Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr4B

Orthogroup ID

OG0006241

Physical Location & Seq

Genomic Coordinates Reverse (-)

13668374 .. 13675434

Gene Structure 7061 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh4BG077100.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 681 bp

ATGGGTTCGTCTTCAACCGACGCTTTTCCACAAATGCAGGAAATTATGCTGGAGTTTCGAGCTGGTAAAATGGCTTTTGAGGGGAAAAGGGTTATTCCCGATACTCGTAAAGGACTTGTTCGCATAGCAAGGGGTGAGGAGGGTTTGGTGCATTTCCAGTGGCTTGATCGGAATCAAAATGTAGTTGAAGATGATCAGATTGTTTTTCCTGATGAGGCAGTTTTTGAAAAGGTTAATCAAGCATCAGGAAGGGTGTACATACTGAAGTTCAACACAGATGATAGGAAGTTTTTCTTTTGGATGCAGGAGCCGAAAGCTGAAGATGACACACAGTTATGTACCTCCGTTAATTACTACATCAATCGACCAATAGAAGAGATACTTGAAGAAGAAGGCCCTGATGGCTCAGTTCCTCTCACAGCTGATGATATGTTTGAAGATGATATTTCATCAAGAGCTGGAATCTTGGTGGAACCAAACTTGGGTGCGGAAGCAAGTAGCGATGTAACCTCTTCATCTGGCCCAGTGAAGCTGGAAGATCTTCAAAGAATCTTGAGTAACATCGATCGTGCAGATAGTGCTGGGGATCCAGATGGAGGTAATAATTTGACTATTCATGTTCTTTCCAACAGATACAAATGCAATGCAATACTTCTGAACTTTTATGATCAATTTGTGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000502 GO:0003674 GO:0005488 GO:0005515 GO:0005575 GO:0005622 GO:0005623 GO:0005838 GO:0006508 GO:0006511 GO:0006807 GO:0008047 GO:0008150 GO:0008152 GO:0008541 GO:0009056 GO:0009057 GO:0009893 GO:0009987 GO:0010604 GO:0010950 GO:0010952 GO:0016043 GO:0016504 GO:0019222 GO:0019538 GO:0019941 GO:0022607 GO:0022624 GO:0030162 GO:0030163 GO:0030234 GO:0031323 GO:0031325 GO:0032182 GO:0032268 GO:0032270 GO:0032991 GO:0034622 GO:0043085 GO:0043130 GO:0043170 GO:0043248 GO:0043632 GO:0043933 GO:0044085 GO:0044093 GO:0044237 GO:0044238 GO:0044248 GO:0044257 GO:0044260 GO:0044265 GO:0044267 GO:0044424 GO:0044464 GO:0044877 GO:0045862 GO:0048518 GO:0048522 GO:0050789 GO:0050790 GO:0050794 GO:0051171 GO:0051173 GO:0051246 GO:0051247 GO:0051336 GO:0051345 GO:0051603 GO:0052547 GO:0052548 GO:0060255 GO:0061133 GO:0061134 GO:0061135 GO:0065003 GO:0065007 GO:0065009 GO:0070628 GO:0071704 GO:0071840 GO:0080090 GO:0098772 GO:1901564 GO:1901565 GO:1901575 GO:1902494 GO:1905368 GO:1905369

KEGG Pathways

Metabolic & Signaling

ko03050 ko05169 map03050 map05169

Pfam Domains

Protein Families

Proteasom_Rpn13 RPN13_C

Protein Analysis

226

Amino Acids

25.44

Weight (kDa)

4.4

Isoelectric Point (pI)

43.23

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Rpn13_ADRM1_Pru	PF04683	17 - 113	2.2e-32	Proteasome complex subunit Rpn13, Pru domain

