Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5A

Orthogroup ID

OG0009193

Physical Location & Seq

Genomic Coordinates Reverse (-)

22693838 .. 22700533

Gene Structure 6696 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5AG195400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 906 bp

ATGGCTGCGGTTGCTGAGATTGCCGGTGAGGCAGCCTCTGCCAACAACCAGAACTTGGATTCAATATCAAAACCCGTGTCTGAATCGAAACCCAAATCGGAATTCGATGTGCAGAAGCTGGTGGATATGTTCACCAAGTTGAACCCTTTAGCCAAAGAGTTCTTCCCTTCATCTTACTCACCTCTGCAAAATCACAATTTTGATAACTCTTTTGCTGTCAATAACAATAAGCTCTTACCCACTGACAATCAGGCCAACAATCGAAGGAGAAGAAATAACTATAATCAGGGGAAGAGAAGGTTGAGTGGGAGAGCTTTCAGAGCTGAGCGCGAAAATAGTATTAGACGAACAGTTTATGTTTCTGATATTGATCAGCAAGTTACCGAAGAGCGTCTTGCTGCCATATTTAGTAATTGTGGACAAGTTGTTGACTGCCGAATTTGTGGTGATCCACATTCAGTGCTCCGTTTTGCATTTGTGGAGTTTGCTGATGAGCATGGTGCGAGAGCAGCCTTGAACCTTGGTGGGACGATGCTAGGGTATTATCCCGTTAGGGTCTTACCTTCAAAAACTGCCATCCTTCCTGTGAATCCTACATTCCTCCCTAGGTCAGAAGATGAACGGGAAATGTGTAGCAGGACTGTATATTGTACAAATATCGATAAGAAGGTTTCTCAAGCTGAAGTCAAGAGTTTCTTTGAAACAGCTTGTGGTGAGGTTACTCGTTTGAGGCTTTTGGGAGATCATGTGCATTCAACCCGTATAGCTTTTGTTGAATTTGCAATGGCAGAAAGTGCCATACTTGCACTGAACTGTAGCGGAATGGTGTTGGGAACACAACCCATCAGGGTAAGTCCTTCAAAGACACCTGTGCGGCCACGGGTCACTCGTCCAACATTGCATTAA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005654 GO:0016604 GO:0016607 GO:0031974 GO:0031981 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044451 GO:0044464 GO:0070013

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PAM2 RRM_1

Protein Analysis

301

Amino Acids

33.58

Weight (kDa)

9.09

Isoelectric Point (pI)

46.33

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
RRM_1	PF00076	118 - 180	1.7e-12	RNA recognition motif
RRM_1	PF00076	215 - 282	7e-09	RNA recognition motif

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0009193)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G53650 AT1G53650 AT3G14450
fragaria_vesca	FvH4_3g16680 FvH4_3g16680
malus_domestica	MD05G1208300.v1.1 MD10G1194800.v1.1
prunus_persica	Prupe.4G149200_v2.0.a1 Prupe.4G149200_v2.0.a1
pyrus_communis	pycom05g19400 pycom10g16820
rosa_chinensis	RchiOBHm_Chr5g0027791
rosa_laevigata	RLG00000033043
rosa_multiflora	Rmu_sc0000920.1_g000007
rosa_roxburghii	Rroxscaffold_1G00051820
rosa_rugosa	Rorug05G0101100 Rorug05G0101200
rosa_samantha	Rh5AG195400 Rh5BG193700 Rh5CG214000 Rh5DG195700
rosa_wichuraiana	Rw5G017830

