Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5D

Orthogroup ID

OG0004387

Physical Location & Seq

Genomic Coordinates Reverse (-)

80661555 .. 80664647

Gene Structure 3093 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5DG519400.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 825 bp

ATGGTGGGATTTGCATATCCTCTTGGTTTCATGTCCACCAGTGGCTATGTCAGCCCAAACAAAGAGTTTCACTGGCTGGCTTCTGCCCTTTTTGGTATGCTTCTCTGCAAAATTGTTTACAAATTAACAGGTCTTATTAGCCTTCATAGCTTCAAGGAATATCAGAAATTGAGCAAAGCAGAAAAAGTTGAATGGAACAACCGGGGGTTCTCAACTGTTCATGCTATTGCTGTAGCAGTTGCATCTTTTTACCTTATACTCTTATCAGATACATTTCATGAGGGTTATAGTGATGAGCTGATCATTAGTAGAAGATCTACTTTTTCAGATACAACACTGGGGATCTCCATTGGTTATTTTCTGGCAGACATAGCAATGATTTTTTGGCATTTTCCTGCTTTAGGTGGACTGGAGTATGTTTTGCACCATGGACTATCTATGTTCTCAATCTTCCTTTCCCTTGTAAGTGGAGAAGGGCAGATTTACATACTAATGGTTCTGTTCTCTGAGAGCACAACTCCTTTTGTAAACCTAAGATGGTACTTGGATATTGCTGGTAAGAAGAACTCTAAGCTGTACGTCTGCAATGGTGTAGCATTGTTCCTGGGGTGGCTGGTTGCAAGGATTTTTTTGTTCATTTACTTTTTCGTCCACATGTTTTTCCATTTTCATCAAGTCAAGACAATTTTTCCGTTGGGATTTTACAGCTTGCTCACGATACCTCCTGTGTTGGCAATCATGAATCTGTTTTGGTTTTGGAAGATTGCCAAAGGTTTGATCAAAACAGTTTCAAAGGGCACACAGAAGACCAAACACAGTCAGTGA

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0003674 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005739 GO:0006950 GO:0006970 GO:0008150 GO:0009628 GO:0009651 GO:0009987 GO:0019725 GO:0042592 GO:0043167 GO:0043169 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044424 GO:0044444 GO:0044464 GO:0045454 GO:0046872 GO:0046914 GO:0050789 GO:0050794 GO:0050896 GO:0050897 GO:0065007 GO:0065008

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

TRAM_LAG1_CLN8

Protein Analysis

274

Amino Acids

31.25

Weight (kDa)

9.36

Isoelectric Point (pI)

24.31

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
TRAM_LAG1_CLN8	PF03798	64 - 257	1.5e-34	TLC domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

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Align Labels (Cladogram)

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Publication-ready

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Orthologous Genes (Group: OG0004387)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT4G10360 AT4G10360 AT4G10360
fragaria_vesca	FvH4_3g41280 FvH4_3g41280 FvH4_3g41280 FvH4_3g41280 FvH4_3g41280 FvH4_3g41280 FvH4_3g41280 FvH4_3g41280 FvH4_3g41280
malus_domestica	MD03G1046000.v1.1 MD11G1048300.v1.1
prunus_persica	Prupe.6G037300_v2.0.a1 Prupe.6G037300_v2.0.a1 Prupe.6G037300_v2.0.a1 Prupe.6G037300_v2.0.a1 Prupe.6G037300_v2.0.a1 Prupe.6G037300_v2.0.a1
pyrus_communis	pycom03g03620 pycom11g03940
rosa_chinensis	RchiOBHm_Chr5g0074081
rosa_laevigata	RLG00000036452
rosa_multiflora	Rmu_sc0000573.1_g000071
rosa_roxburghii	Rroxscaffold_1G00007320
rosa_rugosa	Rorug05G0429100
rosa_samantha	Rh5AG486700 Rh5BG507000 Rh5CG530500 Rh5DG519400
rosa_wichuraiana	Rw5G045170

