Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5B

Orthogroup ID

OG0003092

Physical Location & Seq

Genomic Coordinates Forward (+)

85124176 .. 85127168

Gene Structure 2993 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5BG538000.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 807 bp

ATGGAACGGTTGGTTTTGGCTTGTGGACGGGAGGCAGTGAACTCTGTAGATGATTTAACTCCTGATTGCCTTGGCTGGGTTGGACTTGTATATGAGCACGTCCTTGGTGAAGAGAAGTACACATTTGTCGAAAATGTGAACAACCCTCATTCTTGCACAATCTTAATCAAAGACACCATAGAAATCTTCAAGGGGAGACAAACAAAATTTCCAAGAGTTAAATATGGTGTGGACTTTGTTGCCTACCGCCATCATCCAGCTCTAGTTCACTCTGAATATGCGGTGATTGTATTGTCAGAGGAACATAGTGATGGAAATAAGCTACTGACGGACTGGTTAGAGATTCATTGTACTACTCGTCTTTGTGGAGGTGTTGCAAAGACATTGTTAGTTCTTTATATCAGCAGAAATGGTCAGAGTGTGGACTCCCCATCAAGTGTGGAGAGATTTACTGTTGAAGAGCGTACTATTACAAGATGGAAGCCAGAACAATGCCGTGTTGACAATAGATTAGTTCAAAGTGAAAAGGGAACTGAATTGGAGCAACTCGGTGCTGATATATTCTCCTGCTGTATTCACTCTACCGCCTCAGAACCTCTTGACATAGATGATTCTGAACAGATGTTGAATGACGATGAGCTCTTTTTCAACACTATGGCAGAGGATGGAAGCGATGAGCAGGTAGCTGAAAAATCAACGATTATGAATGAAGAATGTTTAGATGAAGAATATACCAATGACTATGATGAAGAAGAAGAGGAAAACCACTATGCTTCTCGTGCCATATCCAAGATGCAACCCAGATAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000003 GO:0000213 GO:0000214 GO:0000278 GO:0000281 GO:0000379 GO:0000394 GO:0000910 GO:0003006 GO:0003674 GO:0003824 GO:0004518 GO:0004519 GO:0004521 GO:0004540 GO:0004549 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0006139 GO:0006388 GO:0006396 GO:0006399 GO:0006725 GO:0006807 GO:0007049 GO:0007275 GO:0008033 GO:0008150 GO:0008152 GO:0008356 GO:0008380 GO:0009790 GO:0009791 GO:0009793 GO:0009987 GO:0010069 GO:0010070 GO:0010154 GO:0010467 GO:0016070 GO:0016787 GO:0016788 GO:0016892 GO:0016894 GO:0022402 GO:0022414 GO:0032501 GO:0032502 GO:0032991 GO:0034470 GO:0034641 GO:0034660 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0044237 GO:0044238 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0048316 GO:0048608 GO:0048731 GO:0048856 GO:0051301 GO:0061458 GO:0061640 GO:0071704 GO:0090304 GO:0090305 GO:0090501 GO:0090502 GO:0140098 GO:0140101 GO:1901360 GO:1902494 GO:1902555 GO:1903047 GO:1905348

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

tRNA_int_endo tRNA_int_endo_N

Protein Analysis

268

Amino Acids

30.59

Weight (kDa)

4.56

Isoelectric Point (pI)

54.75

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Cpn60_TCP1	PF00118	1 - 58	2.4e-13	TCP-1/cpn60 chaperonin family
tRNA_int_endo	PF01974	73 - 139	1.2e-09	tRNA intron endonuclease, catalytic C-terminal 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)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0003092)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT3G45577 AT3G45590 AT3G45590 AT5G60230 AT5G60230
fragaria_vesca	FvH4_2g14101 FvH4_2g14101 FvH4_2g14101 FvH4_2g14101 FvH4_2g14101 FvH4_2g14101 FvH4_2g14101
rosa_chinensis	RchiOBHm_Chr6g0276201
rosa_laevigata	RLG00000013409 RLG00000025847
rosa_multiflora	Rmu_sc0002063.1_g000007 Rmu_sc0004048.1_g000016 Rmu_sc0008839.1_g000006
rosa_roxburghii	Rroxscaffold_2G00125430 Rroxscaffold_7G00192490
rosa_rugosa	Rorug06G0098800 Rorug06G0098900 Rorug06G0098900 Rorug06G0099000 Rorug06G0099100 Rorug06G0099200 Rorug06G0099300 Rorug06G0124300
rosa_samantha	Rh1AG171200 Rh3BG017000 Rh3DG017300 Rh5BG538000 Rh5CG561900 Rh6AG210700 Rh6BG214900 Rh6DG207200
rosa_wichuraiana	Rw6G018360

