Rh5BG230900

GAG-pre-integrase domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5B
OG0017395
Physical Location & Seq
Reverse (-)
27171514 .. 27172527
1014 bp
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UTR
Exon/CDS
Intron
Rh5BG230900.1

Sequence Viewer

Length: 639 bp
ATGGCGGCTTCTTTGCCCCACAAATTCGGCGATTTGATTCCGTTCAAGCTCGATTTATCGAGCAATTACGTCATCTGGAATTACGCAATGGCGACGCTTCTTCAAGCCTTCAACCTCTACGGTTACGTAGATGGGACCTTCGAGAACGACAACGGCGATGAGGAAGATGTTCGATTTGATGCCGCCGACGACAAGGCAGTCATGGCTCTCATCAACTCCACTCTTGCACCGCCGACCATGGCTCAGGTGACCGGTTGCCGGACGTCGAGGGAACTTTGGGTTAGTCTGGAGCAAAAATTCGAGACTATGAGGGAGTACGCTATCCTCAAGCTCGACCGTCGCCTCAAGAACCTGGAACTCACCGCTTACGTCTCGACTGAGGGTTACGTGGCCGCCATTGAAGATCTCCGAGCAAACTTGGCTGCCTTGGGAAGGAGATACACGGACGCCGAGGTCATTGAGGTCGTCAAGAACAATATAGCTGGGGGACTTCGTTTTGCAATTTTCGGCGGGGAAGCTCAAGCTGAAACTCCTCCTCCTCCTCCCATGGAGTTGCACGACTTCTATGTGAAGCTACTTGATGAAAATTTCAGGCTTTCCAAAATGAGGTTTCCACCCCCTGGCTCTCTCTATGCCTAA
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
RVT_2 gag_pre-integrs rve

Protein Analysis

212

Amino Acids

23.78

Weight (kDa)

4.8

Isoelectric Point (pI)

44.62

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 30 - 153 1.9e-09 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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Publication-ready
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Orthologous Genes (Group: OG0017395)

Species Orthologous Gene IDs
malus_domestica MD11G1266200.v1.1
rosa_chinensis RchiOBHm_Chr5g0033261
rosa_multiflora Rmu_sc0006239.1_g000005
rosa_roxburghii Rroxscaffold_1G00046720 Rroxscaffold_1G00046730
rosa_rugosa Rorug05G0138200 Rorug05G0138200
rosa_samantha Rh5AG230000 Rh5BG230900 Rh5CG258900 Rh5DG236000 Rh5DG236400
rosa_wichuraiana Rw5G021030

