Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr5C

Orthogroup ID

OG0001333

Physical Location & Seq

Genomic Coordinates Reverse (-)

4037903 .. 4038316

Gene Structure 414 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh5CG055600.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 414 bp

ATGTATTTGCAGAGCCAGACGGAGCAGAAATTGGTCACCAGGACTCGCCTGACTTTCGACAGAGCGCTGCCTGCTCTTCCCGTGCAGCTGCACGACTGCTTTTGGGAGCTCTACCTTGCCTTCGTTAGTCAGAAGGGTATCCCAATCGAGACCTCGCTTAGGGTTTACCGGAGGTACTTGCAGTTTGACCCTACTTACGTGGAAGACTACATTAATTTCTTGATGGATTCTACTCTTTGGCAAGAGGCGGCGGAGAAGCTCGCCTCGGTGTTGAATGATGATGAGTTTTGTTCAGTAAAGGGGAAAACTAAGCAGACGCTGTGGTTGGAATATTGTGGTTTGCTTGCTAGGCACGGTACCAAGGTCTCAGGCATCAATGTGGATGCTATCATTGTTAAGACATTTAAAGACTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

GO:0000349 GO:0000375 GO:0000377 GO:0000393 GO:0000398 GO:0000974 GO:0001701 GO:0001824 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005681 GO:0005684 GO:0006139 GO:0006259 GO:0006281 GO:0006283 GO:0006289 GO:0006351 GO:0006396 GO:0006397 GO:0006725 GO:0006807 GO:0006950 GO:0006974 GO:0007275 GO:0008150 GO:0008152 GO:0008380 GO:0009058 GO:0009059 GO:0009790 GO:0009792 GO:0009987 GO:0010467 GO:0016043 GO:0016070 GO:0016071 GO:0018130 GO:0019438 GO:0022607 GO:0022613 GO:0022618 GO:0032501 GO:0032502 GO:0032774 GO:0032991 GO:0033554 GO:0034622 GO:0034641 GO:0034645 GO:0034654 GO:0043009 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043933 GO:0044085 GO:0044237 GO:0044238 GO:0044249 GO:0044260 GO:0044271 GO:0044422 GO:0044424 GO:0044428 GO:0044446 GO:0044464 GO:0046483 GO:0048856 GO:0050896 GO:0051716 GO:0065003 GO:0071007 GO:0071010 GO:0071012 GO:0071013 GO:0071014 GO:0071704 GO:0071826 GO:0071840 GO:0090304 GO:0097659 GO:1901360 GO:1901362 GO:1901576 GO:1902494 GO:1990904

KEGG Pathways

Metabolic & Signaling

ko03040 map03040

Pfam Domains

Protein Families

Suf

Protein Analysis

137

Amino Acids

15.95

Weight (kDa)

6.11

Isoelectric Point (pI)

40.04

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
HAT_Syf1_CNRKL1_N	PF23233	1 - 64	3.4e-17	Pre-mRNA-splicing factor Syf1/CNRKL1 N-terminal HAT repeat
HAT_Syf1_M	PF23220	67 - 133	4.1e-16	Pre-mRNA-splicing factor SYF1 middle HAT repeat

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: OG0001333)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT5G28740
fragaria_vesca	FvH4_3g03910 FvH4_3g04150 FvH4_3g04150 FvH4_3g04150 FvH4_3g04150
malus_domestica	MD05G1324400.v1.1 MD10G1302200.v1.1
prunus_persica	Prupe.5G013200_v2.0.a1
pyrus_communis	pycom05g29860 pycom10g25470
rosa_chinensis	RchiOBHm_Chr5g0006181 RchiOBHm_Chr5g0006191 RchiOBHm_Chr5g0006201 RchiOBHm_Chr5g0006601 RchiOBHm_Chr7g0193971
rosa_laevigata	RLG00000004227 RLG00000031375 RLG00000031376 RLG00000031403
rosa_multiflora	Rmu_co7988368.1_g000001 Rmu_co8257165.1_g000001 Rmu_co8304153.1_g000001 Rmu_co8327759.1_g000001 Rmu_sc0001972.1_g000002 Rmu_sc0002389.1_g000006 Rmu_sc0004331.1_g000002 Rmu_sc0005583.1_g000001 Rmu_sc0009371.1_g000007 Rmu_sc0011154.1_g000005 Rmu_sc0024345.1_g000002 Rmu_sc0032392.1_g000001 Rmu_sc0032393.1_g000001
rosa_roxburghii	Rroxscaffold_1G00069420 Rroxscaffold_1G00069440 Rroxscaffold_1G00069800 Rroxscaffold_2G00122720 Rroxscaffold_3G00261670
rosa_rugosa	Rorug04G0422900
rosa_samantha	Rh5AG050200 Rh5BG046700 Rh5BG046800 Rh5BG049400 Rh5CG055400 Rh5CG055600 Rh5CG057800 Rh5DG046500 Rh5DG048800 Rh7AG139900 Rh7AG140000 Rh7DG141300
rosa_wichuraiana	Rw5G004790 Rw5G005020 Rw7G011940