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AclWI	GGATC	1 cut(s)	350
AfaI	GTAC	2 cut(s)	542, 578
AfiI	CCNNNNNNNGG	1 cut(s)	401
AflIII	ACRYGT	1 cut(s)	654
AgsI	TTSAA	3 cut(s)	154, 191, 792
AjnI	CCWGG	1 cut(s)	603
AluBI	AGCT	4 cut(s)	150, 298, 574, 708
AluI	AGCT	4 cut(s)	150, 298, 574, 708
Alw21I	GWGCWC	1 cut(s)	515
AlwI	GGATC	1 cut(s)	350
AsuC2I	CCSGG	1 cut(s)	203
BaeGI	GKGCMC	1 cut(s)	800
BbsI	GAAGAC	1 cut(s)	812
Bbv12I	GWGCWC	1 cut(s)	515
BccI	CCATC	1 cut(s)	531
BciT130I	CCWGG	1 cut(s)	605
BclI	TGATCA	2 cut(s)	300, 777
BcnI	CCSGG	1 cut(s)	203
BfmI	CTRYAG	1 cut(s)	231
BglII	AGATCT	1 cut(s)	314
Bme1390I	CCNGG	2 cut(s)	203, 605
BmrFI	CCNGG	2 cut(s)	203, 605
BmrI	ACTGGG	1 cut(s)	347
BmsI	GCATC	1 cut(s)	251
BmuI	ACTGGG	1 cut(s)	347
BpiI	GAAGAC	1 cut(s)	812
BplI	GAGNNNNNCTC	2 cut(s)	502, 534
BpmI	CTGGAG	1 cut(s)	431
BpuMI	CCSGG	1 cut(s)	203
BsaJI	CCNNGG	3 cut(s)	202, 427, 604
BsaXI	ACNNNNNCTCC	2 cut(s)	706, 736
Bsc4I	CCNNNNNNNGG	1 cut(s)	401
Bse1I	ACTGG	4 cut(s)	39, 77, 342, 414
Bse3DI	GCAATG	2 cut(s)	381, 592
BseBI	CCWGG	1 cut(s)	605
BseDI	CCNNGG	3 cut(s)	202, 427, 604
BseLI	CCNNNNNNNGG	1 cut(s)	401
BseMI	GCAATG	2 cut(s)	381, 592
BseMII	CTCAG	1 cut(s)	498
BseNI	ACTGG	4 cut(s)	39, 77, 342, 414
BseSI	GKGCMC	1 cut(s)	800
BsiHKAI	GWGCWC	1 cut(s)	515
BsiSI	CCGG	1 cut(s)	202
BslI	CCNNNNNNNGG	1 cut(s)	401
Bsp1286I	GDGCHC	2 cut(s)	515, 800
Bsp143I	GATC	4 cut(s)	300, 314, 342, 777
Bsp19I	CCATGG	1 cut(s)	427
BspCNI	CTCAG	1 cut(s)	499
BspHI	TCATGA	2 cut(s)	277, 738
BspPI	GGATC	1 cut(s)	350
BsrDI	GCAATG	2 cut(s)	381, 592
BsrI	ACTGG	4 cut(s)	39, 77, 342, 414
BssECI	CCNNGG	3 cut(s)	202, 427, 604
BssMI	GATC	4 cut(s)	300, 314, 342, 777
BssT1I	CCWWGG	1 cut(s)	427
Bst2UI	CCWGG	1 cut(s)	605
Bst4CI	ACNGT	3 cut(s)	217, 787, 818
BstC8I	GCNNGC	2 cut(s)	78, 710
BstDEI	CTNAG	3 cut(s)	507, 533, 570
BstDSI	CCRYGG	1 cut(s)	427
BstENI	CCTNNNNNAGG	1 cut(s)	399
BstKTI	GATC	4 cut(s)	303, 317, 345, 780
BstMBI	GATC	4 cut(s)	300, 314, 342, 777
BstMWI	GCNNNNNNNGC	3 cut(s)	51, 147, 371
BstNI	CCWGG	1 cut(s)	605
BstNSI	RCATGY	1 cut(s)	658
BstSCI	CCNGG	2 cut(s)	201, 603
BstSFI	CTRYAG	1 cut(s)	231
BstSLI	GKGCMC	1 cut(s)	800
BstV2I	GAAGAC	1 cut(s)	812
BstX2I	RGATCY	2 cut(s)	314, 342
BstYI	RGATCY	2 cut(s)	314, 342
BtgI	CCRYGG	1 cut(s)	427
BtsIMutI	CAGTG	3 cut(s)	46, 70, 335
Cac8I	GCNNGC	2 cut(s)	78, 710
CciI	TCATGA	2 cut(s)	277, 738
Csp6I	GTAC	2 cut(s)	541, 577
CviAII	CATG	6 cut(s)	31, 221, 278, 428, 655, 739
CviQI	GTAC	2 cut(s)	541, 577
DdeI	CTNAG	3 cut(s)	507, 533, 570
DpnI	GATC	4 cut(s)	302, 316, 344, 779
DpnII	GATC	4 cut(s)	300, 314, 342, 777
Eco130I	CCWWGG	1 cut(s)	427