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 2 cut(s) 197, 452
AatII GACGTC 1 cut(s) 266
AccB7I CCANNNNNTGG 1 cut(s) 620
AciI CCGC 6 cut(s) 5, 183, 230, 363, 393, 510
AcoI YGGCCR 1 cut(s) 390
AcsI RAATTY 3 cut(s) 23, 296, 586
AcyI GRCGYC 2 cut(s) 263, 447
AfaI GTAC 1 cut(s) 317
AfiI CCNNNNNNNGG 4 cut(s) 258, 432, 606, 620
AgeI ACCGGT 1 cut(s) 251
AgsI TTSAA 4 cut(s) 46, 104, 112, 401
AjnI CCWGG 2 cut(s) 351, 619
AluBI AGCT 6 cut(s) 49, 331, 482, 518, 524, 574
AluI AGCT 6 cut(s) 49, 331, 482, 518, 524, 574
Alw26I GTCTC 2 cut(s) 296, 376
AoxI GGCC 1 cut(s) 390
ApeKI GCWGC 1 cut(s) 422
ApoI RAATTY 3 cut(s) 23, 296, 586
AsiGI ACCGGT 1 cut(s) 251
Asp700I GAANNNNTTC 1 cut(s) 168
AspS9I GGNCC 1 cut(s) 135
AsuHPI GGTGA 2 cut(s) 259, 352
AvaII GGWCC 1 cut(s) 135
BbvI GCAGC 1 cut(s) 409
BccI CCATC 1 cut(s) 125
BceAI ACGGC 1 cut(s) 169
BciT130I CCWGG 2 cut(s) 353, 621
BcoDI GTCTC 2 cut(s) 296, 376
BglII AGATCT 1 cut(s) 403
BisI GCNGC 4 cut(s) 6, 183, 393, 423
BlsI GCNGC 4 cut(s) 7, 184, 394, 424
Bme1390I CCNGG 2 cut(s) 353, 621
Bme18I GGWCC 1 cut(s) 135
BmgT120I GGNCC 1 cut(s) 135
BmiI GGNNCC 1 cut(s) 136
BmrFI CCNGG 2 cut(s) 353, 621
BmsI GCATC 1 cut(s) 169
BpmI CTGGAG 1 cut(s) 308
Bpu10I CCTNAGC 1 cut(s) 243
BpuEI CTTGAG 3 cut(s) 311, 329, 504
BsaAI YACGTR 2 cut(s) 127, 388
BsaHI GRCGYC 2 cut(s) 263, 447
BsaJI CCNNGG 5 cut(s) 237, 426, 450, 546, 619
BsaWI WCCGGW 1 cut(s) 251
BsaXI ACNNNNNCTCC 2 cut(s) 520, 550
Bsc4I CCNNNNNNNGG 4 cut(s) 258, 432, 606, 620
Bse118I RCCGGY 1 cut(s) 251
Bse3DI GCAATG 1 cut(s) 93
BseBI CCWGG 2 cut(s) 353, 621
BseDI CCNNGG 5 cut(s) 237, 426, 450, 546, 619
BseLI CCNNNNNNNGG 4 cut(s) 258, 432, 606, 620
BseMI GCAATG 1 cut(s) 93
BseMII CTCAG 2 cut(s) 257, 369
BseRI GAGGAG 4 cut(s) 522, 525, 528, 531
BseXI GCAGC 1 cut(s) 409
BseYI CCCAGC 1 cut(s) 482
Bsh1285I CGRYCG 1 cut(s) 337
BshFI GGCC 1 cut(s) 392
BshTI ACCGGT 1 cut(s) 251
BsiEI CGRYCG 1 cut(s) 337
BsiSI CCGG 2 cut(s) 252, 259
BslFI GGGAC 2 cut(s) 148, 501
BslI CCNNNNNNNGG 4 cut(s) 258, 432, 606, 620
BsmAI GTCTC 2 cut(s) 296, 376
BsmBI CGTCTC 1 cut(s) 376
BsmFI GGGAC 2 cut(s) 148, 501
BsnI GGCC 1 cut(s) 392
Bsp143I GATC 1 cut(s) 403
Bsp19I CCATGG 2 cut(s) 237, 546
BspACI CCGC 6 cut(s) 5, 183, 230, 363, 393, 510
BspANI GGCC 1 cut(s) 392
BspCNI CTCAG 2 cut(s) 256, 370
BspLI GGNNCC 1 cut(s) 136
BsrDI GCAATG 1 cut(s) 93
BsrFI RCCGGY 1 cut(s) 251