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	55
AccII	CGCG	1 cut(s)	330
AciI	CCGC	3 cut(s)	8, 819, 874
AclWI	GGATC	1 cut(s)	443
AcoI	YGGCCR	1 cut(s)	875
AcsI	RAATTY	3 cut(s)	101, 438, 776
AcuI	CTGAAG	1 cut(s)	702
AfaI	GTAC	1 cut(s)	652
AfiI	CCNNNNNNNGG	1 cut(s)	55
AgsI	TTSAA	8 cut(s)	63, 142, 517, 567, 701, 756, 776, 861
AjuI	GAANNNNNNNTTGG	4 cut(s)	86, 118, 146, 178
AluBI	AGCT	7 cut(s)	118, 232, 314, 323, 680, 707, 767
AluI	AGCT	7 cut(s)	118, 232, 314, 323, 680, 707, 767
Alw21I	GWGCWC	1 cut(s)	465
AlwI	GGATC	1 cut(s)	443
AlwNI	CAGNNNCTG	2 cut(s)	38, 118
AoxI	GGCC	2 cut(s)	252, 875
ApeKI	GCWGC	4 cut(s)	5, 32, 398, 509
ApoI	RAATTY	3 cut(s)	101, 438, 776
ArsI	GACNNNNNNTTYG	2 cut(s)	62, 94
AspA2I	CCTAGG	1 cut(s)	605
AspLEI	GCGC	1 cut(s)	330
AsuHPI	GGTGA	5 cut(s)	38, 124, 171, 458, 725
AvrII	CCTAGG	1 cut(s)	605
Bbv12I	GWGCWC	1 cut(s)	465
BbvI	GCAGC	3 cut(s)	44, 385, 521
BccI	CCATC	2 cut(s)	584, 851
BclI	TGATCA	1 cut(s)	370
BfaI	CTAG	2 cut(s)	536, 606
BfmI	CTRYAG	1 cut(s)	814
BglI	GCCNNNNNGGC	1 cut(s)	29
BisI	GCNGC	5 cut(s)	6, 33, 399, 510, 875
BlnI	CCTAGG	1 cut(s)	605
BlpI	GCTNAGC	1 cut(s)	324
BlsI	GCNGC	5 cut(s)	7, 34, 400, 511, 876
BmsI	GCATC	1 cut(s)	522
BplI	GAGNNNNNCTC	2 cut(s)	20, 52
Bpu1102I	GCTNAGC	1 cut(s)	324
BpuEI	CTTGAG	1 cut(s)	660
Bsa29I	ATCGAT	1 cut(s)	660
BsaBI	GATNNNNATC	1 cut(s)	369
BsaJI	CCNNGG	3 cut(s)	520, 605, 878
BsaXI	ACNNNNNCTCC	2 cut(s)	732, 762
Bsc4I	CCNNNNNNNGG	1 cut(s)	55
Bse118I	RCCGGY	1 cut(s)	23
Bse3DI	GCAATG	2 cut(s)	789, 896
Bse8I	GATNNNNATC	1 cut(s)	369
BseCI	ATCGAT	1 cut(s)	660
BseDI	CCNNGG	3 cut(s)	520, 605, 878
BseGI	GGATG	1 cut(s)	576
BseJI	GATNNNNATC	1 cut(s)	369
BseLI	CCNNNNNNNGG	1 cut(s)	55
BseMI	GCAATG	2 cut(s)	789, 896
BseMII	CTCAG	2 cut(s)	6, 315
BseXI	GCAGC	3 cut(s)	44, 385, 521
BsgI	GTGCAG	1 cut(s)	131
Bsh1236I	CGCG	1 cut(s)	330
BshFI	GGCC	2 cut(s)	254, 877
BshVI	ATCGAT	1 cut(s)	660
BsiHKAI	GWGCWC	1 cut(s)	465
BsiSI	CCGG	1 cut(s)	24
BslFI	GGGAC	1 cut(s)	541
BslI	CCNNNNNNNGG	1 cut(s)	55
BsmFI	GGGAC	1 cut(s)	541
BsmI	GAATGC	1 cut(s)	751
BsnI	GGCC	2 cut(s)	254, 877
Bsp1286I	GDGCHC	1 cut(s)	465
Bsp1407I	TGTACA	1 cut(s)	650
Bsp143I	GATC	3 cut(s)	370, 448, 742
Bsp1720I	GCTNAGC	1 cut(s)	324
BspACI	CCGC	3 cut(s)	8, 819, 874
BspANI	GGCC	2 cut(s)	254, 877
BspCNI	CTCAG	2 cut(s)	7, 316
BspDI	ATCGAT	1 cut(s)	660
BspFNI	CGCG	1 cut(s)	330
BspPI	GGATC	1 cut(s)	443