EcoNI	CCTNNNNNAGG	1 cut(s)	399
EcoRII	CCWGG	1 cut(s)	603
EcoT14I	CCWWGG	1 cut(s)	427
ErhI	CCWWGG	1 cut(s)	427
FaeI	CATG	6 cut(s)	34, 224, 281, 431, 658, 742
FalI	AAGNNNNNCTT	2 cut(s)	304, 336
FatI	CATG	6 cut(s)	30, 220, 277, 427, 654, 738
FbaI	TGATCA	2 cut(s)	300, 777
GsuI	CTGGAG	1 cut(s)	431
HapII	CCGG	1 cut(s)	202
Hin1II	CATG	6 cut(s)	34, 224, 281, 431, 658, 742
HinfI	GANTC	1 cut(s)	742
HpaII	CCGG	1 cut(s)	202
Hpy166II	GTNNAC	5 cut(s)	36, 118, 407, 529, 652
Hpy188I	TCNGA	4 cut(s)	165, 268, 328, 508
Hpy188III	TCNNGA	4 cut(s)	278, 679, 715, 739
Hpy8I	GTNNAC	5 cut(s)	36, 118, 407, 529, 652
HpyAV	CCTTC	2 cut(s)	152, 467
HpyCH4III	ACNGT	3 cut(s)	217, 787, 818
HpyCH4IV	ACGT	1 cut(s)	579
HpyCH4V	TGCA	6 cut(s)	14, 108, 242, 424, 585, 620
HpyF10VI	GCNNNNNNNGC	3 cut(s)	51, 147, 371
HpyF3I	CTNAG	3 cut(s)	507, 533, 570
HpySE526I	ACGT	1 cut(s)	579
Hsp92II	CATG	6 cut(s)	34, 224, 281, 431, 658, 742
Ksp22I	TGATCA	2 cut(s)	300, 777
Kzo9I	GATC	4 cut(s)	300, 314, 342, 777
LweI	GCATC	1 cut(s)	251
MaeII	ACGT	1 cut(s)	579
MalI	GATC	4 cut(s)	302, 316, 344, 779
MboI	GATC	4 cut(s)	300, 314, 342, 777
MboII	GAAGA	5 cut(s)	324, 442, 574, 772, 817
MflI	RGATCY	2 cut(s)	314, 342
MhlI	GDGCHC	2 cut(s)	515, 800
MluCI	AATT	4 cut(s)	111, 122, 167, 684
MnlI	CCTC	3 cut(s)	30, 274, 732
MseI	TTAA	1 cut(s)	125
MslI	CAYNNNNRTG	2 cut(s)	374, 491
MspI	CCGG	1 cut(s)	202
MspR9I	CCNGG	2 cut(s)	203, 605
MvaI	CCWGG	1 cut(s)	605
MwoI	GCNNNNNNNGC	3 cut(s)	51, 147, 371
NciI	CCSGG	1 cut(s)	203
NcoI	CCATGG	1 cut(s)	427
NdeII	GATC	4 cut(s)	300, 314, 342, 777
NlaIII	CATG	6 cut(s)	34, 224, 281, 431, 658, 742
NspI	RCATGY	1 cut(s)	658
PagI	TCATGA	2 cut(s)	277, 738
PciI	ACATGT	1 cut(s)	654
PfeI	GAWTC	1 cut(s)	742
PscI	ACATGT	1 cut(s)	654
Psp6I	CCWGG	1 cut(s)	603
PspGI	CCWGG	1 cut(s)	603
PsuI	RGATCY	2 cut(s)	314, 342
RsaI	GTAC	2 cut(s)	542, 578
RsaNI	GTAC	2 cut(s)	541, 577
RseI	CAYNNNNRTG	2 cut(s)	374, 491
SaqAI	TTAA	1 cut(s)	125
Sau3AI	GATC	4 cut(s)	300, 314, 342, 777
ScrFI	CCNGG	2 cut(s)	203, 605
SduI	GDGCHC	2 cut(s)	515, 800
SfaNI	GCATC	1 cut(s)	251
SfcI	CTRYAG	1 cut(s)	231
SmiMI	CAYNNNNRTG	2 cut(s)	374, 491
Sse9I	AATT	4 cut(s)	111, 122, 167, 684
StyD4I	CCNGG	2 cut(s)	201, 603
StyI	CCWWGG	1 cut(s)	427
TaaI	ACNGT	3 cut(s)	217, 787, 818
TaiI	ACGT	1 cut(s)	582
TasI	AATT	4 cut(s)	111, 122, 167, 684
TfiI	GAWTC	1 cut(s)	742
Tru1I	TTAA	1 cut(s)	125
Tru9I	TTAA	1 cut(s)	125
TscAI	CASTG	3 cut(s)	46, 77, 342
TspDTI	ATGAA	7 cut(s)	19, 134, 209, 266, 625, 659, 755
TspGWI	ACGGA	1 cut(s)	681
TspRI	CASTG	3 cut(s)	46, 77, 342
XagI	CCTNNNNNAGG	1 cut(s)	399
XceI	RCATGY	1 cut(s)	658

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