Rw7G025770

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr7
OG0002402
Physical Location & Seq
Reverse (-)
32468059 .. 32469868
1810 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw7G025770.1

Sequence Viewer

Length: 900 bp
ATGTCAGGACATCCTATCACCAAAATTCTCAATGAAAATCGTCTTGAGGGCCCAAACTTCAATGACTGGCTCCGCAATTTGAAAATTGTATTGACATTCGATAAGATCGCTTATGTCTTACAAAATGCACCCCCTCACACCCCTTTGGCTCAAGATGCAACCGATGAGCAACGTTTTGCTTATCAAAAGGATAAGGATGATGACACTCAAGCTAAATGTGTTATGCTTGCATCCATGAACTCACAACTTCAGAAGCAACATGAGAATATGGATAGCGCCAGTTCTATATTACTCCATCTCACTGAATTGTTTGGTAAGAGAAATAGAAATGTGTGCTTCACAGTAGTCAATGAGCTTGTCAAGACAAAACATGTGAGGGGTGCACCTGTGCATCAACATGGTCTAAAAATGATAGGCCTTATTGAGCAAATTCAAGACCTTGGATTTGCACTTGATGCGGAGATAGCTCAAGATCTTCTTCTAGCCTCCCTAGATGATTCATTTTCTCAGTTCATAATAAACTATAATATGCAACAAATGGATCATACTCTTTCTGATCTTCTCAATATGCTGGTAACAGCTGAGAAGCAAATCAAGAAAGAGAGTAGGAGTGCGGCCATTATCGCTTCTTCTTCATCCAGTAAGTCCAAAGGTAAAGGCAAAGGGAAGAAGAATCAAGTGATAAAGCCTAAGGGAGCAGTCCAAAAGAAGAAGAAGAAGGAACAAAAGGAACCAAAAGGTATTTGTTTCTTTTGCAACAAAGATGGGCACTGGAAGAGGAATTGCAAAGCTTATCTTGCATCCTTGAAGAACAAGTCTTCAACAGAAGGTACGATCAATCTCCTCTTGGAACACCACAACTTAATGGTGTCTCTGAAAGGAGAAATCGAACTTTGTTAG
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

299

Amino Acids

33.65

Weight (kDa)

9.2

Isoelectric Point (pI)

