Rmu_sc0006239.1_g000005

GAG-pre-integrase domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0006239.1
OG0017395
Physical Location & Seq
Forward (+)
14659 .. 15303
645 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 645 bp
atggctatggcggcttctttgccccacaaattcggcgatttgattccgttcaagctcgatttatcgagcaattacgtcatctggaattacgcaatggcgacgcttcttcaagccttcaacctctacggttacgtagatgggaccttcgagaacgacaacggcgatgaggaagatgttcgatttgatgccgccgacgacaaggcggtcatggctctcatcaactccactcttgcaccgccgacgatggctcaggtgaccggttgccggacatcgagggaactttgggttagtctggagcaaaaattcgagacgatgagggagtacgctatcctcaagctcgaccgtcgcctcaagaacctggaactcaccgctaacgtctcgactgagggttacgtggccgccattgaagatctccgagcaaacttggctgccttgggaaggagatacacggacgccgaggtcattgaggtcgtcaagaacaatatagctgggggacttcgttttgcagttttcggcggagaagctcaagctgaaactcctcctcctcctcccatggagttgcacgacttctatgtgaagctacttgatgaaaatttcaggctttccaaactgaggttttcaccccctggctctctctatgcctaa
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

214

Amino Acids

23.9

Weight (kDa)

4.8

Isoelectric Point (pI)

