Rw2G001150

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0017871
Physical Location & Seq
Forward (+)
984937 .. 985862
926 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G001150.1

Sequence Viewer

Length: 705 bp
ATGAAAGAAGATGAATTGCTTAAAGAATACTTTACTAGATTGTCTGATGTTGTGAATCAAATGAAAAGCTACGGAGAAGATTTTCCAAATAGAAGAGTTCTGCAAAAAATACTCATAAGCTTAACCCCAAAATATGATCCTATAGTTTCGGTTCTTATAGAAACCAAAGACATGGAAACAGCAGGAATTCAAGAGATTATGGGGTCAATCAAAGTTTTTGATCAGCAATTAGACAGACATGCTGAGAATGCAACATATATAGAGATTGCAACTACAAAAGAAACCAACACAGCCAACTATACTGAGCAAGTAGAAGCAAAGCAAGCAGATGCAGATGGAGATTTATTCTTTGCATGTCAAGCTGCAACGATGCAGACGGATGATAATGTCTGGTATATAGACAGTGGGTGTAGGGATCACATGACAGCAAATAGGTCTCTCCTCATTGATCTTGATACCTCCATAACAGCCCAAGTGAAAATGGGAAATGGAGCCTTGGTTCAAGCAACTGGCAGAGGTACACTTGCAATTGAAACCAAGAAAGGGAAAAGGTATATAAGAGAAGTAATGTTCGTTCCAGGATGGGACCAAAACTTGCTAAGTGTAGGAATGGAATATGGGCACTTCTTATTGTTTGGTGATGAACTGATGATGAAGTCGACATCTATGATGATAGAAAACTCAAGAATCTTGTTGCAAGGATGA
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
DUF4219 Retrotran_gag_2 gag_pre-integrs zf-CCHC

Protein Analysis

234

Amino Acids

26.45

Weight (kDa)

4.79

Isoelectric Point (pI)

31.65

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 1 - 66 6.2e-08 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 131 - 203 2e-21 Pol polyprotein, beta-barrel domain
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: OG0017871)

Species Orthologous Gene IDs
malus_domestica MD09G1281800.v1.1
pyrus_communis pycom12g08370 pycom15g03640 pycom15g18740 pycom15g38670
rosa_chinensis RchiOBHm_Chr1g0356321
rosa_multiflora Rmu_sc0000605.1_g000016
rosa_roxburghii Rroxscaffold_2G00133080 Rroxscaffold_4G00285200 Rroxscaffold_7G00191550
rosa_wichuraiana Rw2G001150

