Basic Information

Type: gene

Biological Identity

Species

rosa_samantha

Chromosome

Chr2B

Orthogroup ID

OG0006436

Physical Location & Seq

Genomic Coordinates Forward (+)

303196 .. 304529

Gene Structure 1334 bp

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UTR

Exon/CDS

Intron

Transcript / Protein ID

Rh2BG003200.1

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1041 bp

ATGGCTTTAGATGATAAGGTCCAATCCATAAGTATTAGGCTAAGCAGAGATAACTATTCATACTGGGCCAGTGTGATGAAAAATTTTCTAATTGGTCGAGGTAGATGGGGTTATGTTACTGGCATAACAGTCAAACCTTCAGATTCCAAAGTTGCAGACTTTGAAAAATCCATTGCCACATGGGAAATGGAGAATGCTCAGGTGCTTACTTGGTTCCATAACTCTGTTGAATCAAGTATTGGTCAGAACTTTTCAAAGTTTGCAACTGCAAAGAGAGTATGGGAGTATTTACAGCTGTTATATCAAGAGTCTAACTTTGCCAAGCACTATCAGCTGGAAATGGAAATTCGAGGTGCCCAGCAAGGTGATAAGACCATTCAAGACTTCTACAATCAGATGACTTGTTTCTGGGATCAATTAGCACTTATGGAACCAGCTGACCTCTTGGCATTTGATAGTTATATTAACTATAGAGAGCGTCAGAGACTTGTCCAATTTCTTATGGCACTTAAGGAACAGTTTGAACCTTTGCGTGGTGCTATGCTGCATCGTGTTCCTCTACCCACTGTTGATGGAGCGGTTAAAGAACTTCTAGCTGAGGAGACTCGATTTAAGGTTGCTCAGAATGTTTCTCCCTCCCCATCTGTATTTGCAACTTCTATTTTGCAACCTCCTTTATTGCAGACTCCACCTCGAAGTCTTATACAGATTACTGGCAAACCAAAGCAACGTGTCAGCAATGATGAATGCAGTTTTTGCCATCAAAAAGGCCACTGGAAGGTTTCTTGCCCAAAATTGCAGAAAGGGCGTCCACTTCATAATCAACGCCCCCCTCACCACAATTCTCAGCGTTTCCCAGCAGCACTTGCTGTTCAAGCTCCTTCAGCAGAGTCCTTACTTGAGCAATTCCAGTCTATTCTTGCTAATGCCACTATGGAGTCTCATGCTTCAACTTCTACCCCATCAGCTTTTCATTCAGGTTTAGCCACTTCTAGCAACACAGGATTGCAAGTCCAAGAAACAGATTGGGACTGGGCGTAG

Functional Annotation

Gene Ontology

Molecular Function
Biological Process
Cellular Component

No ontology terms assigned.

KEGG Pathways

Metabolic & Signaling

No pathways identified.

Pfam Domains

Protein Families

Retrotran_gag_2 Retrotran_gag_3

Protein Analysis

346

Amino Acids

39.34

Weight (kDa)

7.73

Isoelectric Point (pI)

42.24

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
Retrotran_gag_3	PF14244	8 - 47	3e-09	gag-polypeptide of LTR copia-type
Retrotran_gag_2	PF14223	26 - 205	1.1e-08	gag-polypeptide of LTR copia-type

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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Tree File

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Publication-ready

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Orthologous Genes (Group: OG0006436)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G21280
fragaria_vesca	FvH4_3g37931 FvH4_3g37931 FvH4_3g37931
malus_domestica	MD01G1094300.v1.1 MD02G1156200.v1.1 MD10G1309400.v1.1 MD14G1005300.v1.1
pyrus_communis	pycom02g16670 pycom03g10030 pycom04g21390 pycom05g29420 pycom07g08570 pycom08g06430 pycom15g03080 pycom15g21690
rosa_chinensis	RchiOBHm_Chr4g0394011 RchiOBHm_Chr4g0436631
rosa_multiflora	Rmu_sc0002646.1_g000018 Rmu_sc0004135.1_g000007
rosa_roxburghii	Rroxscaffold_2G00099130
rosa_samantha	Rh1AG086000 Rh2BG003200 Rh5DG450100 Rh7AG095400
rosa_wichuraiana	Rw1G012660