35.65

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 36 - 202 4.1e-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 3 cut(s) 73, 458, 614
AclI AACGTT 1 cut(s) 172
AclWI GGATC 1 cut(s) 549
AcoI YGGCCR 1 cut(s) 615
AcsI RAATTY 2 cut(s) 24, 429
AcuI CTGAAG 1 cut(s) 233
AfaI GTAC 1 cut(s) 832
AflIII ACRYGT 1 cut(s) 370
AgsI TTSAA 5 cut(s) 61, 82, 434, 808, 822
AluBI AGCT 5 cut(s) 212, 355, 467, 581, 791
AluI AGCT 5 cut(s) 212, 355, 467, 581, 791
Alw21I GWGCWC 1 cut(s) 385
Alw26I GTCTC 1 cut(s) 876
Alw44I GTGCAC 1 cut(s) 381
AlwI GGATC 1 cut(s) 549
AoxI GGCC 3 cut(s) 49, 415, 615
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) 278
AspS9I GGNCC 2 cut(s) 49, 50
AsuHPI GGTGA 1 cut(s) 10
AxyI CCTNAGG 1 cut(s) 690
BaeGI GKGCMC 3 cut(s) 53, 385, 771
BanII GRGCYC 1 cut(s) 53
BbsI GAAGAC 1 cut(s) 810
Bbv12I GWGCWC 1 cut(s) 385
BccI CCATC 2 cut(s) 303, 758
BcoDI GTCTC 1 cut(s) 876
BfaI CTAG 2 cut(s) 482, 491
BfoI RGCGCY 1 cut(s) 279
BglII AGATCT 1 cut(s) 472
BisI GCNGC 1 cut(s) 615
BlsI GCNGC 1 cut(s) 616
BmgT120I GGNCC 2 cut(s) 49, 50
BmiI GGNNCC 3 cut(s) 51, 71, 732
BmsI GCATC 5 cut(s) 145, 239, 400, 445, 809
BpiI GAAGAC 1 cut(s) 810
BpuEI CTTGAG 4 cut(s) 65, 135, 192, 453
BsaJI CCNNGG 1 cut(s) 439
Bse1I ACTGG 4 cut(s) 71, 279, 639, 776
Bse21I CCTNAGG 1 cut(s) 690
BseDI CCNNGG 1 cut(s) 439
BseGI GGATG 5 cut(s) 10, 202, 230, 635, 800
BseMII CTCAG 2 cut(s) 521, 573
BseNI ACTGG 4 cut(s) 71, 279, 639, 776
BseRI GAGGAG 1 cut(s) 833
BseSI GKGCMC 3 cut(s) 53, 385, 771
BshFI GGCC 3 cut(s) 51, 417, 617
BsiHKAI GWGCWC 1 cut(s) 385
BsmAI GTCTC 1 cut(s) 876
BsnI GGCC 3 cut(s) 51, 417, 617
Bsp120I GGGCCC 1 cut(s) 49
Bsp1286I GDGCHC 3 cut(s) 53, 385, 771
Bsp143I GATC 5 cut(s) 105, 472, 541, 556, 834
BspACI CCGC 3 cut(s) 73, 458, 614
BspANI GGCC 3 cut(s) 51, 417, 617
BspCNI CTCAG 2 cut(s) 520, 574
BspLI GGNNCC 3 cut(s) 51, 71, 732
BspPI GGATC 1 cut(s) 549
BsrI ACTGG 4 cut(s) 71, 279, 639, 776
BssECI CCNNGG 1 cut(s) 439
BssMI GATC 5 cut(s) 105, 472, 541, 556, 834
BssT1I CCWWGG 1 cut(s) 439
Bst4CI ACNGT 1 cut(s) 343
Bst6I CTCTTC 1 cut(s) 770
BstAPI GCANNNNNTGC 1 cut(s) 455
BstC8I GCNNGC 1 cut(s) 228
BstDEI CTNAG 3 cut(s) 507, 582, 690
BstF5I GGATG 5 cut(s) 10, 202, 230, 635, 800
BstH2I RGCGCY 1 cut(s) 279
BstHHI GCGC 1 cut(s) 278
BstKTI GATC 5 cut(s) 108, 475, 544, 559, 837
BstMAI GTCTC 1 cut(s) 876
BstMBI GATC 5 cut(s) 105, 472, 541, 556, 834
BstMWI GCNNNNNNNGC 5 cut(s) 155, 455, 464, 623, 797
BstNSI RCATGY 1 cut(s) 374
BstSLI GKGCMC 3 cut(s) 53, 385, 771
BstV2I GAAGAC 1 cut(s) 810
BstX2I RGATCY 1 cut(s) 472
BstYI RGATCY 1 cut(s) 472
Bsu36I CCTNAGG 1 cut(s) 690
BsuRI GGCC 3 cut(s) 51, 417, 617
BtsCI GGATG 5 cut(s) 10, 202, 230, 635, 800
BtsIMutI CAGTG 2 cut(s) 300, 769
Cac8I GCNNGC 1 cut(s) 228
CfoI GCGC 1 cut(s) 278
Cfr13I GGNCC 2 cut(s) 49, 50
Csp6I GTAC 1 cut(s) 831
CviAII CATG 4 cut(s) 235, 260, 371, 398
CviQI GTAC 1 cut(s) 831
DdeI CTNAG 3 cut(s) 507, 582, 690
DpnI GATC 5 cut(s) 107, 474, 543, 558, 836
DpnII GATC 5 cut(s) 105, 472, 541, 556, 834
EaeI YGGCCR 1 cut(s) 615
Eam1104I CTCTTC 1 cut(s) 770
EarI CTCTTC 1 cut(s) 770
Eco130I CCWWGG 1 cut(s) 439
Eco147I AGGCCT 1 cut(s) 417
Eco24I GRGCYC 1 cut(s) 53