44.46

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 32 - 155 6.4e-10 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) 203, 458
AciI CCGC 7 cut(s) 11, 189, 203, 236, 369, 399, 516
AcoI YGGCCR 1 cut(s) 396
AcsI RAATTY 3 cut(s) 29, 302, 592
AcyI GRCGYC 1 cut(s) 453
AfaI GTAC 1 cut(s) 323
AfiI CCNNNNNNNGG 3 cut(s) 264, 438, 612
AgeI ACCGGT 1 cut(s) 257
AgsI TTSAA 4 cut(s) 52, 110, 118, 407
AjnI CCWGG 2 cut(s) 357, 625
AluBI AGCT 6 cut(s) 55, 337, 488, 524, 530, 580
AluI AGCT 6 cut(s) 55, 337, 488, 524, 530, 580
Alw26I GTCTC 2 cut(s) 302, 382
AoxI GGCC 1 cut(s) 396
ApeKI GCWGC 1 cut(s) 428
ApoI RAATTY 3 cut(s) 29, 302, 592
AsiGI ACCGGT 1 cut(s) 257
Asp700I GAANNNNTTC 1 cut(s) 174
AspS9I GGNCC 1 cut(s) 141
AsuHPI GGTGA 3 cut(s) 265, 358, 612
AvaII GGWCC 1 cut(s) 141
BbvI GCAGC 1 cut(s) 415
BccI CCATC 2 cut(s) 131, 238
BceAI ACGGC 1 cut(s) 175
BciT130I CCWGG 2 cut(s) 359, 627
BcoDI GTCTC 2 cut(s) 302, 382
BglII AGATCT 1 cut(s) 409
BisI GCNGC 4 cut(s) 12, 189, 399, 429
BlsI GCNGC 4 cut(s) 13, 190, 400, 430
Bme1390I CCNGG 2 cut(s) 359, 627
Bme18I GGWCC 1 cut(s) 141
BmgT120I GGNCC 1 cut(s) 141
BmiI GGNNCC 1 cut(s) 142
BmrFI CCNGG 2 cut(s) 359, 627
BmsI GCATC 1 cut(s) 175
BpmI CTGGAG 1 cut(s) 314
Bpu10I CCTNAGC 1 cut(s) 249
BpuEI CTTGAG 3 cut(s) 317, 335, 510
BsaAI YACGTR 2 cut(s) 133, 394
BsaHI GRCGYC 1 cut(s) 453
BsaJI CCNNGG 4 cut(s) 432, 456, 552, 625
BsaWI WCCGGW 1 cut(s) 257
BsaXI ACNNNNNCTCC 2 cut(s) 526, 556
Bsc4I CCNNNNNNNGG 3 cut(s) 264, 438, 612
Bse118I RCCGGY 1 cut(s) 257
Bse3DI GCAATG 1 cut(s) 99
BseBI CCWGG 2 cut(s) 359, 627
BseDI CCNNGG 4 cut(s) 432, 456, 552, 625
BseLI CCNNNNNNNGG 3 cut(s) 264, 438, 612
BseMI GCAATG 1 cut(s) 99
BseMII CTCAG 3 cut(s) 263, 375, 602
BseRI GAGGAG 4 cut(s) 528, 531, 534, 537
BseXI GCAGC 1 cut(s) 415
BseYI CCCAGC 1 cut(s) 488
Bsh1285I CGRYCG 1 cut(s) 343
BshFI GGCC 1 cut(s) 398
BshTI ACCGGT 1 cut(s) 257
BsiEI CGRYCG 1 cut(s) 343
BsiSI CCGG 2 cut(s) 258, 265
BslFI GGGAC 2 cut(s) 154, 507
BslI CCNNNNNNNGG 3 cut(s) 264, 438, 612
BsmAI GTCTC 2 cut(s) 302, 382
BsmBI CGTCTC 2 cut(s) 302, 382
BsmFI GGGAC 2 cut(s) 154, 507
BsnI GGCC 1 cut(s) 398
Bsp143I GATC 1 cut(s) 409
Bsp19I CCATGG 1 cut(s) 552
BspACI CCGC 7 cut(s) 11, 189, 203, 236, 369, 399, 516
BspANI GGCC 1 cut(s) 398
BspCNI CTCAG 3 cut(s) 262, 376, 603
BspLI GGNNCC 1 cut(s) 142
BsrDI GCAATG 1 cut(s) 99
BsrFI RCCGGY 1 cut(s) 257
BssAI RCCGGY 1 cut(s) 257
BssECI CCNNGG 4 cut(s) 432, 456, 552, 625
BssMI GATC 1 cut(s) 409
BssNI GRCGYC 1 cut(s) 453
BssT1I CCWWGG 2 cut(s) 432, 552
Bst2UI CCWGG 2 cut(s) 359, 627
Bst4CI ACNGT 2 cut(s) 128, 344
BstACI GRCGYC 1 cut(s) 453
BstBAI YACGTR 2 cut(s) 133, 394
BstDEI CTNAG 3 cut(s) 249, 384, 611
BstDSI CCRYGG 1 cut(s) 552
BstEII GGTNACC 1 cut(s) 253
BstENI CCTNNNNNAGG 1 cut(s) 436
BstKTI GATC 1 cut(s) 412
BstMAI GTCTC 2 cut(s) 302, 382
BstMBI GATC 1 cut(s) 409
BstMCI CGRYCG 1 cut(s) 343
BstMWI GCNNNNNNNGC 3 cut(s) 11, 209, 425
BstNI CCWGG 2 cut(s) 359, 627
BstPI GGTNACC 1 cut(s) 253
BstSCI CCNGG 2 cut(s) 357, 625
BstSNI TACGTA 1 cut(s) 133
BstV1I GCAGC 1 cut(s) 415
BstX2I RGATCY 1 cut(s) 409
BstYI RGATCY 1 cut(s) 409
BsuRI GGCC 1 cut(s) 398
BtgI CCRYGG 1 cut(s) 552
BtgZI GCGATG 1 cut(s) 177
Cfr10I RCCGGY 1 cut(s) 257
Cfr13I GGNCC 1 cut(s) 141
CseI GACGC 2 cut(s) 109, 461
Csp6I GTAC 1 cut(s) 322
CspAI ACCGGT 1 cut(s) 257
CviAII CATG 2 cut(s) 208, 553
CviQI GTAC 1 cut(s) 322
DdeI CTNAG 3 cut(s) 249, 384, 611
DpnI GATC 1 cut(s) 411
DpnII GATC 1 cut(s) 409
DrdI GACNNNNNNGTC 2 cut(s) 203, 458