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB1I	GGYRCC	1 cut(s)	353
AccBSI	CCGCTC	1 cut(s)	578
AciI	CCGC	1 cut(s)	578
AclWI	GGATC	1 cut(s)	420
AcsI	RAATTY	2 cut(s)	82, 345
AcuI	CTGAAG	2 cut(s)	123, 867
AcyI	GRCGYC	1 cut(s)	808
AfiI	CCNNNNNNNGG	2 cut(s)	533, 778
AflII	CTTAAG	1 cut(s)	509
AflIII	ACRYGT	1 cut(s)	730
AgsI	TTSAA	7 cut(s)	164, 230, 255, 380, 524, 875, 951
AjuI	GAANNNNNNNTTGG	2 cut(s)	222, 254
AluBI	AGCT	6 cut(s)	295, 334, 437, 596, 878, 968
AluI	AGCT	6 cut(s)	295, 334, 437, 596, 878, 968
Alw26I	GTCTC	3 cut(s)	478, 596, 945
AlwI	GGATC	1 cut(s)	420
AoxI	GGCC	2 cut(s)	66, 769
ApeKI	GCWGC	2 cut(s)	544, 860
ApoI	RAATTY	2 cut(s)	82, 345
AspS9I	GGNCC	2 cut(s)	19, 66
AsuHPI	GGTGA	2 cut(s)	377, 827
AvaII	GGWCC	1 cut(s)	19
BaeGI	GKGCMC	1 cut(s)	358
BanI	GGYRCC	1 cut(s)	353
BbvCI	CCTCAGC	1 cut(s)	597
BbvI	GCAGC	2 cut(s)	531, 872
BccI	CCATC	5 cut(s)	99, 566, 649, 768, 970
BcoDI	GTCTC	3 cut(s)	478, 596, 945
BfaI	CTAG	2 cut(s)	593, 993
BfmI	CTRYAG	1 cut(s)	469
BfrI	CTTAAG	1 cut(s)	509
BisI	GCNGC	2 cut(s)	545, 861
BlpI	GCTNAGC	1 cut(s)	41
BlsI	GCNGC	2 cut(s)	546, 862
Bme18I	GGWCC	1 cut(s)	19
BmgT120I	GGNCC	2 cut(s)	19, 66
BmiI	GGNNCC	3 cut(s)	215, 355, 432
BmrI	ACTGGG	1 cut(s)	73
BmsI	GCATC	1 cut(s)	556
BmuI	ACTGGG	1 cut(s)	73
Bpu10I	CCTNAGC	2 cut(s)	198, 597
Bpu1102I	GCTNAGC	1 cut(s)	41
BpuEI	CTTGAG	1 cut(s)	920
BsaHI	GRCGYC	1 cut(s)	808
Bsc4I	CCNNNNNNNGG	2 cut(s)	533, 778
Bse1I	ACTGG	7 cut(s)	68, 69, 124, 718, 779, 910, 1037
Bse3DI	GCAATG	2 cut(s)	171, 745
BseLI	CCNNNNNNNGG	2 cut(s)	533, 778
BseMI	GCAATG	2 cut(s)	171, 745
BseMII	CTCAG	4 cut(s)	212, 588, 635, 860
BseNI	ACTGG	7 cut(s)	68, 69, 124, 718, 779, 910, 1037
BseRI	GAGGAG	1 cut(s)	614
BseSI	GKGCMC	1 cut(s)	358
BseXI	GCAGC	2 cut(s)	531, 872
BseYI	CCCAGC	2 cut(s)	357, 856
BshFI	GGCC	2 cut(s)	68, 771
BshNI	GGYRCC	1 cut(s)	353
BslI	CCNNNNNNNGG	2 cut(s)	533, 778
BsmAI	GTCTC	3 cut(s)	478, 596, 945
BsmI	GAATGC	2 cut(s)	199, 752
BsnI	GGCC	2 cut(s)	68, 771
Bsp1286I	GDGCHC	1 cut(s)	358
Bsp143I	GATC	1 cut(s)	412