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
Acc65I	GGTACC	1 cut(s)	356
AccB1I	GGYRCC	1 cut(s)	356
AciI	CCGC	2 cut(s)	248, 251
AfaI	GTAC	2 cut(s)	176, 358
AfeI	AGCGCT	1 cut(s)	66
AfiI	CCNNNNNNNGG	1 cut(s)	159
AgsI	TTSAA	1 cut(s)	274
AjnI	CCWGG	1 cut(s)	38
AluBI	AGCT	3 cut(s)	88, 109, 259
AluI	AGCT	3 cut(s)	88, 109, 259
Alw21I	GWGCWC	1 cut(s)	111
Alw26I	GTCTC	2 cut(s)	143, 370
AlwNI	CAGNNNCTG	1 cut(s)	319
Aor51HI	AGCGCT	1 cut(s)	66
ApeKI	GCWGC	3 cut(s)	67, 85, 88
AseI	ATTAAT	1 cut(s)	213
Asp718I	GGTACC	1 cut(s)	356
AspLEI	GCGC	1 cut(s)	67
AsuHPI	GGTGA	1 cut(s)	28
BaeI	ACNNNNGTAYC	2 cut(s)	348, 381
BanI	GGYRCC	1 cut(s)	356
BanII	GRGCYC	1 cut(s)	111
BbsI	GAAGAC	1 cut(s)	210
Bbv12I	GWGCWC	1 cut(s)	111
BbvI	GCAGC	3 cut(s)	54, 75, 97
BccI	CCATC	1 cut(s)	217
BciT130I	CCWGG	1 cut(s)	40
BciVI	GTATCC	1 cut(s)	149
BcoDI	GTCTC	2 cut(s)	143, 370
BfaI	CTAG	2 cut(s)	348, 412
BfoI	RGCGCY	1 cut(s)	68
BfuI	GTATCC	1 cut(s)	149
BisI	GCNGC	4 cut(s)	68, 86, 89, 249
BlsI	GCNGC	4 cut(s)	69, 87, 90, 250
Bme1390I	CCNGG	1 cut(s)	40
BmiI	GGNNCC	1 cut(s)	358
BmrFI	CCNGG	1 cut(s)	40
BmsI	GCATC	2 cut(s)	373, 381
BpiI	GAAGAC	1 cut(s)	210
Bpu10I	CCTNAGC	1 cut(s)	158
BsaAI	YACGTR	1 cut(s)	199
BsaI	GGTCTC	2 cut(s)	143, 370
BsaJI	CCNNGG	2 cut(s)	264, 360
BsaWI	WCCGGW	1 cut(s)	168
Bsc4I	CCNNNNNNNGG	1 cut(s)	159
BseBI	CCWGG	1 cut(s)	40
BseDI	CCNNGG	2 cut(s)	264, 360
BseGI	GGATG	1 cut(s)	388
BseLI	CCNNNNNNNGG	1 cut(s)	159
BseMII	CTCAG	1 cut(s)	381
BseXI	GCAGC	3 cut(s)	54, 75, 97
BsgI	GTGCAG	2 cut(s)	74, 104
BshNI	GGYRCC	1 cut(s)	356
BsiHKAI	GWGCWC	1 cut(s)	111
BsiSI	CCGG	1 cut(s)	169
BslI	CCNNNNNNNGG	1 cut(s)	159
BsmAI	GTCTC	2 cut(s)	143, 370
Bso31I	GGTCTC	2 cut(s)	143, 370
Bsp1286I	GDGCHC	1 cut(s)	111
BspACI	CCGC	2 cut(s)	248, 251
BspCNI	CTCAG	1 cut(s)	380
BspLI	GGNNCC	1 cut(s)	358
BspQI	GCTCTTC	1 cut(s)	81
BspT107I	GGYRCC	1 cut(s)	356
BspTNI	GGTCTC	2 cut(s)	143, 370
BssECI	CCNNGG	2 cut(s)	264, 360
BssT1I	CCWWGG	1 cut(s)	360
Bst2UI	CCWGG	1 cut(s)	40
Bst4CI	ACNGT	1 cut(s)	356
Bst6I	CTCTTC	1 cut(s)	81
BstBAI	YACGTR	1 cut(s)	199