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: OG0006241)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT2G26590 AT2G26590 AT2G26590 AT2G26590
fragaria_vesca	FvH4_4g06040 FvH4_4g06040 FvH4_4g06040 FvH4_4g06040 FvH4_4g06040 FvH4_4g06040 FvH4_4g06040
malus_domestica	MD16G1238000.v1.1
prunus_persica	Prupe.1G063800_v2.0.a1 Prupe.1G063800_v2.0.a1 Prupe.1G063800_v2.0.a1 Prupe.1G063800_v2.0.a1
pyrus_communis	pycom16g19920
rosa_chinensis	RchiOBHm_Chr4g0397601
rosa_laevigata	RLG00000009425
rosa_multiflora	Rmu_sc0005653.1_g000003
rosa_roxburghii	Rroxscaffold_5G00342410
rosa_rugosa	Rorug03G0342400
rosa_samantha	Rh4AG079200 Rh4BG077100 Rh4CG084800 Rh4DG072200
rosa_wichuraiana	Rw4G006480

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AciI	CCGC	1 cut(s)	488
AclWI	GGATC	2 cut(s)	581, 594
AcuI	CTGAAG	2 cut(s)	284, 339
AfaI	GTAC	2 cut(s)	257, 340
AfiI	CCNNNNNNNGG	2 cut(s)	482, 596
AgsI	TTSAA	7 cut(s)	15, 188, 227, 271, 386, 437, 545
AluBI	AGCT	5 cut(s)	62, 317, 422, 458, 532
AluI	AGCT	5 cut(s)	62, 317, 422, 458, 532
AlwI	GGATC	2 cut(s)	581, 594
AoxI	GGCC	2 cut(s)	394, 520
Asp700I	GAANNNNTTC	2 cut(s)	290, 540
AspS9I	GGNCC	2 cut(s)	395, 521
AsuHPI	GGTGA	1 cut(s)	146
BamHI	GGATCC	1 cut(s)	586
BbsI	GAAGAC	1 cut(s)	3
BccI	CCATC	2 cut(s)	395, 587
BclI	TGATCA	2 cut(s)	193, 667
BglI	GCCNNNNNGGC	1 cut(s)	402
BglII	AGATCT	1 cut(s)	538
BmgT120I	GGNCC	2 cut(s)	395, 521
BmiI	GGNNCC	3 cut(s)	309, 474, 588
BmrI	ACTGGG	1 cut(s)	518
BmsI	GCATC	2 cut(s)	251, 291
BmuI	ACTGGG	1 cut(s)	518
BpiI	GAAGAC	1 cut(s)	3
BpmI	CTGGAG	1 cut(s)	71
BpuEI	CTTGAG	1 cut(s)	574
Bsa29I	ATCGAT	1 cut(s)	564
BsaBI	GATNNNNATC	1 cut(s)	171
Bsc4I	CCNNNNNNNGG	2 cut(s)	482, 596
Bse1I	ACTGG	2 cut(s)	157, 524
Bse3DI	GCAATG	1 cut(s)	649
Bse8I	GATNNNNATC	1 cut(s)	171
BseCI	ATCGAT	1 cut(s)	564
BseGI	GGATG	1 cut(s)	306
BseJI	GATNNNNATC	1 cut(s)	171
BseLI	CCNNNNNNNGG	2 cut(s)	482, 596
BseMI	GCAATG	1 cut(s)	649
BseMII	CTCAG	1 cut(s)	420
BseNI	ACTGG	2 cut(s)	157, 524
BseRI	GAGGAG	1 cut(s)	152
BseYI	CCCAGC	1 cut(s)	581
BsgI	GTGCAG	1 cut(s)	591
Bsh1285I	CGRYCG	1 cut(s)	568