BssAI RCCGGY 1 cut(s) 251
BssECI CCNNGG 5 cut(s) 237, 426, 450, 546, 619
BssMI GATC 1 cut(s) 403
BssNI GRCGYC 2 cut(s) 263, 447
BssT1I CCWWGG 3 cut(s) 237, 426, 546
Bst2UI CCWGG 2 cut(s) 353, 621
Bst4CI ACNGT 2 cut(s) 122, 338
BstACI GRCGYC 2 cut(s) 263, 447
BstBAI YACGTR 2 cut(s) 127, 388
BstDEI CTNAG 2 cut(s) 243, 378
BstDSI CCRYGG 2 cut(s) 237, 546
BstEII GGTNACC 1 cut(s) 247
BstENI CCTNNNNNAGG 1 cut(s) 430
BstKTI GATC 1 cut(s) 406
BstMAI GTCTC 2 cut(s) 296, 376
BstMBI GATC 1 cut(s) 403
BstMCI CGRYCG 1 cut(s) 337
BstMWI GCNNNNNNNGC 2 cut(s) 203, 419
BstNI CCWGG 2 cut(s) 353, 621
BstPI GGTNACC 1 cut(s) 247
BstSCI CCNGG 2 cut(s) 351, 619
BstSNI TACGTA 1 cut(s) 127
BstV1I GCAGC 1 cut(s) 409
BstX2I RGATCY 1 cut(s) 403
BstYI RGATCY 1 cut(s) 403
BsuRI GGCC 1 cut(s) 392
BtgI CCRYGG 2 cut(s) 237, 546
BtgZI GCGATG 1 cut(s) 171
Cfr10I RCCGGY 1 cut(s) 251
Cfr13I GGNCC 1 cut(s) 135
CseI GACGC 2 cut(s) 103, 455
Csp6I GTAC 1 cut(s) 316
CspAI ACCGGT 1 cut(s) 251
CviAII CATG 3 cut(s) 202, 238, 547
CviQI GTAC 1 cut(s) 316
DdeI CTNAG 2 cut(s) 243, 378
DpnI GATC 1 cut(s) 405
DpnII GATC 1 cut(s) 403
DrdI GACNNNNNNGTC 2 cut(s) 197, 452
DseDI GACNNNNNNGTC 2 cut(s) 197, 452
EaeI YGGCCR 1 cut(s) 390
Eco105I TACGTA 1 cut(s) 127
Eco130I CCWWGG 3 cut(s) 237, 426, 546
Eco47I GGWCC 1 cut(s) 135
Eco91I GGTNACC 1 cut(s) 247
EcoNI CCTNNNNNAGG 1 cut(s) 430
EcoO109I RGGNCCY 1 cut(s) 135
EcoO65I GGTNACC 1 cut(s) 247
EcoRII CCWGG 2 cut(s) 351, 619
EcoT14I CCWWGG 3 cut(s) 237, 426, 546
ErhI CCWWGG 3 cut(s) 237, 426, 546
Esp3I CGTCTC 1 cut(s) 376
FaeI CATG 3 cut(s) 205, 241, 550
FaiI YATR 7 cut(s) 203, 239, 308, 479, 548, 567, 633
FaqI GGGAC 2 cut(s) 148, 501
FatI CATG 3 cut(s) 201, 237, 546
FauI CCCGC 1 cut(s) 503
Fnu4HI GCNGC 4 cut(s) 6, 183, 393, 423
Fsp4HI GCNGC 4 cut(s) 6, 183, 393, 423
GluI GCNGC 4 cut(s) 6, 183, 393, 423
GsaI CCCAGC 1 cut(s) 486
GsuI CTGGAG 1 cut(s) 308
HaeIII GGCC 1 cut(s) 392
HapII CCGG 2 cut(s) 252, 259
HgaI GACGC 2 cut(s) 103, 455
Hin1I GRCGYC 2 cut(s) 263, 447
Hin1II CATG 3 cut(s) 205, 241, 550
HinfI GANTC 1 cut(s) 37
HpaII CCGG 2 cut(s) 252, 259
HphI GGTGA 2 cut(s) 259, 352
Hpy188I TCNGA 1 cut(s) 410
Hpy188III TCNNGA 7 cut(s) 76, 142, 287, 301, 346, 373, 469
Hpy99I CGWCG 4 cut(s) 97, 191, 268, 342
HpyAV CCTTC 3 cut(s) 118, 148, 426
HpyCH4III ACNGT 2 cut(s) 122, 338
HpyCH4IV ACGT 5 cut(s) 69, 126, 263, 369, 387
HpyCH4V TGCA 3 cut(s) 227, 500, 556
