Rw1G011890

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr1
OG0002402
Physical Location & Seq
Forward (+)
26688464 .. 26690784
2321 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw1G011890.1

Sequence Viewer

Length: 513 bp
ATGTCAGGACATCCTATCACCAAAATTCTCAACGAGAATCGTCTTGAGGGCTCAAACTTCAATGAGTGGCTCCGCAATTTGAAAATTGTATTGACATTCGATAAGATCGCTTATGTCTTACAAAATGCACCTCCTCACACTCCTTTGGCTCAAAATGCAACTAGTGAGCAACGTGTTGCTTATCAAAAGCATAAGGATGATGACACTCAAGCCAAATGTGTTATGCTTGCATCCATGAACTCACAACTTCAGAAGCAACATGAGAATGTGGATAACGCCATTTCTATATTACTCCATCTCACTGAATTGTTTGGTGAGAGAAATAGAAATGTGCGCTTCATAGCTGTCAATGAGCTTGTCAAGACAAAACATGTGAGGGGTGCTCCTGTGCATCAACATGTTCTCAAAATGATAGGTCTTATTGAGAAAATTCAAGACCTAGGATTTGCAATTGATCCGGACCTAGCTCAAGATCTTCTTCTATCCTCCCTAGATGATTCATTTTCTCATTAA
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

Protein Analysis

170

Amino Acids

19.28

Weight (kDa)

6.49

Isoelectric Point (pI)