Bsp1720I	GCTNAGC	1 cut(s)	41
BspACI	CCGC	1 cut(s)	578
BspANI	GGCC	2 cut(s)	68, 771
BspCNI	CTCAG	4 cut(s)	211, 589, 634, 859
BspLI	GGNNCC	3 cut(s)	215, 355, 432
BspPI	GGATC	1 cut(s)	420
BspT107I	GGYRCC	1 cut(s)	353
BspTI	CTTAAG	1 cut(s)	509
BsrBI	CCGCTC	1 cut(s)	578
BsrDI	GCAATG	2 cut(s)	171, 745
BsrI	ACTGG	7 cut(s)	68, 69, 124, 718, 779, 910, 1037
BssMI	GATC	1 cut(s)	412
BssNI	GRCGYC	1 cut(s)	808
Bst4CI	ACNGT	3 cut(s)	130, 519, 568
BstACI	GRCGYC	1 cut(s)	808
BstAFI	CTTAAG	1 cut(s)	509
BstAPI	GCANNNNNTGC	2 cut(s)	756, 866
BstDEI	CTNAG	5 cut(s)	41, 198, 597, 621, 846
BstKTI	GATC	1 cut(s)	415
BstMAI	GTCTC	3 cut(s)	478, 596, 945
BstMBI	GATC	1 cut(s)	412
BstMWI	GCNNNNNNNGC	6 cut(s)	331, 756, 805, 866, 875, 884
BstSFI	CTRYAG	1 cut(s)	469
BstSLI	GKGCMC	1 cut(s)	358
BstV1I	GCAGC	2 cut(s)	531, 872
BsuRI	GGCC	2 cut(s)	68, 771
BtsIMutI	CAGTG	3 cut(s)	76, 564, 772
Cfr13I	GGNCC	2 cut(s)	19, 66
CseI	GACGC	2 cut(s)	467, 797
CviAII	CATG	2 cut(s)	180, 944
DdeI	CTNAG	5 cut(s)	41, 198, 597, 621, 846
DpnI	GATC	1 cut(s)	414
DpnII	GATC	1 cut(s)	412
Eco47I	GGWCC	1 cut(s)	19
Eco57I	CTGAAG	2 cut(s)	123, 867
FaeI	CATG	2 cut(s)	183, 947
FatI	CATG	2 cut(s)	179, 943
Fnu4HI	GCNGC	2 cut(s)	545, 861
Fsp4HI	GCNGC	2 cut(s)	545, 861
FspBI	CTAG	2 cut(s)	593, 993
GluI	GCNGC	2 cut(s)	545, 861
GsaI	CCCAGC	2 cut(s)	361, 860
HaeIII	GGCC	2 cut(s)	68, 771
HgaI	GACGC	2 cut(s)	467, 797
Hin1I	GRCGYC	1 cut(s)	808
Hin1II	CATG	2 cut(s)	183, 947
HinfI	GANTC	7 cut(s)	143, 230, 308, 604, 685, 890, 938
HphI	GGTGA	2 cut(s)	377, 827
Hpy166II	GTNNAC	1 cut(s)	812
Hpy188I	TCNGA	5 cut(s)	142, 246, 396, 483, 624
Hpy188III	TCNNGA	2 cut(s)	305, 380
Hpy8I	GTNNAC	1 cut(s)	812
HpyAV	CCTTC	3 cut(s)	147, 772, 891
HpyCH4III	ACNGT	3 cut(s)	130, 519, 568
HpyCH4IV	ACGT	1 cut(s)	730
HpyF10VI	GCNNNNNNNGC	6 cut(s)	331, 756, 805, 866, 875, 884
HpyF3I	CTNAG	5 cut(s)	41, 198, 597, 621, 846
HpySE526I	ACGT	1 cut(s)	730
Hsp92I	GRCGYC	1 cut(s)	808
Hsp92II	CATG	2 cut(s)	183, 947
Kzo9I	GATC	1 cut(s)	412
LmnI	GCTCC	2 cut(s)	575, 883