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc36I	ACCTGC	1 cut(s)	670
AciI	CCGC	3 cut(s)	247, 281, 585
AcsI	RAATTY	1 cut(s)	206
AfaI	GTAC	3 cut(s)	119, 352, 466
AfiI	CCNNNNNNNGG	1 cut(s)	76
AgsI	TTSAA	5 cut(s)	190, 458, 518, 628, 649
AjiI	CACGTC	1 cut(s)	100
AluBI	AGCT	4 cut(s)	260, 322, 640, 686
AluI	AGCT	4 cut(s)	260, 322, 640, 686
Alw21I	GWGCWC	2 cut(s)	99, 642
Alw26I	GTCTC	1 cut(s)	190
ApoI	RAATTY	1 cut(s)	206
AsuHPI	GGTGA	2 cut(s)	119, 295
BanII	GRGCYC	1 cut(s)	642
BauI	CACGAG	1 cut(s)	777
Bbv12I	GWGCWC	2 cut(s)	99, 642
BccI	CCATC	5 cut(s)	258, 305, 439, 471, 659
BceAI	ACGGC	1 cut(s)	480
BcoDI	GTCTC	1 cut(s)	190
BfaI	CTAG	1 cut(s)	263
BfmI	CTRYAG	1 cut(s)	45
BfuAI	ACCTGC	1 cut(s)	670
BmgBI	CACGTC	1 cut(s)	100
BmsI	GCATC	1 cut(s)	783
BsaJI	CCNNGG	2 cut(s)	70, 103
Bsc4I	CCNNNNNNNGG	1 cut(s)	76
Bse1I	ACTGG	1 cut(s)	338
BseDI	CCNNGG	2 cut(s)	70, 103
BseGI	GGATG	2 cut(s)	253, 670
BseLI	CCNNNNNNNGG	1 cut(s)	76
BseMII	CTCAG	1 cut(s)	603
BseNI	ACTGG	1 cut(s)	338
BseYI	CCCAGC	1 cut(s)	75
BsiHKAI	GWGCWC	2 cut(s)	99, 642
BslI	CCNNNNNNNGG	1 cut(s)	76
BsmAI	GTCTC	1 cut(s)	190
Bsp1286I	GDGCHC	2 cut(s)	99, 642
BspACI	CCGC	3 cut(s)	247, 281, 585
BspCNI	CTCAG	1 cut(s)	602
BspMI	ACCTGC	1 cut(s)	670
BspQI	GCTCTTC	1 cut(s)	453
BsrI	ACTGG	1 cut(s)	338
BssECI	CCNNGG	2 cut(s)	70, 103
BssSI	CACGAG	1 cut(s)	777
BssT1I	CCWWGG	2 cut(s)	70, 103
Bst2BI	CACGAG	1 cut(s)	777
Bst4CI	ACNGT	2 cut(s)	9, 454
Bst6I	CTCTTC	3 cut(s)	105, 453, 750
BstDEI	CTNAG	1 cut(s)	589
BstF5I	GGATG	2 cut(s)	253, 670
BstMAI	GTCTC	1 cut(s)	190
BstMWI	GCNNNNNNNGC	1 cut(s)	779
BstSFI	CTRYAG	1 cut(s)	45
BtgZI	GCGATG	1 cut(s)	687
BtrI	CACGTC	1 cut(s)	100
BtsCI	GGATG	2 cut(s)	253, 670
BtsI	GCAGTG	1 cut(s)	42
BtsIMutI	CAGTG	1 cut(s)	42
BveI	ACCTGC	1 cut(s)	670
Csp6I	GTAC	3 cut(s)	118, 351, 465
CviJI	RGCY	7 cut(s)	20, 75, 260, 322, 484, 640, 686
CviKI_1	RGCY	7 cut(s)	20, 75, 260, 322, 484, 640, 686
CviQI	GTAC	3 cut(s)	118, 351, 465
DdeI	CTNAG	1 cut(s)	589
Eam1104I	CTCTTC	3 cut(s)	105, 453, 750
EarI	CTCTTC	3 cut(s)	105, 453, 750
Ecl136II	GAGCTC	1 cut(s)	640
Eco130I	CCWWGG	2 cut(s)	70, 103
Eco24I	GRGCYC	1 cut(s)	642
Eco53kI	GAGCTC	1 cut(s)	640
EcoICRI	GAGCTC	1 cut(s)	640
EcoT14I	CCWWGG	2 cut(s)	70, 103
EcoT38I	GRGCYC	1 cut(s)	642
