Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr6A

Orthogroup ID

OG0001594

Physical Location & Seq

Genomic Coordinates Reverse (-)

4634057 .. 4635776

Gene Structure 1720 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh6AG035800.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 429 bp

ATGGTGTTTGTACAGGGCGGTATTGGAATCAAAAGGAGTTTAGATGAACTGGCTGCCACTTGTTTAAGTTACGGCTTTTCAGAACCCCCTCGTCTGGTACACAGACTTGACAGAGATTGTAGTGGTATCCTTGTGATGGGACGGACACAAACAAGTGCAACAGTTTTGCATTCCCTCTTCCGTGAGAAAACTTTTAGAGCTTCAGATGATGTTATCGACCATGCTAAAGCCATTCTGCAAAGAAGGTATTGGGCACTCGTCGTTGGATCTCCCAGACAACAAGAGGGGTTAATCTCCGTGCCTTTAGGAAAGGTGGTGGTAGACAATGGTAAATCAGATAGGATCACCATTGTGAATAAGGCACAATGTTTTCCATCTCAACATGCACTTACAAAGTACGAAGTGATTGGATCATCATGTCCTGGTTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0001522 GO:0003674 GO:0003824 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0006139 GO:0006396 GO:0006399 GO:0006400 GO:0006725 GO:0006807 GO:0008033 GO:0008150 GO:0008152 GO:0009451 GO:0009982 GO:0009987 GO:0010467 GO:0016070 GO:0016853 GO:0016866 GO:0031119 GO:0034470 GO:0034641 GO:0034660 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043412 GO:0044237 GO:0044238 GO:0044424 GO:0044444 GO:0044464 GO:0046483 GO:0071704 GO:0090304 GO:1901360

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

PseudoU_synth_2

Protein Analysis

142

Amino Acids

15.58

Weight (kDa)

9.23

Isoelectric Point (pI)

36.66

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
PseudoU_synth_2	PF00849	27 - 137	2.4e-09	RNA pseudouridylate synthase

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

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Orthologous Genes (Group: OG0001594)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G19440 AT3G19440
fragaria_vesca	FvH4_2g05120 FvH4_2g05120 FvH4_2g05120 FvH4_2g05120
malus_domestica	MD10G1097600.v1.1
prunus_persica	Prupe.8G135400_v2.0.a1 Prupe.8G135400_v2.0.a1 Prupe.8G135400_v2.0.a1
pyrus_communis	pycom01g14220 pycom10g08370
rosa_chinensis	RchiOBHm_Chr4g0415551 RchiOBHm_Chr6g0255041
rosa_laevigata	RLG00000003460 RLG00000014859 RLG00000014868 RLG00000018864 RLG00000024043 RLG00000027684
rosa_multiflora	Rmu_ssc0000011.1_g000078
rosa_roxburghii	Rroxscaffold_2G00121110 Rroxscaffold_6G00396470 Rroxscaffold_6G00402590 Rroxscaffold_7G00210260
rosa_rugosa	Rorug03G0278700 Rorug03G0278800 Rorug03G0278900 Rorug05G0556400 Rorug05G0556500
rosa_samantha	Rh1AG091300 Rh1AG167900 Rh1DG094800 Rh2BG117700 Rh2BG330200 Rh2DG118600 Rh3BG349000 Rh4CG206700 Rh5BG449900 Rh6AG035800 Rh6AG073700 Rh6BG065900 Rh6BG066100 Rh6BG131700 Rh7AG357100 Rh7CG374500
rosa_wichuraiana	Rw2G034900 Rw6G006400 Rw6G006410 Rw6G026380

