Rw5G015820

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0002402
Physical Location & Seq
Forward (+)
19660058 .. 19662395
2338 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G015820.1

Sequence Viewer

Length: 513 bp
ATGTCAGGACATCCTATCACCAAAATTCTCAATGAAAATCGTCTTGAGGGCCCAAACTTCAATGGCTGGCTCCGCAATTTGAAAATTGTATTGACATTCGATAAGATTGCTTATGTCTTACAAAATGCACCCCCTCACACTCCTTTGGCTCAAGATGCAACCGATGAGCAACGTGTTGCTTATCAAAAGCATAAGGATGATGACACTCAAGCTAAATGTGTTATGCTTGCATCCATGAACTCACAACTTCAGAAGCAACATGAGAATATGGATAGTGCCAGTTCTATATTACTCCATCTCACTGAATTGTTTGGTGAAAGAAATAGAAATGTGCGCTTCACAGTAGTCAATGAGCTTGTCAAGACAAAACATGTGAGGGGTGCACCTGTGCATCAACATGGTCTAAAAATGATAGACCTTATTGAGCAAATTCAAGACCTTGGATTTGCACTTGATGCAGAGCTAGCTCAAGATCTTCTTCTAACCTCCCTAGATGATTCATTTTCTCATTAA
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 zf-CCHC

Protein Analysis

170

Amino Acids

19.26

Weight (kDa)

5.95

Isoelectric Point (pI)