BspQI	GCTCTTC	1 cut(s)	381
BsrDI	GCAATG	2 cut(s)	789, 896
BsrFI	RCCGGY	1 cut(s)	23
BsrGI	TGTACA	1 cut(s)	650
BssAI	RCCGGY	1 cut(s)	23
BssECI	CCNNGG	3 cut(s)	520, 605, 878
BssMI	GATC	3 cut(s)	370, 448, 742
BssT1I	CCWWGG	2 cut(s)	520, 605
Bst4CI	ACNGT	3 cut(s)	352, 643, 815
Bst6I	CTCTTC	2 cut(s)	287, 381
BstAPI	GCANNNNNTGC	2 cut(s)	38, 794
BstAUI	TGTACA	1 cut(s)	650
BstDEI	CTNAG	2 cut(s)	15, 324
BstDSI	CCRYGG	1 cut(s)	878
BstF5I	GGATG	1 cut(s)	576
BstFNI	CGCG	1 cut(s)	330
BstHHI	GCGC	1 cut(s)	330
BstKTI	GATC	3 cut(s)	373, 451, 745
BstMBI	GATC	3 cut(s)	370, 448, 742
BstMWI	GCNNNNNNNGC	8 cut(s)	11, 20, 29, 38, 320, 509, 794, 803
BstSFI	CTRYAG	1 cut(s)	814
BstUI	CGCG	1 cut(s)	330
BstV1I	GCAGC	3 cut(s)	44, 385, 521
Bsu15I	ATCGAT	1 cut(s)	660
BsuRI	GGCC	2 cut(s)	254, 877
BsuTUI	ATCGAT	1 cut(s)	660
BtgI	CCRYGG	1 cut(s)	878
BtsCI	GGATG	1 cut(s)	576
BtsIMutI	CAGTG	3 cut(s)	240, 465, 806
CaiI	CAGNNNCTG	2 cut(s)	38, 118
CfoI	GCGC	1 cut(s)	330
Cfr10I	RCCGGY	1 cut(s)	23
ClaI	ATCGAT	1 cut(s)	660
CseI	GACGC	1 cut(s)	380
Csp6I	GTAC	1 cut(s)	651
CviAII	CATG	2 cut(s)	497, 746
CviQI	GTAC	1 cut(s)	651
DdeI	CTNAG	2 cut(s)	15, 324
DpnI	GATC	3 cut(s)	372, 450, 744
DpnII	GATC	3 cut(s)	370, 448, 742
EaeI	YGGCCR	1 cut(s)	875
Eam1104I	CTCTTC	2 cut(s)	287, 381
EarI	CTCTTC	2 cut(s)	287, 381
Eco130I	CCWWGG	2 cut(s)	520, 605
Eco57I	CTGAAG	1 cut(s)	702
EcoRI	GAATTC	1 cut(s)	101
EcoT14I	CCWWGG	2 cut(s)	520, 605
ErhI	CCWWGG	2 cut(s)	520, 605
FaeI	CATG	2 cut(s)	500, 749
FaiI	YATR	9 cut(s)	128, 282, 357, 404, 498, 646, 747, 764, 800
FalI	AAGNNNNNCTT	4 cut(s)	378, 410, 680, 712
FaqI	GGGAC	1 cut(s)	541
FatI	CATG	2 cut(s)	496, 745
FbaI	TGATCA	1 cut(s)	370
Fnu4HI	GCNGC	5 cut(s)	6, 33, 399, 510, 875
FokI	GGATG	1 cut(s)	563
Fsp4HI	GCNGC	5 cut(s)	6, 33, 399, 510, 875
FspBI	CTAG	2 cut(s)	536, 606
GlaI	GCGC	1 cut(s)	329
GluI	GCNGC	5 cut(s)	6, 33, 399, 510, 875
HaeIII	GGCC	2 cut(s)	254, 877
HapII	CCGG	1 cut(s)	24
HgaI	GACGC	1 cut(s)	380
HhaI	GCGC	1 cut(s)	330
Hin1II	CATG	2 cut(s)	500, 749
Hin6I	GCGC	1 cut(s)	328
HinP1I	GCGC	1 cut(s)	328
HincII	GTYRAC	1 cut(s)	430
HindII	GTYRAC	1 cut(s)	430
HinfI	GANTC	3 cut(s)	59, 83, 589
HpaII	CCGG	1 cut(s)	24
HphI	GGTGA	5 cut(s)	38, 124, 171, 458, 725
Hpy166II	GTNNAC	3 cut(s)	132, 419, 430
Hpy188I	TCNGA	5 cut(s)	82, 100, 320, 364, 613
Hpy188III	TCNNGA	1 cut(s)	688
Hpy8I	GTNNAC	3 cut(s)	132, 419, 430
