Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4D

Orthogroup ID

OG0000288

Physical Location & Seq

Genomic Coordinates Reverse (-)

38892090 .. 38893499

Gene Structure 1410 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4DG200000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 330 bp

ATGGTCCGTGATAAGCTTCTAGGAAAAAAATTCAAGGACATCGATATTGCTTTGGAAAATATGATGGGCAGCAAATTTGTTGAGAAGGTGAGAGACTACTTGTTGTCTATGGGGGAAGAGGTTCAAGGAATCGCTATCATTCCAAGCAATCCCGATCAATCAAAACATTTGGAAATGGCGAGGATGTGCATCTTAAATGTATGGGTTGATTTTGTGAACTTACGCTGTGAAGAGTACAGTGATGATAGCCGCATTCCTGCTATGCACCCAACCTCCTCCTCCATCTCCGAACAGCACCGAACCAACCTCTTCTTACTTCGCCGCCTCTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001680 GO:0003674 GO:0003824 GO:0004652 GO:0004810 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0005739 GO:0005759 GO:0006139 GO:0006396 GO:0006399 GO:0006725 GO:0006807 GO:0008033 GO:0008150 GO:0008152 GO:0009987 GO:0010467 GO:0016070 GO:0016740 GO:0016772 GO:0016779 GO:0031123 GO:0031974 GO:0034470 GO:0034641 GO:0034660 GO:0042780 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043628 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044429 GO:0044444 GO:0044446 GO:0044464 GO:0046483 GO:0052928 GO:0052929 GO:0070013 GO:0070566 GO:0071704 GO:0090304 GO:0140098 GO:0140101 GO:1901360 GO:1990817

KEGG Pathways

Metabolic & Signaling

ko03013 map03013

Pfam Domains

Protein Families

PolyA_pol PolyA_pol_RNAbd

Protein Analysis

109

Amino Acids

12.64

Weight (kDa)

6.28

Isoelectric Point (pI)

38.79

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PolyA_pol	PF01743	1 - 81	7.9e-10	Poly A polymerase head domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Orthologous Genes (Group: OG0000288)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G22660 AT1G22660 AT1G22660 AT1G22660 AT1G22660
fragaria_vesca	FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440 FvH4_4g33440
malus_domestica	MD05G1045700.v1.1 MD10G1052700.v1.1
prunus_persica	Prupe.6G147900_v2.0.a1 Prupe.6G147900_v2.0.a1
pyrus_communis	pycom05g03810 pycom10g03770
rosa_chinensis	RchiOBHm_Chr3g0457671 RchiOBHm_Chr4g0411681 RchiOBHm_Chr4g0411871 RchiOBHm_Chr4g0412011 RchiOBHm_Chr4g0442691 RchiOBHm_Chr5g0054011 RchiOBHm_Chr7g0192731 RchiOBHm_Chr7g0217301 RchiOBHm_Chr7g0217311
rosa_laevigata	RLG00000002496 RLG00000002497 RLG00000004333 RLG00000005141 RLG00000005991 RLG00000008329 RLG00000008334
rosa_multiflora	Rmu_co8052866.1_g000001 Rmu_sc0000124.1_g000041 Rmu_sc0000711.1_g000018 Rmu_sc0000711.1_g000026 Rmu_sc0000711.1_g000049 Rmu_sc0001260.1_g000024 Rmu_sc0002040.1_g000016 Rmu_sc0003311.1_g000009 Rmu_sc0003541.1_g000049 Rmu_sc0007633.1_g000011 Rmu_sc0007784.1_g000001 Rmu_sc0007843.1_g000002 Rmu_sc0018873.1_g000007 Rmu_sc0037239.1_g000001 Rmu_ssc0000204.1_g000025
rosa_roxburghii	Rroxscaffold_1G00010150 Rroxscaffold_2G00085070 Rroxscaffold_3G00237950 Rroxscaffold_3G00238000 Rroxscaffold_3G00238060 Rroxscaffold_3G00242460 Rroxscaffold_5G00356230 Rroxscaffold_5G00356320 Rroxscaffold_5G00357990 Rroxscaffold_5G00383500
rosa_rugosa	Rorug04G0107400 Rorug04G0107400 Rorug04G0342400.1 Rorug04G0342500.1 Rorug04G0342600.1 Rorug06G0053100 Rorug06G0099700 Rorug07G0004300 Rorug07G0167800 Rorug07G0167900
rosa_samantha	Rh2CG570300 Rh2DG609200 Rh4AG068500 Rh4AG169600 Rh4AG169900 Rh4AG170200 Rh4AG170600 Rh4AG202600 Rh4AG394800 Rh4BG066700 Rh4BG066800 Rh4BG166500 Rh4BG166600 Rh4BG166700 Rh4BG167000 Rh4BG167300 Rh4BG168500 Rh4BG169200 Rh4BG208600 Rh4BG407700 Rh4CG074000 Rh4CG181100 Rh4CG181200 Rh4CG181700 Rh4CG423100 Rh4DG163900 Rh4DG164400 Rh4DG165100 Rh4DG165200 Rh4DG200000 Rh4DG401800 Rh6BG194500 Rh6CG100200 Rh7AG129300 Rh7AG307100 Rh7BG130700 Rh7BG298000 Rh7CG134100 Rh7DG131500 Rh7DG306700
rosa_wichuraiana	Rw0G007750 Rw4G014080 Rw4G014120 Rw4G014180 Rw4G017150 Rw4G034120 Rw7G011060

