Rmu_sc0001188.1_g000026

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0001188.1
OG0019088
Physical Location & Seq
Reverse (-)
92130 .. 94753
2624 bp
Loading structure...
UTR
Exon/CDS
Intron
Rmu_sc0001188.1_g000026.1.cds

Sequence Viewer

Length: 1056 bp
ctgttatctggccaatgggcatcgtcatctccggtccggcgagtggtagcgtatccacgacagtgctgcggcggcggtgaaggctcgatcgccggatggtggtgggtgtgcgacggtgggaatggggctggaactcttccgggcttgcgcaccttgcgtgccatgtctgctctaagtaggaggcgagttccttgctttgtcaaattgtcacagccttttagtggcagaatgaaactaagtgtcaccgggttatatttccggtggcagcatactaggaaagctgatagtattggttactcatggctcaacgcccgcaagccctgcttgccttccaccttcccgcgagctcgcctaccctctcgaccgcgaatcaccagcgaccccgcggcatatccgcagcgtccacaaggccctgtggcatccccgcagcgtcctcactgccccgcgactccgcattcccgtgactcgcccgcgaccgtgcgaccaccacagctcctacgtacccctgtgcttgctatccctgtgagggcaccctgcatctgctgcccccgcatccctaggctcgtatgctgcccctgcaaccctacgctcacccgctgccccagcagctcctataagcccctgcgcttactgctccctcctgcgtgcattgcatctgctgtccctgcggccctgcagcaccaacagcctatccccgctgcctgttttccaacatgcgcttgttctcaagccctaaatcaacaaatttctcggaagcgactatgctcagaaatccctacatttcttggaagcgactacactcagaaatttctatttaacctgaacaaattggacttttctccattgggaataactggctctggatatcactggtgggttcgtgatgtccgccagcatctcaaggccgatggaatcttggataagattctcaagcctagccaagacgtgctaactgttgagcaagctcaagctttggaagcaaatagagcagccttagaggcaaataaggcgaaagccatcatcctaataactcgtcatatggatgattcactctag
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

351

Amino Acids

38.58

Weight (kDa)

10.02

Isoelectric Point (pI)