BshFI	GGCC	2 cut(s)	396, 522
BshVI	ATCGAT	1 cut(s)	564
BsiEI	CGRYCG	1 cut(s)	568
BslI	CCNNNNNNNGG	2 cut(s)	482, 596
BsnI	GGCC	2 cut(s)	396, 522
Bsp1407I	TGTACA	1 cut(s)	255
Bsp143I	GATC	6 cut(s)	166, 193, 538, 565, 586, 667
BspACI	CCGC	1 cut(s)	488
BspANI	GGCC	2 cut(s)	396, 522
BspCNI	CTCAG	1 cut(s)	419
BspDI	ATCGAT	1 cut(s)	564
BspLI	GGNNCC	3 cut(s)	309, 474, 588
BspPI	GGATC	2 cut(s)	581, 594
BsrDI	GCAATG	1 cut(s)	649
BsrGI	TGTACA	1 cut(s)	255
BsrI	ACTGG	2 cut(s)	157, 524
BssMI	GATC	6 cut(s)	166, 193, 538, 565, 586, 667
Bst4CI	ACNGT	1 cut(s)	333
Bst6I	CTCTTC	2 cut(s)	369, 517
BstAPI	GCANNNNNTGC	1 cut(s)	578
BstAUI	TGTACA	1 cut(s)	255
BstDEI	CTNAG	1 cut(s)	406
BstF5I	GGATG	1 cut(s)	306
BstKTI	GATC	6 cut(s)	169, 196, 541, 568, 589, 670
BstMBI	GATC	6 cut(s)	166, 193, 538, 565, 586, 667
BstMCI	CGRYCG	1 cut(s)	568
BstMWI	GCNNNNNNNGC	2 cut(s)	402, 578
BstV2I	GAAGAC	1 cut(s)	3
BstX2I	RGATCY	2 cut(s)	538, 586
BstYI	RGATCY	2 cut(s)	538, 586
Bsu15I	ATCGAT	1 cut(s)	564
BsuRI	GGCC	2 cut(s)	396, 522
BsuTUI	ATCGAT	1 cut(s)	564
BtgZI	GCGATG	1 cut(s)	516
BtsCI	GGATG	1 cut(s)	306
BtsIMutI	CAGTG	2 cut(s)	164, 531
Cfr13I	GGNCC	2 cut(s)	395, 521
ClaI	ATCGAT	1 cut(s)	564
CseI	GACGC	1 cut(s)	29
Csp6I	GTAC	2 cut(s)	256, 339
CviAII	CATG	1 cut(s)	617
CviQI	GTAC	2 cut(s)	256, 339
DdeI	CTNAG	1 cut(s)	406
DpnI	GATC	6 cut(s)	168, 195, 540, 567, 588, 669
DpnII	GATC	6 cut(s)	166, 193, 538, 565, 586, 667
Eam1104I	CTCTTC	2 cut(s)	369, 517
EarI	CTCTTC	2 cut(s)	369, 517
Eco57I	CTGAAG	2 cut(s)	284, 339
EcoO109I	RGGNCCY	1 cut(s)	395
FaeI	CATG	1 cut(s)	620
FaiI	YATR	7 cut(s)	47, 125, 260, 337, 431, 618, 666
FalI	AAGNNNNNCTT	4 cut(s)	278, 310, 366, 398
FatI	CATG	1 cut(s)	616
FbaI	TGATCA	2 cut(s)	193, 667
FokI	GGATG	1 cut(s)	313
GsaI	CCCAGC	1 cut(s)	585
GsuI	CTGGAG	1 cut(s)	71
HaeIII	GGCC	2 cut(s)	396, 522
HgaI	GACGC	1 cut(s)	29
Hin1II	CATG	1 cut(s)	620
HinfI	GANTC	3 cut(s)	172, 462, 549
HphI	GGTGA	1 cut(s)	146
Hpy166II	GTNNAC	1 cut(s)	256
Hpy188I	TCNGA	3 cut(s)	171, 198, 657
Hpy188III	TCNNGA	6 cut(s)	98, 209, 246, 453, 553, 590