33.91

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 30 - 169 3.4e-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)
AccIII TCCGGA 1 cut(s) 457
AciI CCGC 1 cut(s) 73
AclWI GGATC 1 cut(s) 449
AcsI RAATTY 2 cut(s) 24, 429
AcuI CTGAAG 1 cut(s) 233
AflIII ACRYGT 3 cut(s) 172, 370, 397
AgsI TTSAA 3 cut(s) 61, 82, 434
AhlI ACTAGT 1 cut(s) 161
AluBI AGCT 3 cut(s) 344, 355, 467
AluI AGCT 3 cut(s) 344, 355, 467
Alw21I GWGCWC 1 cut(s) 385
AlwI GGATC 1 cut(s) 449
Aor13HI TCCGGA 1 cut(s) 457
ApoI RAATTY 2 cut(s) 24, 429
ArsI GACNNNNNNTTYG 2 cut(s) 428, 460
AspA2I CCTAGG 1 cut(s) 439
AspLEI GCGC 1 cut(s) 336
AspS9I GGNCC 1 cut(s) 460
AsuHPI GGTGA 2 cut(s) 10, 326
AvaII GGWCC 1 cut(s) 460
AvrII CCTAGG 1 cut(s) 439
BanII GRGCYC 1 cut(s) 53
Bbv12I GWGCWC 1 cut(s) 385
BccI CCATC 1 cut(s) 303
BcuI ACTAGT 1 cut(s) 161
BfaI CTAG 4 cut(s) 162, 440, 464, 491
BglII AGATCT 1 cut(s) 472
BlnI CCTAGG 1 cut(s) 439
Bme18I GGWCC 1 cut(s) 460
BmgT120I GGNCC 1 cut(s) 460
BmiI GGNNCC 1 cut(s) 71
BmsI GCATC 2 cut(s) 239, 400
BplI GAGNNNNNCTC 2 cut(s) 367, 399
BpuEI CTTGAG 3 cut(s) 65, 192, 453
BsaJI CCNNGG 1 cut(s) 439
BsaWI WCCGGW 1 cut(s) 457
BseAI TCCGGA 1 cut(s) 457
BseDI CCNNGG 1 cut(s) 439
BseGI GGATG 3 cut(s) 10, 202, 230
BseRI GAGGAG 1 cut(s) 123
BsiHKAI GWGCWC 1 cut(s) 385
BsiSI CCGG 1 cut(s) 458
Bsp1286I GDGCHC 2 cut(s) 53, 385
Bsp13I TCCGGA 1 cut(s) 457
Bsp143I GATC 3 cut(s) 105, 454, 472
BspACI CCGC 1 cut(s) 73
BspEI TCCGGA 1 cut(s) 457
BspLI GGNNCC 1 cut(s) 71
BspPI GGATC 1 cut(s) 449
BssECI CCNNGG 1 cut(s) 439
BssMI GATC 3 cut(s) 105, 454, 472
BssT1I CCWWGG 1 cut(s) 439
BstC8I GCNNGC 1 cut(s) 228
BstF5I GGATG 3 cut(s) 10, 202, 230
BstHHI GCGC 1 cut(s) 336
BstKTI GATC 3 cut(s) 108, 457, 475
BstMBI GATC 3 cut(s) 105, 454, 472
BstMWI GCNNNNNNNGC 1 cut(s) 155
BstNSI RCATGY 2 cut(s) 374, 401
BstX2I RGATCY 1 cut(s) 472
BstYI RGATCY 1 cut(s) 472
BtsCI GGATG 3 cut(s) 10, 202, 230
BtsIMutI CAGTG 1 cut(s) 300
Cac8I GCNNGC 1 cut(s) 228
CfoI GCGC 1 cut(s) 336
Cfr13I GGNCC 1 cut(s) 460
CviAII CATG 4 cut(s) 235, 260, 371, 398
CviJI RGCY 7 cut(s) 51, 70, 149, 212, 344, 355, 467
CviKI_1 RGCY 7 cut(s) 51, 70, 149, 212, 344, 355, 467
DpnI GATC 3 cut(s) 107, 456, 474
DpnII GATC 3 cut(s) 105, 454, 472
Eco130I CCWWGG 1 cut(s) 439
Eco24I GRGCYC 1 cut(s) 53
Eco47I GGWCC 1 cut(s) 460
Eco57I CTGAAG 1 cut(s) 233
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, 287, 341, 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 4 cut(s) 162, 440, 464, 491
GlaI GCGC 1 cut(s) 335
HapII CCGG 1 cut(s) 458
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 2 cut(s) 37, 497
HpaII CCGG 1 cut(s) 458
HphI GGTGA 2 cut(s) 10, 326
Hpy188I TCNGA 1 cut(s) 252
Hpy188III TCNNGA 6 cut(s) 6, 44, 361, 434, 458, 470
HpyCH4IV ACGT 1 cut(s) 172
HpyCH4V TGCA 5 cut(s) 128, 158, 230, 391, 449
HpyF10VI GCNNNNNNNGC 1 cut(s) 155
HpySE526I ACGT 1 cut(s) 172
Hsp92II CATG 4 cut(s) 238, 263, 374, 401
HspAI GCGC 1 cut(s) 334
Kpn2I TCCGGA 1 cut(s) 457
Kzo9I GATC 3 cut(s) 105, 454, 472
LmnI GCTCC 2 cut(s) 75, 388
LpnPI CCDG 2 cut(s) 399, 471
LweI GCATC 2 cut(s) 239, 400
MaeI CTAG 4 cut(s) 162, 440, 464, 491
MaeII ACGT 1 cut(s) 172
MalI GATC 3 cut(s) 107, 456, 474
MboI GATC 3 cut(s) 105, 454, 472
MboII GAAGA 2 cut(s) 467, 470
MfeI CAATTG 1 cut(s) 450
MflI RGATCY 1 cut(s) 472
MhlI GDGCHC 2 cut(s) 53, 385
MluCI AATT 6 cut(s) 24, 76, 84, 305, 429, 450
MnlI CCTC 5 cut(s) 40, 141, 144, 369, 496
MroI TCCGGA 1 cut(s) 457
MseI TTAA 1 cut(s) 511
MslI CAYNNNNRTG 3 cut(s) 195, 264, 396
MspI CCGG 1 cut(s) 458
MunI CAATTG 1 cut(s) 450
MwoI GCNNNNNNNGC 1 cut(s) 155
NdeII GATC 3 cut(s) 105, 454, 472
NlaIII CATG 4 cut(s) 238, 263, 374, 401
NlaIV GGNNCC 1 cut(s) 71
NspI RCATGY 2 cut(s) 374, 401
PciI ACATGT 2 cut(s) 370, 397
PfeI GAWTC 2 cut(s) 37, 497
PscI ACATGT 2 cut(s) 370, 397
PspN4I GGNNCC 1 cut(s) 71
PspPI GGNCC 1 cut(s) 460
PsuI RGATCY 1 cut(s) 472
RseI CAYNNNNRTG 3 cut(s) 195, 264, 396
SaqAI TTAA 1 cut(s) 511
Sau3AI GATC 3 cut(s) 105, 454, 472
Sau96I GGNCC 1 cut(s) 460
SduI GDGCHC 2 cut(s) 53, 385
SetI ASST 8 cut(s) 133, 175, 346, 357, 418, 441, 465, 469
SfaNI GCATC 2 cut(s) 239, 400
SinI GGWCC 1 cut(s) 460
SmiMI CAYNNNNRTG 3 cut(s) 195, 264, 396
SmlI CTYRAG 3 cut(s) 44, 207, 468
SmoI CTYRAG 3 cut(s) 44, 207, 468
SpeI ACTAGT 1 cut(s) 161
Sse9I AATT 6 cut(s) 24, 76, 84, 305, 429, 450
SsiI CCGC 1 cut(s) 73
SspMI CTAG 4 cut(s) 162, 440, 464, 491
StyI CCWWGG 1 cut(s) 439
TaiI ACGT 1 cut(s) 175
TaqI TCGA 1 cut(s) 99
TasI AATT 6 cut(s) 24, 76, 84, 305, 429, 450
TfiI GAWTC 2 cut(s) 37, 497
Tru1I TTAA 1 cut(s) 511
Tru9I TTAA 1 cut(s) 511
TscAI CASTG 1 cut(s) 307
TspDTI ATGAA 3 cut(s) 251, 328, 489
TspRI CASTG 1 cut(s) 307
VpaK11BI GGWCC 1 cut(s) 460
XapI RAATTY 2 cut(s) 24, 429
XceI RCATGY 2 cut(s) 374, 401
XmaJI CCTAGG 1 cut(s) 439
XspI CTAG 4 cut(s) 162, 440, 464, 491
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.