HpyF10VI GCNNNNNNNGC 2 cut(s) 203, 419
HpyF3I CTNAG 2 cut(s) 243, 378
HpySE526I ACGT 5 cut(s) 69, 126, 263, 369, 387
Hsp92I GRCGYC 2 cut(s) 263, 447
Hsp92II CATG 3 cut(s) 205, 241, 550
Kzo9I GATC 1 cut(s) 403
LmnI GCTCC 1 cut(s) 289
Lsp1109I GCAGC 1 cut(s) 409
LweI GCATC 1 cut(s) 169
MaeII ACGT 5 cut(s) 69, 126, 263, 369, 387
MaeIII GTNAC 3 cut(s) 122, 247, 383
MalI GATC 1 cut(s) 405
MboI GATC 1 cut(s) 403
MboII GAAGA 3 cut(s) 92, 176, 413
MflI RGATCY 1 cut(s) 403
MluCI AATT 6 cut(s) 23, 64, 79, 296, 501, 586
MroXI GAANNNNTTC 1 cut(s) 168
MspI CCGG 2 cut(s) 252, 259
MspR9I CCNGG 2 cut(s) 353, 621
MvaI CCWGG 2 cut(s) 353, 621
MwoI GCNNNNNNNGC 2 cut(s) 203, 419
NcoI CCATGG 2 cut(s) 237, 546
NdeII GATC 1 cut(s) 403
NlaIII CATG 3 cut(s) 205, 241, 550
NlaIV GGNNCC 1 cut(s) 136
NmeAIII GCCGAG 1 cut(s) 475
NmuCI GTSAC 1 cut(s) 247
PcsI WCGNNNNNNNCGW 1 cut(s) 153
PdmI GAANNNNTTC 1 cut(s) 168
PfeI GAWTC 1 cut(s) 37
PflMI CCANNNNNTGG 1 cut(s) 620
PinAI ACCGGT 1 cut(s) 251
PkrI GCNGC 4 cut(s) 7, 184, 394, 424
Ppu21I YACGTR 2 cut(s) 127, 388
PpuMI RGGWCCY 1 cut(s) 135
Psp5II RGGWCCY 1 cut(s) 135
Psp6I CCWGG 2 cut(s) 351, 619
PspEI GGTNACC 1 cut(s) 247
PspFI CCCAGC 1 cut(s) 482
PspGI CCWGG 2 cut(s) 351, 619
PspN4I GGNNCC 1 cut(s) 136
PspPI GGNCC 1 cut(s) 135
PspPPI RGGWCCY 1 cut(s) 135
PsuI RGATCY 1 cut(s) 403
RsaI GTAC 1 cut(s) 317
RsaNI GTAC 1 cut(s) 316
SatI GCNGC 4 cut(s) 6, 183, 393, 423
Sau3AI GATC 1 cut(s) 403
Sau96I GGNCC 1 cut(s) 135
ScrFI CCNGG 2 cut(s) 353, 621
SfaNI GCATC 1 cut(s) 169
SinI GGWCC 1 cut(s) 135
SmlI CTYRAG 3 cut(s) 326, 344, 519
SmoI CTYRAG 3 cut(s) 326, 344, 519
SnaBI TACGTA 1 cut(s) 127
Sse9I AATT 6 cut(s) 23, 64, 79, 296, 501, 586
SsiI CCGC 6 cut(s) 5, 183, 230, 363, 393, 510
StyD4I CCNGG 2 cut(s) 351, 619
StyI CCWWGG 3 cut(s) 237, 426, 546
TaaI ACNGT 2 cut(s) 122, 338
TaiI ACGT 5 cut(s) 72, 129, 266, 372, 390
TaqI TCGA 8 cut(s) 51, 59, 141, 172, 266, 300, 333, 374
TasI AATT 6 cut(s) 23, 64, 79, 296, 501, 586
TauI GCSGC 3 cut(s) 8, 185, 395
TfiI GAWTC 1 cut(s) 37
TseFI GTSAC 1 cut(s) 247
TseI GCWGC 1 cut(s) 422
Tsp45I GTSAC 1 cut(s) 247
TspDTI ATGAA 1 cut(s) 597
TspGWI ACGGA 2 cut(s) 30, 458
Van91I CCANNNNNTGG 1 cut(s) 620
VpaK11BI GGWCC 1 cut(s) 135
XagI CCTNNNNNAGG 1 cut(s) 430
XapI RAATTY 3 cut(s) 23, 296, 586
XmnI GAANNNNTTC 1 cut(s) 168
ZraI GACGTC 1 cut(s) 264
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.