38.12

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 36 - 169 6e-11 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 73
AcsI RAATTY 2 cut(s) 24, 429
AcuI CTGAAG 1 cut(s) 233
AflIII ACRYGT 2 cut(s) 172, 370
AgsI TTSAA 3 cut(s) 61, 82, 434
AluBI AGCT 4 cut(s) 212, 355, 463, 467
AluI AGCT 4 cut(s) 212, 355, 463, 467
Alw21I GWGCWC 1 cut(s) 385
Alw44I GTGCAC 1 cut(s) 381
AoxI GGCC 1 cut(s) 49
ApaI GGGCCC 1 cut(s) 53
ApaLI GTGCAC 1 cut(s) 381
ApoI RAATTY 2 cut(s) 24, 429
ArsI GACNNNNNNTTYG 2 cut(s) 428, 460
AspLEI GCGC 1 cut(s) 336
AspS9I GGNCC 2 cut(s) 49, 50
AsuHPI GGTGA 2 cut(s) 10, 326
AsuNHI GCTAGC 1 cut(s) 463
BaeGI GKGCMC 2 cut(s) 53, 385
BanII GRGCYC 1 cut(s) 53
Bbv12I GWGCWC 1 cut(s) 385
BccI CCATC 1 cut(s) 303
BcgI CGANNNNNNTGC 2 cut(s) 89, 123
BfaI CTAG 2 cut(s) 464, 491
BglII AGATCT 1 cut(s) 472
BmgT120I GGNCC 2 cut(s) 49, 50
BmiI GGNNCC 2 cut(s) 51, 71
BmsI GCATC 4 cut(s) 145, 239, 400, 445
BmtI GCTAGC 1 cut(s) 467
BpuEI CTTGAG 4 cut(s) 65, 135, 192, 453
BsaJI CCNNGG 1 cut(s) 439
Bse1I ACTGG 1 cut(s) 279
BseDI CCNNGG 1 cut(s) 439
BseGI GGATG 3 cut(s) 10, 202, 230
BseNI ACTGG 1 cut(s) 279
BseSI GKGCMC 2 cut(s) 53, 385
BshFI GGCC 1 cut(s) 51
BsiHKAI GWGCWC 1 cut(s) 385
BsnI GGCC 1 cut(s) 51
Bsp120I GGGCCC 1 cut(s) 49
Bsp1286I GDGCHC 2 cut(s) 53, 385
Bsp143I GATC 1 cut(s) 472
BspACI CCGC 1 cut(s) 73
BspANI GGCC 1 cut(s) 51
BspLI GGNNCC 2 cut(s) 51, 71
BspOI GCTAGC 1 cut(s) 467
BsrI ACTGG 1 cut(s) 279
BssECI CCNNGG 1 cut(s) 439
BssMI GATC 1 cut(s) 472
BssT1I CCWWGG 1 cut(s) 439
Bst4CI ACNGT 1 cut(s) 343
BstAPI GCANNNNNTGC 1 cut(s) 455
BstC8I GCNNGC 3 cut(s) 68, 228, 465
BstF5I GGATG 3 cut(s) 10, 202, 230
BstHHI GCGC 1 cut(s) 336
BstKTI GATC 1 cut(s) 475
BstMBI GATC 1 cut(s) 472
BstMWI GCNNNNNNNGC 4 cut(s) 72, 155, 455, 464
BstNSI RCATGY 1 cut(s) 374
BstSLI GKGCMC 2 cut(s) 53, 385
BstX2I RGATCY 1 cut(s) 472
BstYI RGATCY 1 cut(s) 472
BsuRI GGCC 1 cut(s) 51
BtsCI GGATG 3 cut(s) 10, 202, 230
BtsIMutI CAGTG 1 cut(s) 300
Cac8I GCNNGC 3 cut(s) 68, 228, 465
CfoI GCGC 1 cut(s) 336
Cfr13I GGNCC 2 cut(s) 49, 50
CviAII CATG 4 cut(s) 235, 260, 371, 398
CviJI RGCY 8 cut(s) 51, 66, 70, 149, 212, 355, 463, 467
CviKI_1 RGCY 8 cut(s) 51, 66, 70, 149, 212, 355, 463, 467
DpnI GATC 1 cut(s) 474
DpnII GATC 1 cut(s) 472
Eco130I CCWWGG 1 cut(s) 439
Eco24I GRGCYC 1 cut(s) 53
Eco57I CTGAAG 1 cut(s) 233
EcoO109I RGGNCCY 1 cut(s) 49
EcoT14I CCWWGG 1 cut(s) 439
EcoT38I GRGCYC 1 cut(s) 53
ErhI CCWWGG 1 cut(s) 439
FaeI CATG 4 cut(s) 238, 263, 374, 401
FaiI YATR 9 cut(s) 114, 192, 224, 236, 261, 269, 287, 372, 399
FalI AAGNNNNNCTT 2 cut(s) 462, 494
FatI CATG 4 cut(s) 234, 259, 370, 397
FokI GGATG 2 cut(s) 209, 217
FriOI GRGCYC 1 cut(s) 53
FspBI CTAG 2 cut(s) 464, 491
GlaI GCGC 1 cut(s) 335
HaeIII GGCC 1 cut(s) 51
HhaI GCGC 1 cut(s) 336
Hin1II CATG 4 cut(s) 238, 263, 374, 401
Hin6I GCGC 1 cut(s) 334
HinP1I GCGC 1 cut(s) 334
HinfI GANTC 1 cut(s) 497
HphI GGTGA 2 cut(s) 10, 326
Hpy166II GTNNAC 1 cut(s) 383
Hpy188I TCNGA 1 cut(s) 252
Hpy188III TCNNGA 6 cut(s) 6, 44, 152, 361, 434, 470
Hpy8I GTNNAC 1 cut(s) 383
HpyCH4III ACNGT 1 cut(s) 343
HpyCH4IV ACGT 1 cut(s) 172
HpyCH4V TGCA 7 cut(s) 128, 158, 230, 383, 391, 449, 458
HpyF10VI GCNNNNNNNGC 4 cut(s) 72, 155, 455, 464
HpySE526I ACGT 1 cut(s) 172
Hsp92II CATG 4 cut(s) 238, 263, 374, 401
HspAI GCGC 1 cut(s) 334
Kzo9I GATC 1 cut(s) 472
LmnI GCTCC 1 cut(s) 75
LpnPI CCDG 3 cut(s) 52, 292, 399
LweI GCATC 4 cut(s) 145, 239, 400, 445
MaeI CTAG 2 cut(s) 464, 491
MaeII ACGT 1 cut(s) 172
MalI GATC 1 cut(s) 474
MboI GATC 1 cut(s) 472
MboII GAAGA 2 cut(s) 467, 470
MflI RGATCY 1 cut(s) 472
MhlI GDGCHC 2 cut(s) 53, 385
MluCI AATT 5 cut(s) 24, 76, 84, 305, 429
MnlI CCTC 4 cut(s) 40, 144, 369, 496
MseI TTAA 1 cut(s) 511
MslI CAYNNNNRTG 2 cut(s) 195, 396
MwoI GCNNNNNNNGC 4 cut(s) 72, 155, 455, 464
NdeII GATC 1 cut(s) 472
NheI GCTAGC 1 cut(s) 463
NlaIII CATG 4 cut(s) 238, 263, 374, 401
NlaIV GGNNCC 2 cut(s) 51, 71
NspI RCATGY 1 cut(s) 374
PciI ACATGT 1 cut(s) 370
PfeI GAWTC 1 cut(s) 497
PscI ACATGT 1 cut(s) 370
PspN4I GGNNCC 2 cut(s) 51, 71
PspOMI GGGCCC 1 cut(s) 49
PspPI GGNCC 2 cut(s) 49, 50
PsuI RGATCY 1 cut(s) 472
RseI CAYNNNNRTG 2 cut(s) 195, 396
SaqAI TTAA 1 cut(s) 511
Sau3AI GATC 1 cut(s) 472
Sau96I GGNCC 2 cut(s) 49, 50
SduI GDGCHC 2 cut(s) 53, 385
SetI ASST 9 cut(s) 175, 214, 357, 388, 420, 441, 465, 469, 488
SfaNI GCATC 4 cut(s) 145, 239, 400, 445
SmiMI CAYNNNNRTG 2 cut(s) 195, 396
SmlI CTYRAG 4 cut(s) 44, 150, 207, 468
SmoI CTYRAG 4 cut(s) 44, 150, 207, 468
Sse9I AATT 5 cut(s) 24, 76, 84, 305, 429
SsiI CCGC 1 cut(s) 73
SspMI CTAG 2 cut(s) 464, 491
StyI CCWWGG 1 cut(s) 439
TaaI ACNGT 1 cut(s) 343
TaiI ACGT 1 cut(s) 175
TaqI TCGA 1 cut(s) 99
TasI AATT 5 cut(s) 24, 76, 84, 305, 429
TfiI GAWTC 1 cut(s) 497
Tru1I TTAA 1 cut(s) 511
Tru9I TTAA 1 cut(s) 511
TscAI CASTG 1 cut(s) 307
TspDTI ATGAA 3 cut(s) 48, 251, 489
TspRI CASTG 1 cut(s) 307
VneI GTGCAC 1 cut(s) 381
XapI RAATTY 2 cut(s) 24, 429
XceI RCATGY 1 cut(s) 374
XspI CTAG 2 cut(s) 464, 491
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.