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccI	GTMKAC	1 cut(s)	321
AciI	CCGC	1 cut(s)	18
AclWI	GGATC	3 cut(s)	274, 350, 418
AcuI	CTGAAG	1 cut(s)	186
AfaI	GTAC	3 cut(s)	12, 99, 398
AfiI	CCNNNNNNNGG	2 cut(s)	94, 136
AjnI	CCWGG	1 cut(s)	421
AleI	CACNNNNGTG	1 cut(s)	350
AluBI	AGCT	1 cut(s)	200
AluI	AGCT	1 cut(s)	200
AlwI	GGATC	3 cut(s)	274, 350, 418
ApeKI	GCWGC	1 cut(s)	53
AsuHPI	GGTGA	1 cut(s)	337
BaeGI	GKGCMC	1 cut(s)	256
BbvI	GCAGC	1 cut(s)	40
BccI	CCATC	2 cut(s)	130, 382
BceAI	ACGGC	1 cut(s)	88
BciT130I	CCWGG	1 cut(s)	423
BciVI	GTATCC	1 cut(s)	137
BfuI	GTATCC	1 cut(s)	137
BisI	GCNGC	1 cut(s)	54
BlsI	GCNGC	1 cut(s)	55
Bme1390I	CCNGG	1 cut(s)	423
BmrFI	CCNGG	1 cut(s)	423
Bsc4I	CCNNNNNNNGG	2 cut(s)	94, 136
Bse1I	ACTGG	1 cut(s)	54
BseBI	CCWGG	1 cut(s)	423
BseLI	CCNNNNNNNGG	2 cut(s)	94, 136
BseNI	ACTGG	1 cut(s)	54
BseSI	GKGCMC	1 cut(s)	256
BseXI	GCAGC	1 cut(s)	40
BslFI	GGGAC	1 cut(s)	153
BslI	CCNNNNNNNGG	2 cut(s)	94, 136
BsmFI	GGGAC	1 cut(s)	153
BsmI	GAATGC	1 cut(s)	169
Bsp1286I	GDGCHC	1 cut(s)	256
Bsp1407I	TGTACA	1 cut(s)	10
Bsp143I	GATC	3 cut(s)	266, 342, 410
BspACI	CCGC	1 cut(s)	18
BspPI	GGATC	3 cut(s)	274, 350, 418
BsrGI	TGTACA	1 cut(s)	10
BsrI	ACTGG	1 cut(s)	54
BssMI	GATC	3 cut(s)	266, 342, 410
Bst2UI	CCWGG	1 cut(s)	423
Bst4CI	ACNGT	1 cut(s)	163
Bst6I	CTCTTC	1 cut(s)	182
BstAUI	TGTACA	1 cut(s)	10
BstKTI	GATC	3 cut(s)	269, 345, 413
BstMBI	GATC	3 cut(s)	266, 342, 410
BstNI	CCWGG	1 cut(s)	423
BstNSI	RCATGY	1 cut(s)	386
BstSCI	CCNGG	1 cut(s)	421
BstSLI	GKGCMC	1 cut(s)	256
BstV1I	GCAGC	1 cut(s)	40
BstX2I	RGATCY	1 cut(s)	266
BstYI	RGATCY	1 cut(s)	266
BsuI	GTATCC	1 cut(s)	137
Csp6I	GTAC	3 cut(s)	11, 98, 397
CviAII	CATG	3 cut(s)	221, 383, 417
CviJI	RGCY	4 cut(s)	53, 75, 200, 230
CviKI_1	RGCY	4 cut(s)	53, 75, 200, 230
CviQI	GTAC	3 cut(s)	11, 98, 397
DpnI	GATC	3 cut(s)	268, 344, 412
DpnII	GATC	3 cut(s)	266, 342, 410
Eam1104I	CTCTTC	1 cut(s)	182
EarI	CTCTTC	1 cut(s)	182
Eco57I	CTGAAG	1 cut(s)	186
EcoRII	CCWGG	1 cut(s)	421
FaeI	CATG	3 cut(s)	224, 386, 420
FaiI	YATR	3 cut(s)	222, 384, 418
FaqI	GGGAC	1 cut(s)	153
FatI	CATG	3 cut(s)	220, 382, 416
FblI	GTMKAC	1 cut(s)	321
Fnu4HI	GCNGC	1 cut(s)	54
Fsp4HI	GCNGC	1 cut(s)	54
GluI	GCNGC	1 cut(s)	54
Hin1II	CATG	3 cut(s)	224, 386, 420
HinfI	GANTC	1 cut(s)	27
HphI	GGTGA	1 cut(s)	337
Hpy166II	GTNNAC	2 cut(s)	100, 322
Hpy188I	TCNGA	3 cut(s)	82, 205, 337
Hpy8I	GTNNAC	2 cut(s)	100, 322
Hpy99I	CGWCG	1 cut(s)	263
HpyAV	CCTTC	1 cut(s)	237
HpyCH4III	ACNGT	1 cut(s)	163
HpyCH4V	TGCA	4 cut(s)	158, 169, 238, 386
Hsp92II	CATG	3 cut(s)	224, 386, 420
Kzo9I	GATC	3 cut(s)	266, 342, 410
LpnPI	CCDG	4 cut(s)	35, 80, 286, 408
Lsp1109I	GCAGC	1 cut(s)	40
MaeIII	GTNAC	1 cut(s)	68
MalI	GATC	3 cut(s)	268, 344, 412
MboI	GATC	3 cut(s)	266, 342, 410
MboII	GAAGA	1 cut(s)	169
MflI	RGATCY	1 cut(s)	266
MhlI	GDGCHC	1 cut(s)	256
MmeI	TCCRAC	1 cut(s)	244
MnlI	CCTC	3 cut(s)	99, 185, 277
MseI	TTAA	2 cut(s)	65, 290
MslI	CAYNNNNRTG	1 cut(s)	350
MspR9I	CCNGG	1 cut(s)	423
Mva1269I	GAATGC	1 cut(s)	169
MvaI	CCWGG	1 cut(s)	423
NdeII	GATC	3 cut(s)	266, 342, 410
NlaIII	CATG	3 cut(s)	224, 386, 420
NspI	RCATGY	1 cut(s)	386
OliI	CACNNNNGTG	1 cut(s)	350
PctI	GAATGC	1 cut(s)	169
PfeI	GAWTC	1 cut(s)	27
PkrI	GCNGC	1 cut(s)	55
Psp6I	CCWGG	1 cut(s)	421
PspGI	CCWGG	1 cut(s)	421
PsuI	RGATCY	1 cut(s)	266
RsaI	GTAC	3 cut(s)	12, 99, 398
RsaNI	GTAC	3 cut(s)	11, 98, 397
RseI	CAYNNNNRTG	1 cut(s)	350
SaqAI	TTAA	2 cut(s)	65, 290
SatI	GCNGC	1 cut(s)	54
Sau3AI	GATC	3 cut(s)	266, 342, 410
ScrFI	CCNGG	1 cut(s)	423
SduI	GDGCHC	1 cut(s)	256
SetI	ASST	3 cut(s)	202, 248, 315
SmiMI	CAYNNNNRTG	1 cut(s)	350
SsiI	CCGC	1 cut(s)	18
StyD4I	CCNGG	1 cut(s)	421
TaaI	ACNGT	1 cut(s)	163
TaqI	TCGA	1 cut(s)	216
TatI	WGTACW	1 cut(s)	10
TfiI	GAWTC	1 cut(s)	27
Tru1I	TTAA	2 cut(s)	65, 290
Tru9I	TTAA	2 cut(s)	65, 290
TseI	GCWGC	1 cut(s)	53
TspDTI	ATGAA	1 cut(s)	60
TspGWI	ACGGA	3 cut(s)	157, 170, 286
XceI	RCATGY	1 cut(s)	386
XmiI	GTMKAC	1 cut(s)	321

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