ErhI	CCWWGG	2 cut(s)	70, 103
FokI	GGATG	2 cut(s)	240, 677
FriOI	GRGCYC	1 cut(s)	642
FspBI	CTAG	1 cut(s)	263
GsaI	CCCAGC	1 cut(s)	79
HincII	GTYRAC	1 cut(s)	502
HindII	GTYRAC	1 cut(s)	502
HinfI	GANTC	3 cut(s)	343, 425, 611
HphI	GGTGA	2 cut(s)	119, 295
Hpy166II	GTNNAC	8 cut(s)	26, 40, 120, 139, 232, 268, 424, 502
Hpy188I	TCNGA	5 cut(s)	274, 298, 417, 592, 616
Hpy188III	TCNNGA	2 cut(s)	62, 599
Hpy8I	GTNNAC	8 cut(s)	26, 40, 120, 139, 232, 268, 424, 502
HpyCH4III	ACNGT	2 cut(s)	9, 454
HpyCH4IV	ACGT	1 cut(s)	99
HpyCH4V	TGCA	3 cut(s)	156, 377, 796
HpyF10VI	GCNNNNNNNGC	1 cut(s)	779
HpyF3I	CTNAG	1 cut(s)	589
HpySE526I	ACGT	1 cut(s)	99
LguI	GCTCTTC	1 cut(s)	453
LmnI	GCTCC	1 cut(s)	541
LpnPI	CCDG	7 cut(s)	61, 75, 270, 319, 498, 580, 665
LweI	GCATC	1 cut(s)	783
MaeI	CTAG	1 cut(s)	263
MaeII	ACGT	1 cut(s)	99
MboII	GAAGA	8 cut(s)	122, 178, 470, 722, 737, 761, 764, 767
MhlI	GDGCHC	2 cut(s)	99, 642
MluCI	AATT	2 cut(s)	206, 536
MlyI	GAGTC	1 cut(s)	419
MmeI	TCCRAC	1 cut(s)	61
MnlI	CCTC	8 cut(s)	25, 156, 292, 362, 598, 606, 655, 751
MseI	TTAA	3 cut(s)	56, 164, 219
MslI	CAYNNNNRTG	1 cut(s)	309
MwoI	GCNNNNNNNGC	1 cut(s)	779
PciSI	GCTCTTC	1 cut(s)	453
PfeI	GAWTC	2 cut(s)	343, 611
PleI	GAGTC	1 cut(s)	419
PpsI	GAGTC	1 cut(s)	419
Psp124BI	GAGCTC	1 cut(s)	642
PspFI	CCCAGC	1 cut(s)	75
RsaI	GTAC	3 cut(s)	119, 352, 466
RsaNI	GTAC	3 cut(s)	118, 351, 465
RseI	CAYNNNNRTG	1 cut(s)	309
SacI	GAGCTC	1 cut(s)	642
SapI	GCTCTTC	1 cut(s)	453
SaqAI	TTAA	3 cut(s)	56, 164, 219
SchI	GAGTC	1 cut(s)	419
SduI	GDGCHC	2 cut(s)	99, 642
SetI	ASST	8 cut(s)	102, 262, 324, 373, 598, 642, 684, 688
SfaNI	GCATC	1 cut(s)	783
SfcI	CTRYAG	1 cut(s)	45
SmiMI	CAYNNNNRTG	1 cut(s)	309
Sse9I	AATT	2 cut(s)	206, 536
SsiI	CCGC	3 cut(s)	247, 281, 585
SspMI	CTAG	1 cut(s)	263
SstI	GAGCTC	1 cut(s)	642
StyI	CCWWGG	2 cut(s)	70, 103
TaaI	ACNGT	2 cut(s)	9, 454
TaiI	ACGT	1 cut(s)	102
TaqI	TCGA	1 cut(s)	129
TasI	AATT	2 cut(s)	206, 536
TatI	WGTACW	2 cut(s)	117, 350
TfiI	GAWTC	2 cut(s)	343, 611
Tru1I	TTAA	3 cut(s)	56, 164, 219
Tru9I	TTAA	3 cut(s)	56, 164, 219
TscAI	CASTG	1 cut(s)	42
TspDTI	ATGAA	5 cut(s)	335, 719, 723, 738, 762
TspGWI	ACGGA	1 cut(s)	344
TspRI	CASTG	1 cut(s)	42
XapI	RAATTY	1 cut(s)	206
XspI	CTAG	1 cut(s)	263

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