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	2 cut(s)	250, 322
AcsI	RAATTY	2 cut(s)	29, 74
AfaI	GTAC	1 cut(s)	236
AgsI	TTSAA	2 cut(s)	34, 125
AluBI	AGCT	1 cut(s)	16
AluI	AGCT	1 cut(s)	16
Alw26I	GTCTC	1 cut(s)	87
ApeKI	GCWGC	1 cut(s)	69
ApoI	RAATTY	2 cut(s)	29, 74
Asp700I	GAANNNNTTC	1 cut(s)	120
AspS9I	GGNCC	1 cut(s)	4
AsuHPI	GGTGA	1 cut(s)	100
AvaII	GGWCC	1 cut(s)	4
BbvI	GCAGC	1 cut(s)	81
BccI	CCATC	2 cut(s)	58, 290
BcoDI	GTCTC	1 cut(s)	87
BfaI	CTAG	1 cut(s)	20
BisI	GCNGC	3 cut(s)	70, 250, 322
BlsI	GCNGC	3 cut(s)	71, 251, 323
Bme18I	GGWCC	1 cut(s)	4
BmgT120I	GGNCC	1 cut(s)	4
BmsI	GCATC	1 cut(s)	198
Bsa29I	ATCGAT	1 cut(s)	42
BsaBI	GATNNNNATC	1 cut(s)	188
BsaXI	ACNNNNNCTCC	2 cut(s)	257, 287
Bse8I	GATNNNNATC	1 cut(s)	188
BseCI	ATCGAT	1 cut(s)	42
BseGI	GGATG	1 cut(s)	189
BseJI	GATNNNNATC	1 cut(s)	188
BseRI	GAGGAG	2 cut(s)	265, 268
BseXI	GCAGC	1 cut(s)	81
BshVI	ATCGAT	1 cut(s)	42
BsmAI	GTCTC	1 cut(s)	87
BsmI	GAATGC	1 cut(s)	252
Bsp143I	GATC	1 cut(s)	154
BspACI	CCGC	2 cut(s)	250, 322
BspDI	ATCGAT	1 cut(s)	42
BssMI	GATC	1 cut(s)	154
Bst4CI	ACNGT	1 cut(s)	239
Bst6I	CTCTTC	3 cut(s)	111, 225, 314
BstF5I	GGATG	1 cut(s)	189
BstKTI	GATC	1 cut(s)	157
BstMAI	GTCTC	1 cut(s)	87
BstMBI	GATC	1 cut(s)	154
BstV1I	GCAGC	1 cut(s)	81
Bsu15I	ATCGAT	1 cut(s)	42
BsuTUI	ATCGAT	1 cut(s)	42
BtsCI	GGATG	1 cut(s)	189
BtsIMutI	CAGTG	1 cut(s)	244
Cfr13I	GGNCC	1 cut(s)	4
ClaI	ATCGAT	1 cut(s)	42
Csp6I	GTAC	1 cut(s)	235
CviJI	RGCY	2 cut(s)	16, 249
CviKI_1	RGCY	2 cut(s)	16, 249
CviQI	GTAC	1 cut(s)	235
DpnI	GATC	1 cut(s)	156
DpnII	GATC	1 cut(s)	154
Eam1104I	CTCTTC	3 cut(s)	111, 225, 314
EarI	CTCTTC	3 cut(s)	111, 225, 314
Eco47I	GGWCC	1 cut(s)	4
FaiI	YATR	4 cut(s)	62, 110, 202, 263
Fnu4HI	GCNGC	3 cut(s)	70, 250, 322