Eco57I CTGAAG 1 cut(s) 233
Eco81I CCTNAGG 1 cut(s) 690
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
FalI AAGNNNNNCTT 4 cut(s) 462, 494, 780, 812
FatI CATG 4 cut(s) 234, 259, 370, 397
Fnu4HI GCNGC 1 cut(s) 615
FokI GGATG 4 cut(s) 209, 217, 622, 787
FriOI GRGCYC 1 cut(s) 53
Fsp4HI GCNGC 1 cut(s) 615
FspBI CTAG 2 cut(s) 482, 491
GlaI GCGC 1 cut(s) 277
GluI GCNGC 1 cut(s) 615
HaeII RGCGCY 1 cut(s) 279
HaeIII GGCC 3 cut(s) 51, 417, 617
HhaI GCGC 1 cut(s) 278
Hin1II CATG 4 cut(s) 238, 263, 374, 401
Hin6I GCGC 1 cut(s) 276
HinP1I GCGC 1 cut(s) 276
HindIII AAGCTT 1 cut(s) 789
HinfI GANTC 2 cut(s) 497, 673
HphI GGTGA 1 cut(s) 10
Hpy166II GTNNAC 1 cut(s) 383
Hpy188I TCNGA 3 cut(s) 252, 556, 876
Hpy188III TCNNGA 7 cut(s) 6, 44, 152, 361, 434, 470, 595
Hpy8I GTNNAC 1 cut(s) 383
HpyAV CCTTC 2 cut(s) 712, 821
HpyCH4III ACNGT 1 cut(s) 343
HpyCH4IV ACGT 1 cut(s) 172
HpyF10VI GCNNNNNNNGC 5 cut(s) 155, 455, 464, 623, 797
HpyF3I CTNAG 3 cut(s) 507, 582, 690
HpySE526I ACGT 1 cut(s) 172
Hsp92II CATG 4 cut(s) 238, 263, 374, 401
HspAI GCGC 1 cut(s) 276
Kzo9I GATC 5 cut(s) 105, 472, 541, 556, 834
LmnI GCTCC 2 cut(s) 75, 695
LpnPI CCDG 6 cut(s) 52, 292, 399, 557, 652, 757
LweI GCATC 5 cut(s) 145, 239, 400, 445, 809
MaeI CTAG 2 cut(s) 482, 491
MaeII ACGT 1 cut(s) 172
MaeIII GTNAC 1 cut(s) 574
MalI GATC 5 cut(s) 107, 474, 543, 558, 836
MboI GATC 5 cut(s) 105, 472, 541, 556, 834
MflI RGATCY 1 cut(s) 472
MhlI GDGCHC 3 cut(s) 53, 385, 771
MluCI AATT 6 cut(s) 24, 76, 84, 305, 429, 781
MnlI CCTC 6 cut(s) 40, 144, 369, 496, 771, 854
MseI TTAA 1 cut(s) 863
MslI CAYNNNNRTG 1 cut(s) 396
MspA1I CMGCKG 1 cut(s) 581
MwoI GCNNNNNNNGC 5 cut(s) 155, 455, 464, 623, 797
NdeII GATC 5 cut(s) 105, 472, 541, 556, 834
NlaIII CATG 4 cut(s) 238, 263, 374, 401
NlaIV GGNNCC 3 cut(s) 51, 71, 732
NspI RCATGY 1 cut(s) 374
PceI AGGCCT 1 cut(s) 417
PciI ACATGT 1 cut(s) 370
PfeI GAWTC 2 cut(s) 497, 673
PkrI GCNGC 1 cut(s) 616
PscI ACATGT 1 cut(s) 370
Psp1406I AACGTT 1 cut(s) 172
PspN4I GGNNCC 3 cut(s) 51, 71, 732
PspOMI GGGCCC 1 cut(s) 49
PspPI GGNCC 2 cut(s) 49, 50
PsuI RGATCY 1 cut(s) 472
PvuII CAGCTG 1 cut(s) 581
RsaI GTAC 1 cut(s) 832
RsaNI GTAC 1 cut(s) 831
RseI CAYNNNNRTG 1 cut(s) 396
SaqAI TTAA 1 cut(s) 863
SatI GCNGC 1 cut(s) 615
Sau3AI GATC 5 cut(s) 105, 472, 541, 556, 834
Sau96I GGNCC 2 cut(s) 49, 50
SduI GDGCHC 3 cut(s) 53, 385, 771
SfaNI GCATC 5 cut(s) 145, 239, 400, 445, 809
SmiMI CAYNNNNRTG 1 cut(s) 396
SmlI CTYRAG 4 cut(s) 44, 150, 207, 468
SmoI CTYRAG 4 cut(s) 44, 150, 207, 468
Sse9I AATT 6 cut(s) 24, 76, 84, 305, 429, 781
SseBI AGGCCT 1 cut(s) 417
SsiI CCGC 3 cut(s) 73, 458, 614
SspMI CTAG 2 cut(s) 482, 491
StuI AGGCCT 1 cut(s) 417
StyI CCWWGG 1 cut(s) 439
TaaI ACNGT 1 cut(s) 343
TaiI ACGT 1 cut(s) 175
TaqI TCGA 2 cut(s) 99, 888
TasI AATT 6 cut(s) 24, 76, 84, 305, 429, 781
TauI GCSGC 1 cut(s) 617
TfiI GAWTC 2 cut(s) 497, 673
Tru1I TTAA 1 cut(s) 863
Tru9I TTAA 1 cut(s) 863
TscAI CASTG 2 cut(s) 307, 776
TspDTI ATGAA 5 cut(s) 48, 251, 489, 502, 624
TspRI CASTG 2 cut(s) 307, 776
VneI GTGCAC 1 cut(s) 381
XapI RAATTY 2 cut(s) 24, 429
XceI RCATGY 1 cut(s) 374
XspI CTAG 2 cut(s) 482, 491
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.