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 659
AclWI GGATC 2 cut(s) 131, 423
AcsI RAATTY 1 cut(s) 186
AfaI GTAC 1 cut(s) 520
AfiI CCNNNNNNNGG 1 cut(s) 543
AgsI TTSAA 3 cut(s) 191, 503, 533
AjnI CCWGG 1 cut(s) 577
AloI GAACNNNNNNTCC 2 cut(s) 483, 515
AluBI AGCT 3 cut(s) 69, 120, 362
AluI AGCT 3 cut(s) 69, 120, 362
Alw26I GTCTC 1 cut(s) 441
AlwI GGATC 2 cut(s) 131, 423
ApeKI GCWGC 1 cut(s) 362
ApoI RAATTY 1 cut(s) 186
Asp700I GAANNNNTTC 1 cut(s) 81
AspS9I GGNCC 1 cut(s) 586
AsuHPI GGTGA 1 cut(s) 650
AvaII GGWCC 1 cut(s) 586
BaeGI GKGCMC 1 cut(s) 624
BbvI GCAGC 1 cut(s) 349
BccI CCATC 2 cut(s) 329, 576
BciT130I CCWGG 1 cut(s) 579
BclI TGATCA 1 cut(s) 220
BcoDI GTCTC 1 cut(s) 441
BfaI CTAG 1 cut(s) 36
BfmI CTRYAG 1 cut(s) 141
BisI GCNGC 1 cut(s) 363
BlsI GCNGC 1 cut(s) 364
Bme1390I CCNGG 1 cut(s) 579
Bme18I GGWCC 1 cut(s) 586
BmgT120I GGNCC 1 cut(s) 586
BmiI GGNNCC 2 cut(s) 493, 587
BmrFI CCNGG 1 cut(s) 579
BmsI GCATC 2 cut(s) 319, 360
BpuEI CTTGAG 1 cut(s) 667
BsaI GGTCTC 1 cut(s) 441
BsaJI CCNNGG 1 cut(s) 495
BsaXI ACNNNNNCTCC 2 cut(s) 483, 513
Bsc4I CCNNNNNNNGG 1 cut(s) 543
Bse1I ACTGG 1 cut(s) 514
BseBI CCWGG 1 cut(s) 579
BseDI CCNNGG 1 cut(s) 495
BseGI GGATG 2 cut(s) 385, 587
BseLI CCNNNNNNNGG 1 cut(s) 543
BseMII CTCAG 2 cut(s) 234, 294
BseNI ACTGG 1 cut(s) 514
BseRI GAGGAG 1 cut(s) 431
BseSI GKGCMC 1 cut(s) 624
BseXI GCAGC 1 cut(s) 349
BslFI GGGAC 1 cut(s) 599
BslI CCNNNNNNNGG 1 cut(s) 543
BsmAI GTCTC 1 cut(s) 441
BsmFI GGGAC 1 cut(s) 599
BsmI GAATGC 1 cut(s) 253
Bso31I GGTCTC 1 cut(s) 441
Bsp1286I GDGCHC 1 cut(s) 624
Bsp143I GATC 4 cut(s) 136, 220, 415, 448
BspCNI CTCAG 2 cut(s) 235, 295
BspLI GGNNCC 2 cut(s) 493, 587
BspPI GGATC 2 cut(s) 131, 423
BspTNI GGTCTC 1 cut(s) 441
BsrI ACTGG 1 cut(s) 514
BssECI CCNNGG 1 cut(s) 495
BssMI GATC 4 cut(s) 136, 220, 415, 448
BssT1I CCWWGG 1 cut(s) 495
Bst2UI CCWGG 1 cut(s) 579
Bst4CI ACNGT 1 cut(s) 404
Bst6I CTCTTC 1 cut(s) 88
BstC8I GCNNGC 1 cut(s) 324
BstDEI CTNAG 3 cut(s) 243, 303, 599
BstF5I GGATG 2 cut(s) 385, 587
BstKTI GATC 4 cut(s) 139, 223, 418, 451
BstMAI GTCTC 1 cut(s) 441
BstMBI GATC 4 cut(s) 136, 220, 415, 448
BstMWI GCNNNNNNNGC 3 cut(s) 248, 323, 359
BstNI CCWGG 1 cut(s) 579
BstNSI RCATGY 2 cut(s) 242, 357
BstSCI CCNGG 1 cut(s) 577
BstSFI CTRYAG 1 cut(s) 141
BstSLI GKGCMC 1 cut(s) 624
BstV1I GCAGC 1 cut(s) 349
BstXI CCANNNNNNTGG 1 cut(s) 172
BtsCI GGATG 2 cut(s) 385, 587
BtsIMutI CAGTG 1 cut(s) 409
Cac8I GCNNGC 1 cut(s) 324
Cfr13I GGNCC 1 cut(s) 586
Csp6I GTAC 1 cut(s) 519
CviAII CATG 4 cut(s) 172, 239, 354, 421
CviJI RGCY 6 cut(s) 69, 120, 293, 362, 470, 494
CviKI_1 RGCY 6 cut(s) 69, 120, 293, 362, 470, 494
CviQI GTAC 1 cut(s) 519
DdeI CTNAG 3 cut(s) 243, 303, 599
DpnI GATC 4 cut(s) 138, 222, 417, 450
DpnII GATC 4 cut(s) 136, 220, 415, 448
Eam1104I CTCTTC 1 cut(s) 88
EarI CTCTTC 1 cut(s) 88
Eco130I CCWWGG 1 cut(s) 495
Eco31I GGTCTC 1 cut(s) 441
Eco47I GGWCC 1 cut(s) 586
EcoRI GAATTC 1 cut(s) 186
EcoRII CCWGG 1 cut(s) 577
EcoT14I CCWWGG 1 cut(s) 495
