 730
BsmAI	GTCTC	3 cut(s)	567, 737, 848
BsmFI	GGGAC	1 cut(s)	221
Bsp143I	GATC	5 cut(s)	116, 231, 263, 379, 595
BspACI	CCGC	1 cut(s)	767
BspCNI	CTCAG	1 cut(s)	106
BspDI	ATCGAT	1 cut(s)	262
BspLI	GGNNCC	2 cut(s)	99, 209
BspPI	GGATC	2 cut(s)	258, 374
BspT107I	GGYRCC	1 cut(s)	97
BsrI	ACTGG	2 cut(s)	322, 800
BssMI	GATC	5 cut(s)	116, 231, 263, 379, 595
Bst4CI	ACNGT	1 cut(s)	571
Bst6I	CTCTTC	1 cut(s)	484
BstC8I	GCNNGC	1 cut(s)	459
BstDEI	CTNAG	1 cut(s)	93
BstF5I	GGATG	1 cut(s)	664
BstHHI	GCGC	1 cut(s)	730
BstKTI	GATC	5 cut(s)	119, 234, 266, 382, 598
BstMAI	GTCTC	3 cut(s)	567, 737, 848
BstMBI	GATC	5 cut(s)	116, 231, 263, 379, 595
BstMWI	GCNNNNNNNGC	2 cut(s)	727, 764
BstPAI	GACNNNNGTC	2 cut(s)	336, 824
BstSCI	CCNGG	1 cut(s)	686
BstX2I	RGATCY	1 cut(s)	379
BstYI	RGATCY	1 cut(s)	379
Bsu15I	ATCGAT	1 cut(s)	262
BsuTUI	ATCGAT	1 cut(s)	262
BtsCI	GGATG	1 cut(s)	664
BtsI	GCAGTG	1 cut(s)	177
BtsIMutI	CAGTG	3 cut(s)	177, 334, 534
Cac8I	GCNNGC	1 cut(s)	459
CfoI	GCGC	1 cut(s)	730
Cfr13I	GGNCC	3 cut(s)	208, 474, 690
ClaI	ATCGAT	1 cut(s)	262
CseI	GACGC	1 cut(s)	840
Csp6I	GTAC	3 cut(s)	319, 567, 739
CspCI	CAANNNNNGTGG	1 cut(s)	35
CviAII	CATG	4 cut(s)	46, 334, 370, 725
CviJI	RGCY	3 cut(s)	289, 487, 721
CviKI_1	RGCY	3 cut(s)	289, 487, 721
CviQI	GTAC	3 cut(s)	319, 567, 739
DdeI	CTNAG	1 cut(s)	93
DpnI	GATC	5 cut(s)	118, 233, 265, 381, 597
DpnII	GATC	5 cut(s)	116, 231, 263, 379, 595
Eam1104I	CTCTTC	1 cut(s)	484
EarI	CTCTTC	1 cut(s)	484
Eco32I	GATATC	1 cut(s)	402
Eco47I	GGWCC	3 cut(s)	208, 474, 690
Eco57I	CTGAAG	2 cut(s)	275, 405
EcoRV	GATATC	1 cut(s)	402
FaeI	CATG	4 cut(s)	49, 337, 373, 728
FaqI	GGGAC	1 cut(s)	221
FatI	CATG	4 cut(s)	45, 333, 369, 724
FauNDI	CATATG	1 cut(s)	453
FokI	GGATG	1 cut(s)	651
FspBI	CTAG	1 cut(s)	614
GlaI	GCGC	1 cut(s)	729
GsuI	CTGGAG	1 cut(s)	817
HapII	CCGG	2 cut(s)	472, 688
HgaI	GACGC	1 cut(s)	840
HhaI	GCGC	1 cut(s)	730
Hin1II	CATG	4 cut(s)	49, 337, 373, 728
Hin6I	GCGC	1 cut(s)	728
HinP1I	GCGC	1 cut(s)	728
HindIII	AAGCTT	1 cut(s)	485
HinfI	GANTC	5 cut(s)	35, 337, 353, 674, 807
HpaII	CCGG	2 cut(s)	472, 688
HphI	GGTGA	2 cut(s)	185, 710
Hpy188I	TCNGA	5 cut(s)	43, 399, 656, 812, 830
Hpy188III	TCNNGA	1 cut(s)	383
HpyAV	CCTTC	3 cut(s)	88, 380, 505
HpyCH4III	ACNGT	1 cut(s)	571
HpyCH4IV	ACGT	1 cut(s)	520
HpyCH4V	TGCA	2 cut(s)	461, 559
HpyF10VI	GCNNNNNNNGC	2 cut(s)	727, 764