HpyAV	CCTTC	7 cut(s)	177, 258, 291, 573, 590, 661, 867
HpyCH4III	ACNGT	3 cut(s)	352, 643, 815
HpyCH4V	TGCA	7 cut(s)	112, 187, 473, 751, 782, 806, 901
HpyF10VI	GCNNNNNNNGC	8 cut(s)	11, 20, 29, 38, 320, 509, 794, 803
HpyF3I	CTNAG	2 cut(s)	15, 324
Hsp92II	CATG	2 cut(s)	500, 749
HspAI	GCGC	1 cut(s)	328
Ksp22I	TGATCA	1 cut(s)	370
Kzo9I	GATC	3 cut(s)	370, 448, 742
LguI	GCTCTTC	1 cut(s)	381
LmnI	GCTCC	1 cut(s)	468
LpnPI	CCDG	9 cut(s)	37, 62, 104, 236, 272, 597, 622, 832, 882
Lsp1109I	GCAGC	3 cut(s)	44, 385, 521
LweI	GCATC	1 cut(s)	522
MaeI	CTAG	2 cut(s)	536, 606
MaeIII	GTNAC	3 cut(s)	379, 718, 883
MalI	GATC	3 cut(s)	372, 450, 744
MboI	GATC	3 cut(s)	370, 448, 742
MboII	GAAGA	5 cut(s)	154, 282, 304, 398, 626
MhlI	GDGCHC	1 cut(s)	465
MluCI	AATT	5 cut(s)	101, 196, 412, 438, 776
MnlI	CCTC	6 cut(s)	22, 46, 192, 611, 709, 723
MseI	TTAA	1 cut(s)	904
MspI	CCGG	1 cut(s)	24
Mva1269I	GAATGC	1 cut(s)	751
MvnI	CGCG	1 cut(s)	330
MwoI	GCNNNNNNNGC	8 cut(s)	11, 20, 29, 38, 320, 509, 794, 803
NdeII	GATC	3 cut(s)	370, 448, 742
NlaIII	CATG	2 cut(s)	500, 749
NmuCI	GTSAC	1 cut(s)	883
PciSI	GCTCTTC	1 cut(s)	381
PcsI	WCGNNNNNNNCGW	1 cut(s)	886
PctI	GAATGC	1 cut(s)	751
PfeI	GAWTC	3 cut(s)	59, 83, 589
PflMI	CCANNNNNTGG	1 cut(s)	55
PkrI	GCNGC	5 cut(s)	7, 34, 400, 511, 876
PstNI	CAGNNNCTG	2 cut(s)	38, 118
RsaI	GTAC	1 cut(s)	652
RsaNI	GTAC	1 cut(s)	651
SapI	GCTCTTC	1 cut(s)	381
SaqAI	TTAA	1 cut(s)	904
SatI	GCNGC	5 cut(s)	6, 33, 399, 510, 875
Sau3AI	GATC	3 cut(s)	370, 448, 742
SduI	GDGCHC	1 cut(s)	465
SfaNI	GCATC	1 cut(s)	522
SfcI	CTRYAG	1 cut(s)	814
SmlI	CTYRAG	1 cut(s)	675
SmoI	CTYRAG	1 cut(s)	675
Sse9I	AATT	5 cut(s)	101, 196, 412, 438, 776
SsiI	CCGC	3 cut(s)	8, 819, 874
SspMI	CTAG	2 cut(s)	536, 606
StyI	CCWWGG	2 cut(s)	520, 605
TaaI	ACNGT	3 cut(s)	352, 643, 815
TaqI	TCGA	4 cut(s)	86, 105, 262, 660
TasI	AATT	5 cut(s)	101, 196, 412, 438, 776
TatI	WGTACW	1 cut(s)	650
TauI	GCSGC	1 cut(s)	877
TfiI	GAWTC	3 cut(s)	59, 83, 589
Tru1I	TTAA	1 cut(s)	904
Tru9I	TTAA	1 cut(s)	904
TscAI	CASTG	3 cut(s)	247, 465, 813
TseFI	GTSAC	1 cut(s)	883
TseI	GCWGC	4 cut(s)	5, 32, 398, 509
Tsp45I	GTSAC	1 cut(s)	883
TspDTI	ATGAA	2 cut(s)	159, 633
TspGWI	ACGGA	1 cut(s)	455
TspRI	CASTG	3 cut(s)	247, 465, 813
Van91I	CCANNNNNTGG	1 cut(s)	55
XapI	RAATTY	3 cut(s)	101, 438, 776
XmaJI	CCTAGG	1 cut(s)	605
XspI	CTAG	2 cut(s)	536, 606

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