ErhI CCWWGG 1 cut(s) 495
FaeI CATG 4 cut(s) 175, 242, 357, 424
FaqI GGGAC 1 cut(s) 599
FatI CATG 4 cut(s) 171, 238, 353, 420
FbaI TGATCA 1 cut(s) 220
FblI GTMKAC 1 cut(s) 659
Fnu4HI GCNGC 1 cut(s) 363
FokI GGATG 2 cut(s) 392, 594
Fsp4HI GCNGC 1 cut(s) 363
FspBI CTAG 1 cut(s) 36
GluI GCNGC 1 cut(s) 363
Hin1II CATG 4 cut(s) 175, 242, 357, 424
HincII GTYRAC 1 cut(s) 660
HindII GTYRAC 1 cut(s) 660
HindIII AAGCTT 1 cut(s) 118
HinfI GANTC 2 cut(s) 55, 687
HphI GGTGA 1 cut(s) 650
Hpy166II GTNNAC 2 cut(s) 521, 660
Hpy188I TCNGA 1 cut(s) 46
Hpy188III TCNNGA 3 cut(s) 191, 452, 684
Hpy8I GTNNAC 2 cut(s) 521, 660
HpyCH4III ACNGT 1 cut(s) 404
HpyCH4V TGCA 9 cut(s) 103, 251, 269, 332, 353, 365, 373, 527, 697
HpyF10VI GCNNNNNNNGC 3 cut(s) 248, 323, 359
HpyF3I CTNAG 3 cut(s) 243, 303, 599
Hsp92II CATG 4 cut(s) 175, 242, 357, 424
Ksp22I TGATCA 1 cut(s) 220
Kzo9I GATC 4 cut(s) 136, 220, 415, 448
LmnI GCTCC 1 cut(s) 491
LpnPI CCDG 5 cut(s) 168, 376, 495, 564, 591
Lsp1109I GCAGC 1 cut(s) 349
LweI GCATC 2 cut(s) 319, 360
MaeI CTAG 1 cut(s) 36
MalI GATC 4 cut(s) 138, 222, 417, 450
MboI GATC 4 cut(s) 136, 220, 415, 448
MboII GAAGA 3 cut(s) 20, 89, 105
MfeI CAATTG 1 cut(s) 528
MhlI GDGCHC 1 cut(s) 624
MluCI AATT 4 cut(s) 14, 186, 227, 528
MnlI CCTC 3 cut(s) 452, 469, 509
MroXI GAANNNNTTC 1 cut(s) 81
MseI TTAA 2 cut(s) 21, 122
MspR9I CCNGG 1 cut(s) 579
MunI CAATTG 1 cut(s) 528
Mva1269I GAATGC 1 cut(s) 253
MvaI CCWGG 1 cut(s) 579
MwoI GCNNNNNNNGC 3 cut(s) 248, 323, 359
NdeII GATC 4 cut(s) 136, 220, 415, 448
NlaIII CATG 4 cut(s) 175, 242, 357, 424
NlaIV GGNNCC 2 cut(s) 493, 587
NspI RCATGY 2 cut(s) 242, 357
PctI GAATGC 1 cut(s) 253
PdmI GAANNNNTTC 1 cut(s) 81
PfeI GAWTC 2 cut(s) 55, 687
PfoI TCCNGGA 1 cut(s) 577
PkrI GCNGC 1 cut(s) 364
Psp6I CCWGG 1 cut(s) 577
PspGI CCWGG 1 cut(s) 577
PspN4I GGNNCC 2 cut(s) 493, 587
PspPI GGNCC 1 cut(s) 586
PsrI GAACNNNNNNTAC 2 cut(s) 558, 590
RsaI GTAC 1 cut(s) 520
RsaNI GTAC 1 cut(s) 519
SalI GTCGAC 1 cut(s) 658
SaqAI TTAA 2 cut(s) 21, 122
SatI GCNGC 1 cut(s) 363
Sau3AI GATC 4 cut(s) 136, 220, 415, 448
Sau96I GGNCC 1 cut(s) 586
ScrFI CCNGG 1 cut(s) 579
SduI GDGCHC 1 cut(s) 624
SetI ASST 7 cut(s) 71, 122, 364, 437, 461, 520, 554
SfaNI GCATC 2 cut(s) 319, 360
SfcI CTRYAG 1 cut(s) 141
SinI GGWCC 1 cut(s) 586
SmlI CTYRAG 1 cut(s) 682
SmoI CTYRAG 1 cut(s) 682
Sse9I AATT 4 cut(s) 14, 186, 227, 528
SspMI CTAG 1 cut(s) 36
StyD4I CCNGG 1 cut(s) 577
StyI CCWWGG 1 cut(s) 495
TaaI ACNGT 1 cut(s) 404
TaqI TCGA 1 cut(s) 659
TasI AATT 4 cut(s) 14, 186, 227, 528
TfiI GAWTC 2 cut(s) 55, 687
Tru1I TTAA 2 cut(s) 21, 122
Tru9I TTAA 2 cut(s) 21, 122
TscAI CASTG 1 cut(s) 409
TseI GCWGC 1 cut(s) 362
TspDTI ATGAA 5 cut(s) 17, 27, 77, 657, 668
TspGWI ACGGA 2 cut(s) 87, 392
TspRI CASTG 1 cut(s) 409
VpaK11BI GGWCC 1 cut(s) 586
XapI RAATTY 1 cut(s) 186
XceI RCATGY 2 cut(s) 242, 357
XmiI GTMKAC 1 cut(s) 659
XmnI GAANNNNTTC 1 cut(s) 81
XspI CTAG 1 cut(s) 36
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.