62.13

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc16I TGCGCA 1 cut(s) 149
AccB1I GGYRCC 1 cut(s) 529
AccII CGCG 5 cut(s) 343, 367, 386, 446, 473
AcoI YGGCCR 1 cut(s) 10
AcsI RAATTY 2 cut(s) 744, 806
AfaI GTAC 1 cut(s) 502
AfiI CCNNNNNNNGG 4 cut(s) 43, 99, 221, 526
AjiI CACGTC 1 cut(s) 946
AleI CACNNNNGTG 1 cut(s) 61
AluBI AGCT 6 cut(s) 281, 347, 493, 609, 965, 971
AluI AGCT 6 cut(s) 281, 347, 493, 609, 965, 971
Alw21I GWGCWC 1 cut(s) 349
AoxI GGCC 4 cut(s) 10, 409, 669, 903
ApoI RAATTY 2 cut(s) 744, 806
AspA2I CCTAGG 1 cut(s) 557
AspLEI GCGC 3 cut(s) 150, 627, 719
AspS9I GGNCC 3 cut(s) 34, 410, 670
AsuC2I CCSGG 2 cut(s) 141, 247
AsuHPI GGTGA 4 cut(s) 89, 235, 364, 583
AvaII GGWCC 1 cut(s) 34
AvrII CCTAGG 1 cut(s) 557
BaeGI GKGCMC 1 cut(s) 532
BalI TGGCCA 1 cut(s) 12
BanI GGYRCC 1 cut(s) 529
BanII GRGCYC 1 cut(s) 349
Bbv12I GWGCWC 1 cut(s) 349
BccI CCATC 3 cut(s) 90, 902, 1025
BcgI CGANNNNNNTGC 4 cut(s) 48, 82, 174, 208
BciVI GTATCC 1 cut(s) 63
BcnI CCSGG 2 cut(s) 141, 247
BfaI CTAG 4 cut(s) 273, 558, 936, 1054
BfmI CTRYAG 1 cut(s) 674
BfuI GTATCC 1 cut(s) 63
BglI GCCNNNNNGGC 1 cut(s) 998
BlnI CCTAGG 1 cut(s) 557
Bme1390I CCNGG 2 cut(s) 141, 247
Bme18I GGWCC 1 cut(s) 34
BmgBI CACGTC 1 cut(s) 946
BmgT120I GGNCC 3 cut(s) 34, 410, 670
BmiI GGNNCC 1 cut(s) 531
BmrFI CCNGG 2 cut(s) 141, 247
BmsI GCATC 6 cut(s) 29, 428, 546, 561, 662, 904
BpuEI CTTGAG 4 cut(s) 711, 884, 914, 951
BpuMI CCSGG 2 cut(s) 141, 247
BsaAI YACGTR 1 cut(s) 500
BsaJI CCNNGG 2 cut(s) 384, 557
BsaWI WCCGGW 2 cut(s) 31, 258
BsaXI ACNNNNNCTCC 2 cut(s) 477, 507
Bsc4I CCNNNNNNNGG 4 cut(s) 43, 99, 221, 526
Bse1I ACTGG 2 cut(s) 859, 875
Bse3DI GCAATG 1 cut(s) 648
BseDI CCNNGG 2 cut(s) 384, 557
BseGI GGATG 5 cut(s) 101, 419, 552, 1020, 1048
BseLI CCNNNNNNNGG 4 cut(s) 43, 99, 221, 526
BseMI GCAATG 1 cut(s) 648
BseMII CTCAG 2 cut(s) 780, 815
BseNI ACTGG 2 cut(s) 859, 875
BseSI GKGCMC 1 cut(s) 532
BseYI CCCAGC 1 cut(s) 602
Bsh1236I CGCG 5 cut(s) 343, 367, 386, 446, 473
Bsh1285I CGRYCG 3 cut(s) 90, 365, 477
BshFI GGCC 4 cut(s) 12, 411, 671, 905
BshNI GGYRCC 1 cut(s) 529
BsiEI CGRYCG 3 cut(s) 90, 365, 477
BsiHKAI GWGCWC 1 cut(s) 349
BsiSI CCGG 6 cut(s) 32, 37, 93, 140, 246, 259
BslFI GGGAC 1 cut(s) 647
BslI CCNNNNNNNGG 4 cut(s) 43, 99, 221, 526
BsmFI GGGAC 1 cut(s) 647
BsmI GAATGC 1 cut(s) 454
BsnI GGCC 4 cut(s) 12, 411, 671, 905
Bsp1286I GDGCHC 2 cut(s) 349, 532
Bsp143I GATC 1 cut(s) 87
BspANI GGCC 4 cut(s) 12, 411, 671, 905
BspCNI CTCAG 2 cut(s) 779, 814
BspFNI CGCG 5 cut(s) 343, 367, 386, 446, 473
BspLI GGNNCC 1 cut(s) 531
BspMAI CTGCAG 1 cut(s) 678
BspT107I GGYRCC 1 cut(s) 529
BsrDI GCAATG 1 cut(s) 648
BsrI ACTGG 2 cut(s) 859, 875
BssECI CCNNGG 2 cut(s) 384, 557