FokI	GGATG	1 cut(s)	196
Fsp4HI	GCNGC	3 cut(s)	70, 250, 322
FspBI	CTAG	1 cut(s)	20
GluI	GCNGC	3 cut(s)	70, 250, 322
HindIII	AAGCTT	1 cut(s)	14
HinfI	GANTC	1 cut(s)	129
HphI	GGTGA	1 cut(s)	100
Hpy166II	GTNNAC	1 cut(s)	217
Hpy188I	TCNGA	2 cut(s)	289, 329
Hpy188III	TCNNGA	1 cut(s)	152
Hpy8I	GTNNAC	1 cut(s)	217
HpyAV	CCTTC	1 cut(s)	79
HpyCH4III	ACNGT	1 cut(s)	239
HpyCH4V	TGCA	2 cut(s)	189, 265
Kzo9I	GATC	1 cut(s)	154
LpnPI	CCDG	1 cut(s)	270
Lsp1109I	GCAGC	1 cut(s)	81
LweI	GCATC	1 cut(s)	198
MaeI	CTAG	1 cut(s)	20
MalI	GATC	1 cut(s)	156
MboI	GATC	1 cut(s)	154
MboII	GAAGA	3 cut(s)	128, 242, 301
MluCI	AATT	2 cut(s)	29, 74
MnlI	CCTC	6 cut(s)	112, 174, 283, 286, 289, 317
MroXI	GAANNNNTTC	1 cut(s)	120
MseI	TTAA	1 cut(s)	194
Mva1269I	GAATGC	1 cut(s)	252
NdeII	GATC	1 cut(s)	154
PctI	GAATGC	1 cut(s)	252
PdmI	GAANNNNTTC	1 cut(s)	120
PfeI	GAWTC	1 cut(s)	129
PkrI	GCNGC	3 cut(s)	71, 251, 323
PspPI	GGNCC	1 cut(s)	4
RsaI	GTAC	1 cut(s)	236
RsaNI	GTAC	1 cut(s)	235
SaqAI	TTAA	1 cut(s)	194
SatI	GCNGC	3 cut(s)	70, 250, 322
Sau3AI	GATC	1 cut(s)	154
Sau96I	GGNCC	1 cut(s)	4
SetI	ASST	5 cut(s)	18, 90, 123, 275, 309
SfaNI	GCATC	1 cut(s)	198
SgeI	CNNG	9 cut(s)	20, 32, 46, 112, 137, 156, 164, 192, 269
SinI	GGWCC	1 cut(s)	4
Sse9I	AATT	2 cut(s)	29, 74
SsiI	CCGC	2 cut(s)	250, 322
SspMI	CTAG	1 cut(s)	20
TaaI	ACNGT	1 cut(s)	239
TaqI	TCGA	1 cut(s)	42
TasI	AATT	2 cut(s)	29, 74
TatI	WGTACW	1 cut(s)	234
TauI	GCSGC	2 cut(s)	252, 324
TfiI	GAWTC	1 cut(s)	129
Tru1I	TTAA	1 cut(s)	194
Tru9I	TTAA	1 cut(s)	194
TscAI	CASTG	1 cut(s)	244
TseI	GCWGC	1 cut(s)	69
TspRI	CASTG	1 cut(s)	244
VpaK11BI	GGWCC	1 cut(s)	4
XapI	RAATTY	2 cut(s)	29, 74
XmnI	GAANNNNTTC	1 cut(s)	120
XspI	CTAG	1 cut(s)	20

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