BstC8I	GCNNGC	3 cut(s)	72, 261, 345
BstDEI	CTNAG	3 cut(s)	158, 309, 367
BstEII	GGTNACC	1 cut(s)	34
BstENI	CCTNNNNNAGG	1 cut(s)	157
BstF5I	GGATG	1 cut(s)	388
BstH2I	RGCGCY	1 cut(s)	68
BstHHI	GCGC	1 cut(s)	67
BstMAI	GTCTC	2 cut(s)	143, 370
BstMWI	GCNNNNNNNGC	2 cut(s)	71, 349
BstNI	CCWGG	1 cut(s)	40
BstPI	GGTNACC	1 cut(s)	34
BstSCI	CCNGG	1 cut(s)	38
BstV1I	GCAGC	3 cut(s)	54, 75, 97
BstV2I	GAAGAC	1 cut(s)	210
BsuI	GTATCC	1 cut(s)	149
BtsCI	GGATG	1 cut(s)	388
Cac8I	GCNNGC	3 cut(s)	72, 261, 345
CaiI	CAGNNNCTG	1 cut(s)	319
CfoI	GCGC	1 cut(s)	67
CseI	GACGC	1 cut(s)	325
Csp6I	GTAC	2 cut(s)	175, 357
CviJI	RGCY	4 cut(s)	15, 88, 109, 259
CviKI_1	RGCY	4 cut(s)	15, 88, 109, 259
CviQI	GTAC	2 cut(s)	175, 357
DdeI	CTNAG	3 cut(s)	158, 309, 367
DraI	TTTAAA	1 cut(s)	406
Eam1104I	CTCTTC	1 cut(s)	81
EarI	CTCTTC	1 cut(s)	81
EciI	GGCGGA	1 cut(s)	266
Ecl136II	GAGCTC	1 cut(s)	109
Eco130I	CCWWGG	1 cut(s)	360
Eco24I	GRGCYC	1 cut(s)	111
Eco31I	GGTCTC	2 cut(s)	143, 370
Eco47III	AGCGCT	1 cut(s)	66
Eco53kI	GAGCTC	1 cut(s)	109
Eco91I	GGTNACC	1 cut(s)	34
EcoICRI	GAGCTC	1 cut(s)	109
EcoNI	CCTNNNNNAGG	1 cut(s)	157
EcoO65I	GGTNACC	1 cut(s)	34
EcoRII	CCWGG	1 cut(s)	38
EcoT14I	CCWWGG	1 cut(s)	360
EcoT38I	GRGCYC	1 cut(s)	111
ErhI	CCWWGG	1 cut(s)	360
Fnu4HI	GCNGC	4 cut(s)	68, 86, 89, 249
FokI	GGATG	1 cut(s)	395
FriOI	GRGCYC	1 cut(s)	111
Fsp4HI	GCNGC	4 cut(s)	68, 86, 89, 249
FspBI	CTAG	2 cut(s)	348, 412
GlaI	GCGC	1 cut(s)	66
GluI	GCNGC	4 cut(s)	68, 86, 89, 249
HaeII	RGCGCY	1 cut(s)	68
HapII	CCGG	1 cut(s)	169
HgaI	GACGC	1 cut(s)	325
HhaI	GCGC	1 cut(s)	67
Hin6I	GCGC	1 cut(s)	65
HinP1I	GCGC	1 cut(s)	65
HinfI	GANTC	2 cut(s)	43, 227
HpaII	CCGG	1 cut(s)	169
HphI	GGTGA	1 cut(s)	28
Hpy166II	GTNNAC	1 cut(s)	166
Hpy188I	TCNGA	1 cut(s)	132
Hpy188III	TCNNGA	2 cut(s)	148, 220
Hpy8I	GTNNAC	1 cut(s)	166
HpyAV	CCTTC	2 cut(s)	127, 130
HpyCH4III	ACNGT	1 cut(s)	356
HpyCH4IV	ACGT	1 cut(s)	198
HpyCH4V	TGCA	4 cut(s)	10, 85, 91, 181
HpyF10VI	GCNNNNNNNGC	2 cut(s)	71, 349
HpyF3I	CTNAG	3 cut(s)	158, 309, 367
HpySE526I	ACGT	1 cut(s)	198
HspAI	GCGC	1 cut(s)	65
KpnI	GGTACC	1 cut(s)	360
LguI	GCTCTTC	1 cut(s)	81