BssMI GATC 1 cut(s) 87
BssT1I CCWWGG 1 cut(s) 557
Bst4CI ACNGT 4 cut(s) 63, 116, 478, 955
Bst6I CTCTTC 1 cut(s) 141
BstAPI GCANNNNNTGC 2 cut(s) 321, 543
BstBAI YACGTR 1 cut(s) 500
BstDEI CTNAG 5 cut(s) 173, 236, 766, 801, 994
BstDSI CCRYGG 1 cut(s) 384
BstF5I GGATG 5 cut(s) 101, 419, 552, 1020, 1048
BstFNI CGCG 5 cut(s) 343, 367, 386, 446, 473
BstHHI GCGC 3 cut(s) 150, 627, 719
BstKTI GATC 1 cut(s) 90
BstMBI GATC 1 cut(s) 87
BstMCI CGRYCG 3 cut(s) 90, 365, 477
BstNSI RCATGY 1 cut(s) 717
BstSCI CCNGG 2 cut(s) 139, 245
BstSFI CTRYAG 1 cut(s) 674
BstSLI GKGCMC 1 cut(s) 532
BstSNI TACGTA 1 cut(s) 500
BstUI CGCG 5 cut(s) 343, 367, 386, 446, 473
BsuI GTATCC 1 cut(s) 63
BsuRI GGCC 4 cut(s) 12, 411, 671, 905
BtgI CCRYGG 1 cut(s) 384
BtrI CACGTC 1 cut(s) 946
BtsCI GGATG 5 cut(s) 101, 419, 552, 1020, 1048
BtsI GCAGTG 1 cut(s) 436
BtsIMutI CAGTG 3 cut(s) 68, 436, 868
CfoI GCGC 3 cut(s) 150, 627, 719
Cfr13I GGNCC 3 cut(s) 34, 410, 670
Cfr42I CCGCGG 1 cut(s) 387
CpoI CGGWCCG 1 cut(s) 34
CseI GACGC 2 cut(s) 389, 419
Csp6I GTAC 1 cut(s) 501
CspI CGGWCCG 1 cut(s) 34
CviAII CATG 3 cut(s) 163, 300, 714
CviQI GTAC 1 cut(s) 501
DdeI CTNAG 5 cut(s) 173, 236, 766, 801, 994
DpnI GATC 1 cut(s) 89
DpnII GATC 1 cut(s) 87
EaeI YGGCCR 1 cut(s) 10
Eam1104I CTCTTC 1 cut(s) 141
EarI CTCTTC 1 cut(s) 141
EciI GGCGGA 1 cut(s) 878
Ecl136II GAGCTC 1 cut(s) 347
Eco105I TACGTA 1 cut(s) 500
Eco130I CCWWGG 1 cut(s) 557
Eco24I GRGCYC 1 cut(s) 349
Eco32I GATATC 1 cut(s) 866
Eco47I GGWCC 1 cut(s) 34
Eco53kI GAGCTC 1 cut(s) 347
EcoICRI GAGCTC 1 cut(s) 347
EcoO109I RGGNCCY 1 cut(s) 410
EcoRV GATATC 1 cut(s) 866
EcoT14I CCWWGG 1 cut(s) 557
EcoT38I GRGCYC 1 cut(s) 349
ErhI CCWWGG 1 cut(s) 557
FaeI CATG 3 cut(s) 166, 303, 717
FalI AAGNNNNNCTT 2 cut(s) 308, 340
FaqI GGGAC 1 cut(s) 647
FatI CATG 3 cut(s) 162, 299, 713
FauI CCCGC 9 cut(s) 320, 348, 391, 432, 451, 478, 557, 602, 703
FauNDI CATATG 1 cut(s) 1038
FokI GGATG 4 cut(s) 108, 406, 539, 1007
FriOI GRGCYC 1 cut(s) 349
FspBI CTAG 4 cut(s) 273, 558, 936, 1054
FspI TGCGCA 1 cut(s) 149
GlaI GCGC 3 cut(s) 149, 626, 718
GsaI CCCAGC 1 cut(s) 606
HaeIII GGCC 4 cut(s) 12, 411, 671, 905
HapII CCGG 6 cut(s) 32, 37, 93, 140, 246, 259
HgaI GACGC 2 cut(s) 389, 419
HhaI GCGC 3 cut(s) 150, 627, 719
Hin1II CATG 3 cut(s) 166, 303, 717
Hin6I GCGC 3 cut(s) 148, 625, 717
HinP1I GCGC 3 cut(s) 148, 625, 717
HindIII AAGCTT 1 cut(s) 969
HinfI GANTC 6 cut(s) 369, 448, 464, 912, 925, 1046
HpaII CCGG 6 cut(s) 32, 37, 93, 140, 246, 259
HphI GGTGA 4 cut(s) 89, 235, 364, 583
Hpy166II GTNNAC 1 cut(s) 404
Hpy188I TCNGA 3 cut(s) 753, 769, 804
Hpy188III TCNNGA 3 cut(s) 360, 861, 881
Hpy8I GTNNAC 1 cut(s) 404
Hpy99I CGWCG 1 cut(s) 116
HpyAV CCTTC 3 cut(s) 74, 339, 346