HpyF3I	CTNAG	1 cut(s)	93
HpySE526I	ACGT	1 cut(s)	520
Hsp92II	CATG	4 cut(s)	49, 337, 373, 728
HspAI	GCGC	1 cut(s)	728
Kzo9I	GATC	5 cut(s)	116, 231, 263, 379, 595
LmnI	GCTCC	1 cut(s)	726
LweI	GCATC	1 cut(s)	120
MaeI	CTAG	1 cut(s)	614
MaeII	ACGT	1 cut(s)	520
MaeIII	GTNAC	4 cut(s)	173, 329, 432, 443
MalI	GATC	5 cut(s)	118, 233, 265, 381, 597
MboI	GATC	5 cut(s)	116, 231, 263, 379, 595
MboII	GAAGA	5 cut(s)	471, 563, 605, 631, 675
MflI	RGATCY	1 cut(s)	379
MluCI	AATT	6 cut(s)	83, 104, 190, 215, 554, 679
MlyI	GAGTC	2 cut(s)	346, 801
MnlI	CCTC	4 cut(s)	49, 231, 487, 783
MroXI	GAANNNNTTC	1 cut(s)	108
MseI	TTAA	1 cut(s)	516
MslI	CAYNNNNRTG	1 cut(s)	50
MspI	CCGG	2 cut(s)	472, 688
MspR9I	CCNGG	1 cut(s)	688
MwoI	GCNNNNNNNGC	2 cut(s)	727, 764
NciI	CCSGG	1 cut(s)	688
NdeI	CATATG	1 cut(s)	453
NdeII	GATC	5 cut(s)	116, 231, 263, 379, 595
NlaIII	CATG	4 cut(s)	49, 337, 373, 728
NlaIV	GGNNCC	2 cut(s)	99, 209
NmuCI	GTSAC	3 cut(s)	173, 329, 432
PdmI	GAANNNNTTC	1 cut(s)	108
PfeI	GAWTC	3 cut(s)	35, 353, 674
PflMI	CCANNNNNTGG	1 cut(s)	730
PleI	GAGTC	2 cut(s)	345, 801
PpsI	GAGTC	2 cut(s)	345, 801
PshAI	GACNNNNGTC	2 cut(s)	336, 824
PspN4I	GGNNCC	2 cut(s)	99, 209
PspPI	GGNCC	3 cut(s)	208, 474, 690
PsuI	RGATCY	1 cut(s)	379
RsaI	GTAC	3 cut(s)	320, 568, 740
RsaNI	GTAC	3 cut(s)	319, 567, 739
RseI	CAYNNNNRTG	1 cut(s)	50
SaqAI	TTAA	1 cut(s)	516
Sau3AI	GATC	5 cut(s)	116, 231, 263, 379, 595
Sau96I	GGNCC	3 cut(s)	208, 474, 690
SchI	GAGTC	2 cut(s)	346, 801
ScrFI	CCNGG	1 cut(s)	688
SfaNI	GCATC	1 cut(s)	120
SinI	GGWCC	3 cut(s)	208, 474, 690
SmiMI	CAYNNNNRTG	1 cut(s)	50
Sse9I	AATT	6 cut(s)	83, 104, 190, 215, 554, 679
SsiI	CCGC	1 cut(s)	767
SspI	AATATT	1 cut(s)	247
SspMI	CTAG	1 cut(s)	614
StyD4I	CCNGG	1 cut(s)	686
TaaI	ACNGT	1 cut(s)	571
TaiI	ACGT	1 cut(s)	523
TaqI	TCGA	1 cut(s)	262
TasI	AATT	6 cut(s)	83, 104, 190, 215, 554, 679
TfiI	GAWTC	3 cut(s)	35, 353, 674
Tru1I	TTAA	1 cut(s)	516
Tru9I	TTAA	1 cut(s)	516
TscAI	CASTG	3 cut(s)	184, 334, 541
TseFI	GTSAC	3 cut(s)	173, 329, 432
Tsp45I	GTSAC	3 cut(s)	173, 329, 432
TspDTI	ATGAA	4 cut(s)	366, 443, 694, 864
TspRI	CASTG	3 cut(s)	184, 334, 541
Van91I	CCANNNNNTGG	1 cut(s)	730
VpaK11BI	GGWCC	3 cut(s)	208, 474, 690
XapI	RAATTY	2 cut(s)	83, 104
XmnI	GAANNNNTTC	1 cut(s)	108
XspI	CTAG	1 cut(s)	614

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