LmnI	GCTCC	2 cut(s)	22, 106
LpnPI	CCDG	7 cut(s)	25, 29, 52, 62, 84, 182, 354
Lsp1109I	GCAGC	3 cut(s)	54, 75, 97
LweI	GCATC	2 cut(s)	373, 381
MaeI	CTAG	2 cut(s)	348, 412
MaeII	ACGT	1 cut(s)	198
MaeIII	GTNAC	1 cut(s)	34
MboII	GAAGA	2 cut(s)	68, 215
MhlI	GDGCHC	1 cut(s)	111
MluCI	AATT	2 cut(s)	29, 214
MlyI	GAGTC	1 cut(s)	37
MmeI	TCCRAC	1 cut(s)	306
MnlI	CCTC	4 cut(s)	163, 165, 238, 274
MseI	TTAA	3 cut(s)	213, 396, 405
MslI	CAYNNNNRTG	1 cut(s)	377
MspA1I	CMGCKG	1 cut(s)	88
MspI	CCGG	1 cut(s)	169
MspR9I	CCNGG	1 cut(s)	40
MvaI	CCWGG	1 cut(s)	40
MwoI	GCNNNNNNNGC	2 cut(s)	71, 349
NlaIV	GGNNCC	1 cut(s)	358
NmuCI	GTSAC	1 cut(s)	34
PciSI	GCTCTTC	1 cut(s)	81
PfeI	GAWTC	1 cut(s)	227
PkrI	GCNGC	4 cut(s)	69, 87, 90, 250
PleI	GAGTC	1 cut(s)	37
PpsI	GAGTC	1 cut(s)	37
Ppu21I	YACGTR	1 cut(s)	199
PshBI	ATTAAT	1 cut(s)	213
Psp124BI	GAGCTC	1 cut(s)	111
Psp6I	CCWGG	1 cut(s)	38
PspEI	GGTNACC	1 cut(s)	34
PspGI	CCWGG	1 cut(s)	38
PspN4I	GGNNCC	1 cut(s)	358
PstNI	CAGNNNCTG	1 cut(s)	319
PvuII	CAGCTG	1 cut(s)	88
RsaI	GTAC	2 cut(s)	176, 358
RsaNI	GTAC	2 cut(s)	175, 357
RseI	CAYNNNNRTG	1 cut(s)	377
SacI	GAGCTC	1 cut(s)	111
SapI	GCTCTTC	1 cut(s)	81
SaqAI	TTAA	3 cut(s)	213, 396, 405
SatI	GCNGC	4 cut(s)	68, 86, 89, 249
SchI	GAGTC	1 cut(s)	37
ScrFI	CCNGG	1 cut(s)	40
SduI	GDGCHC	1 cut(s)	111
SetI	ASST	8 cut(s)	90, 111, 117, 155, 176, 201, 261, 366
SfaNI	GCATC	2 cut(s)	373, 381
SmiMI	CAYNNNNRTG	1 cut(s)	377
Sse9I	AATT	2 cut(s)	29, 214
SsiI	CCGC	2 cut(s)	248, 251
SspI	AATATT	1 cut(s)	332
SspMI	CTAG	2 cut(s)	348, 412
SstI	GAGCTC	1 cut(s)	111
StyD4I	CCNGG	1 cut(s)	38
StyI	CCWWGG	1 cut(s)	360
TaaI	ACNGT	1 cut(s)	356
TaiI	ACGT	1 cut(s)	201
TaqI	TCGA	2 cut(s)	57, 147
TasI	AATT	2 cut(s)	29, 214
TauI	GCSGC	1 cut(s)	251
TfiI	GAWTC	1 cut(s)	227
Tru1I	TTAA	3 cut(s)	213, 396, 405
Tru9I	TTAA	3 cut(s)	213, 396, 405
TseFI	GTSAC	1 cut(s)	34
TseI	GCWGC	3 cut(s)	67, 85, 88
Tsp45I	GTSAC	1 cut(s)	34
TspGWI	ACGGA	1 cut(s)	35
VspI	ATTAAT	1 cut(s)	213
XagI	CCTNNNNNAGG	1 cut(s)	157
XspI	CTAG	2 cut(s)	348, 412

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