Lsp1109I	GCAGC	2 cut(s)	531, 872
LweI	GCATC	1 cut(s)	556
MaeI	CTAG	2 cut(s)	593, 993
MaeII	ACGT	1 cut(s)	730
MaeIII	GTNAC	1 cut(s)	115
MalI	GATC	1 cut(s)	414
MbiI	CCGCTC	1 cut(s)	578
MboI	GATC	1 cut(s)	412
MhlI	GDGCHC	1 cut(s)	358
MluCI	AATT	8 cut(s)	82, 90, 345, 416, 494, 794, 841, 905
MlyI	GAGTC	5 cut(s)	317, 598, 679, 899, 947
MnlI	CCTC	9 cut(s)	92, 344, 452, 567, 592, 646, 681, 702, 843
MseI	TTAA	4 cut(s)	465, 510, 582, 612
MspA1I	CMGCKG	3 cut(s)	295, 334, 437
MspCI	CTTAAG	1 cut(s)	509
Mva1269I	GAATGC	2 cut(s)	199, 752
MwoI	GCNNNNNNNGC	6 cut(s)	331, 756, 805, 866, 875, 884
NdeII	GATC	1 cut(s)	412
NlaIII	CATG	2 cut(s)	183, 947
NlaIV	GGNNCC	3 cut(s)	215, 355, 432
PctI	GAATGC	2 cut(s)	199, 752
PfeI	GAWTC	2 cut(s)	143, 230
PkrI	GCNGC	2 cut(s)	546, 862
PleI	GAGTC	5 cut(s)	316, 598, 679, 898, 946
PpsI	GAGTC	5 cut(s)	316, 598, 679, 898, 946
PspFI	CCCAGC	2 cut(s)	357, 856
PspN4I	GGNNCC	3 cut(s)	215, 355, 432
PspPI	GGNCC	2 cut(s)	19, 66
PvuII	CAGCTG	3 cut(s)	295, 334, 437
SaqAI	TTAA	4 cut(s)	465, 510, 582, 612
SatI	GCNGC	2 cut(s)	545, 861
Sau3AI	GATC	1 cut(s)	412
Sau96I	GGNCC	2 cut(s)	19, 66
SchI	GAGTC	5 cut(s)	317, 598, 679, 899, 947
SduI	GDGCHC	1 cut(s)	358
SfaNI	GCATC	1 cut(s)	556
SfcI	CTRYAG	1 cut(s)	469
SinI	GGWCC	1 cut(s)	19
SmlI	CTYRAG	2 cut(s)	509, 899
SmoI	CTYRAG	2 cut(s)	509, 899
Sse9I	AATT	8 cut(s)	82, 90, 345, 416, 494, 794, 841, 905
SsiI	CCGC	1 cut(s)	578
SspMI	CTAG	2 cut(s)	593, 993
TaaI	ACNGT	3 cut(s)	130, 519, 568
TaiI	ACGT	1 cut(s)	733
TaqI	TCGA	4 cut(s)	97, 349, 607, 694
TasI	AATT	8 cut(s)	82, 90, 345, 416, 494, 794, 841, 905
TfiI	GAWTC	2 cut(s)	143, 230
Tru1I	TTAA	4 cut(s)	465, 510, 582, 612
Tru9I	TTAA	4 cut(s)	465, 510, 582, 612
TscAI	CASTG	3 cut(s)	76, 571, 779
TseI	GCWGC	2 cut(s)	544, 860
TspDTI	ATGAA	5 cut(s)	48, 92, 759, 806, 962
TspRI	CASTG	3 cut(s)	76, 571, 779
Vha464I	CTTAAG	1 cut(s)	509
VpaK11BI	GGWCC	1 cut(s)	19
XapI	RAATTY	2 cut(s)	82, 345
XcmI	CCANNNNNNNNNTGG	1 cut(s)	184
XspI	CTAG	2 cut(s)	593, 993

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