DseDI GACNNNNNNGTC 2 cut(s) 203, 458
EaeI YGGCCR 1 cut(s) 396
EciI GGCGGA 1 cut(s) 531
Eco105I TACGTA 1 cut(s) 133
Eco130I CCWWGG 2 cut(s) 432, 552
Eco47I GGWCC 1 cut(s) 141
Eco91I GGTNACC 1 cut(s) 253
EcoNI CCTNNNNNAGG 1 cut(s) 436
EcoO109I RGGNCCY 1 cut(s) 141
EcoO65I GGTNACC 1 cut(s) 253
EcoRII CCWGG 2 cut(s) 357, 625
EcoT14I CCWWGG 2 cut(s) 432, 552
ErhI CCWWGG 2 cut(s) 432, 552
Esp3I CGTCTC 2 cut(s) 302, 382
FaeI CATG 2 cut(s) 211, 556
FaiI YATR 6 cut(s) 8, 209, 485, 554, 573, 639
FaqI GGGAC 2 cut(s) 154, 507
FatI CATG 2 cut(s) 207, 552
Fnu4HI GCNGC 4 cut(s) 12, 189, 399, 429
Fsp4HI GCNGC 4 cut(s) 12, 189, 399, 429
GluI GCNGC 4 cut(s) 12, 189, 399, 429
GsaI CCCAGC 1 cut(s) 492
GsuI CTGGAG 1 cut(s) 314
HaeIII GGCC 1 cut(s) 398
HapII CCGG 2 cut(s) 258, 265
HgaI GACGC 2 cut(s) 109, 461
Hin1I GRCGYC 1 cut(s) 453
Hin1II CATG 2 cut(s) 211, 556
HinfI GANTC 1 cut(s) 43
HpaII CCGG 2 cut(s) 258, 265
HphI GGTGA 3 cut(s) 265, 358, 612
Hpy188I TCNGA 1 cut(s) 416
Hpy188III TCNNGA 7 cut(s) 82, 148, 293, 307, 352, 379, 475
Hpy99I CGWCG 4 cut(s) 103, 197, 244, 348
HpyAV CCTTC 3 cut(s) 124, 154, 432
HpyCH4III ACNGT 2 cut(s) 128, 344
HpyCH4IV ACGT 4 cut(s) 75, 132, 375, 393
HpyCH4V TGCA 3 cut(s) 233, 506, 562
HpyF10VI GCNNNNNNNGC 3 cut(s) 11, 209, 425
HpyF3I CTNAG 3 cut(s) 249, 384, 611
HpySE526I ACGT 4 cut(s) 75, 132, 375, 393
Hsp92I GRCGYC 1 cut(s) 453
Hsp92II CATG 2 cut(s) 211, 556
Kzo9I GATC 1 cut(s) 409
LmnI GCTCC 1 cut(s) 295
Lsp1109I GCAGC 1 cut(s) 415
LweI GCATC 1 cut(s) 175
MaeII ACGT 4 cut(s) 75, 132, 375, 393
MaeIII GTNAC 3 cut(s) 128, 253, 389
MalI GATC 1 cut(s) 411
MboI GATC 1 cut(s) 409
MboII GAAGA 3 cut(s) 98, 182, 419
MflI RGATCY 1 cut(s) 409
MluCI AATT 5 cut(s) 29, 70, 85, 302, 592
MroXI GAANNNNTTC 1 cut(s) 174
MspI CCGG 2 cut(s) 258, 265
MspR9I CCNGG 2 cut(s) 359, 627
MvaI CCWGG 2 cut(s) 359, 627
MwoI GCNNNNNNNGC 3 cut(s) 11, 209, 425
NcoI CCATGG 1 cut(s) 552
NdeII GATC 1 cut(s) 409
NlaIII CATG 2 cut(s) 211, 556
NlaIV GGNNCC 1 cut(s) 142
NmeAIII GCCGAG 1 cut(s) 481
NmuCI GTSAC 1 cut(s) 253
PcsI WCGNNNNNNNCGW 1 cut(s) 159
PdmI GAANNNNTTC 1 cut(s) 174
PfeI GAWTC 1 cut(s) 43
PinAI ACCGGT 1 cut(s) 257
PkrI GCNGC 4 cut(s) 13, 190, 400, 430
Ppu21I YACGTR 2 cut(s) 133, 394
PpuMI RGGWCCY 1 cut(s) 141
Psp5II RGGWCCY 1 cut(s) 141
Psp6I CCWGG 2 cut(s) 357, 625
PspEI GGTNACC 1 cut(s) 253
PspFI CCCAGC 1 cut(s) 488
PspGI CCWGG 2 cut(s) 357, 625
PspN4I GGNNCC 1 cut(s) 142
PspPI GGNCC 1 cut(s) 141
PspPPI RGGWCCY 1 cut(s) 141
PsuI RGATCY 1 cut(s) 409
RsaI GTAC 1 cut(s) 323
RsaNI GTAC 1 cut(s) 322
SatI GCNGC 4 cut(s) 12, 189, 399, 429
Sau3AI GATC 1 cut(s) 409
Sau96I GGNCC 1 cut(s) 141
ScrFI CCNGG 2 cut(s) 359, 627
SfaNI GCATC 1 cut(s) 175
SinI GGWCC 1 cut(s) 141
SmlI CTYRAG 3 cut(s) 332, 350, 525
SmoI CTYRAG 3 cut(s) 332, 350, 525
SnaBI TACGTA 1 cut(s) 133
Sse9I AATT 5 cut(s) 29, 70, 85, 302, 592
SsiI CCGC 7 cut(s) 11, 189, 203, 236, 369, 399, 516
StyD4I CCNGG 2 cut(s) 357, 625
StyI CCWWGG 2 cut(s) 432, 552
TaaI ACNGT 2 cut(s) 128, 344
TaiI ACGT 4 cut(s) 78, 135, 378, 396
TaqI TCGA 8 cut(s) 57, 65, 147, 178, 272, 306, 339, 380
TasI AATT 5 cut(s) 29, 70, 85, 302, 592
TauI GCSGC 3 cut(s) 14, 191, 401
TfiI GAWTC 1 cut(s) 43
TseFI GTSAC 1 cut(s) 253
TseI GCWGC 1 cut(s) 428
Tsp45I GTSAC 1 cut(s) 253
TspDTI ATGAA 1 cut(s) 603
TspGWI ACGGA 2 cut(s) 36, 464
VpaK11BI GGWCC 1 cut(s) 141
XagI CCTNNNNNAGG 1 cut(s) 436
XapI RAATTY 3 cut(s) 29, 302, 592
XmnI GAANNNNTTC 1 cut(s) 174
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.