Hpy8I	GTNNAC	1 cut(s)	256
Hpy99I	CGWCG	1 cut(s)	23
HpyAV	CCTTC	2 cut(s)	243, 386
HpyCH4III	ACNGT	1 cut(s)	333
HpyCH4V	TGCA	6 cut(s)	37, 151, 304, 572, 642, 647
HpyF10VI	GCNNNNNNNGC	2 cut(s)	402, 578
HpyF3I	CTNAG	1 cut(s)	406
Hsp92II	CATG	1 cut(s)	620
Ksp22I	TGATCA	2 cut(s)	193, 667
Kzo9I	GATC	6 cut(s)	166, 193, 538, 565, 586, 667
LmnI	GCTCC	1 cut(s)	307
LweI	GCATC	2 cut(s)	251, 291
MaeIII	GTNAC	2 cut(s)	505, 557
MalI	GATC	6 cut(s)	168, 195, 540, 567, 588, 669
MboI	GATC	6 cut(s)	166, 193, 538, 565, 586, 667
MflI	RGATCY	2 cut(s)	538, 586
MluCI	AATT	4 cut(s)	42, 349, 604, 671
MmeI	TCCRAC	1 cut(s)	651
MnlI	CCTC	8 cut(s)	73, 130, 133, 208, 352, 423, 520, 590
MroXI	GAANNNNTTC	2 cut(s)	290, 540
MseI	TTAA	2 cut(s)	234, 348
MslI	CAYNNNNRTG	1 cut(s)	334
MspA1I	CMGCKG	1 cut(s)	422
MwoI	GCNNNNNNNGC	2 cut(s)	402, 578
NdeII	GATC	6 cut(s)	166, 193, 538, 565, 586, 667
NlaIII	CATG	1 cut(s)	620
NlaIV	GGNNCC	3 cut(s)	309, 474, 588
PdmI	GAANNNNTTC	2 cut(s)	290, 540
PfeI	GAWTC	3 cut(s)	172, 462, 549
Ple19I	CGATCG	1 cut(s)	568
PspFI	CCCAGC	1 cut(s)	581
PspN4I	GGNNCC	3 cut(s)	309, 474, 588
PspPI	GGNCC	2 cut(s)	395, 521
PsuI	RGATCY	2 cut(s)	538, 586
PvuI	CGATCG	1 cut(s)	568
PvuII	CAGCTG	1 cut(s)	422
RsaI	GTAC	2 cut(s)	257, 340
RsaNI	GTAC	2 cut(s)	256, 339
RseI	CAYNNNNRTG	1 cut(s)	334
SaqAI	TTAA	2 cut(s)	234, 348
Sau3AI	GATC	6 cut(s)	166, 193, 538, 565, 586, 667
Sau96I	GGNCC	2 cut(s)	395, 521
SetI	ASST	9 cut(s)	64, 234, 319, 344, 424, 460, 512, 534, 601
SfaNI	GCATC	2 cut(s)	251, 291
SmiMI	CAYNNNNRTG	1 cut(s)	334
SmlI	CTYRAG	1 cut(s)	553
SmoI	CTYRAG	1 cut(s)	553
Sse9I	AATT	4 cut(s)	42, 349, 604, 671
SsiI	CCGC	1 cut(s)	488
TaaI	ACNGT	1 cut(s)	333
TaqI	TCGA	3 cut(s)	58, 364, 564
TasI	AATT	4 cut(s)	42, 349, 604, 671
TatI	WGTACW	1 cut(s)	255
TfiI	GAWTC	3 cut(s)	172, 462, 549
Tru1I	TTAA	2 cut(s)	234, 348
Tru9I	TTAA	2 cut(s)	234, 348
TscAI	CASTG	2 cut(s)	164, 531
TspDTI	ATGAA	3 cut(s)	438, 504, 605
TspGWI	ACGGA	1 cut(s)	334
TspRI	CASTG	2 cut(s)	164, 531
XmnI	GAANNNNTTC	2 cut(s)	290, 540

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