HpyCH4III ACNGT 4 cut(s) 63, 116, 478, 955
HpyCH4IV ACGT 2 cut(s) 499, 945
HpyCH4V TGCA 5 cut(s) 537, 579, 648, 653, 676
HpyF3I CTNAG 5 cut(s) 173, 236, 766, 801, 994
HpySE526I ACGT 2 cut(s) 499, 945
Hsp92II CATG 3 cut(s) 166, 303, 717
HspAI GCGC 3 cut(s) 148, 625, 717
KspI CCGCGG 1 cut(s) 387
Kzo9I GATC 1 cut(s) 87
LmnI GCTCC 3 cut(s) 498, 614, 639
LweI GCATC 6 cut(s) 29, 428, 546, 561, 662, 904
MaeI CTAG 4 cut(s) 273, 558, 936, 1054
MaeII ACGT 2 cut(s) 499, 945
MaeIII GTNAC 4 cut(s) 207, 241, 293, 461
MalI GATC 1 cut(s) 89
MboI GATC 1 cut(s) 87
MboII GAAGA 1 cut(s) 128
MhlI GDGCHC 2 cut(s) 349, 532
MlsI TGGCCA 1 cut(s) 12
MluCI AATT 4 cut(s) 203, 744, 806, 827
MluNI TGGCCA 1 cut(s) 12
MlyI GAGTC 2 cut(s) 442, 458
MmeI TCCRAC 1 cut(s) 734
MnlI CCTC 6 cut(s) 174, 367, 444, 519, 648, 991
Mox20I TGGCCA 1 cut(s) 12
MscI TGGCCA 1 cut(s) 12
MseI TTAA 1 cut(s) 816
MslI CAYNNNNRTG 3 cut(s) 61, 459, 1041
Msp20I TGGCCA 1 cut(s) 12
MspA1I CMGCKG 3 cut(s) 386, 597, 698
MspI CCGG 6 cut(s) 32, 37, 93, 140, 246, 259
MspR9I CCNGG 2 cut(s) 141, 247
Mva1269I GAATGC 1 cut(s) 454
MvnI CGCG 5 cut(s) 343, 367, 386, 446, 473
NciI CCSGG 2 cut(s) 141, 247
NdeI CATATG 1 cut(s) 1038
NdeII GATC 1 cut(s) 87
NlaIII CATG 3 cut(s) 166, 303, 717
NlaIV GGNNCC 1 cut(s) 531
NmuCI GTSAC 3 cut(s) 207, 241, 461
NsbI TGCGCA 1 cut(s) 149
NspI RCATGY 1 cut(s) 717
OliI CACNNNNGTG 1 cut(s) 61
PctI GAATGC 1 cut(s) 454
PfeI GAWTC 4 cut(s) 369, 912, 925, 1046
Ple19I CGATCG 1 cut(s) 90
PleI GAGTC 2 cut(s) 442, 458
PpsI GAGTC 2 cut(s) 442, 458
Ppu21I YACGTR 1 cut(s) 500
Psp124BI GAGCTC 1 cut(s) 349
PspFI CCCAGC 1 cut(s) 602
PspN4I GGNNCC 1 cut(s) 531
PspPI GGNCC 3 cut(s) 34, 410, 670
PstI CTGCAG 1 cut(s) 678
PvuI CGATCG 1 cut(s) 90
RsaI GTAC 1 cut(s) 502
RsaNI GTAC 1 cut(s) 501
RseI CAYNNNNRTG 3 cut(s) 61, 459, 1041
Rsr2I CGGWCCG 1 cut(s) 34
RsrII CGGWCCG 1 cut(s) 34
SacI GAGCTC 1 cut(s) 349
SacII CCGCGG 1 cut(s) 387
SaqAI TTAA 1 cut(s) 816
Sau3AI GATC 1 cut(s) 87
Sau96I GGNCC 3 cut(s) 34, 410, 670
SchI GAGTC 2 cut(s) 442, 458
ScrFI CCNGG 2 cut(s) 141, 247
SduI GDGCHC 2 cut(s) 349, 532
SfaNI GCATC 6 cut(s) 29, 428, 546, 561, 662, 904
SfcI CTRYAG 1 cut(s) 674
Sfr303I CCGCGG 1 cut(s) 387
SgrBI CCGCGG 1 cut(s) 387
SinI GGWCC 1 cut(s) 34
SmiMI CAYNNNNRTG 3 cut(s) 61, 459, 1041
SmlI CTYRAG 4 cut(s) 726, 899, 929, 966
SmoI CTYRAG 4 cut(s) 726, 899, 929, 966
SnaBI TACGTA 1 cut(s) 500
Sse9I AATT 4 cut(s) 203, 744, 806, 827
SspMI CTAG 4 cut(s) 273, 558, 936, 1054
SstI GAGCTC 1 cut(s) 349
StyD4I CCNGG 2 cut(s) 139, 245
StyI CCWWGG 1 cut(s) 557
TaaI ACNGT 4 cut(s) 63, 116, 478, 955
TaiI ACGT 2 cut(s) 502, 948
TaqI TCGA 2 cut(s) 86, 361
TasI AATT 4 cut(s) 203, 744, 806, 827
TauI GCSGC 4 cut(s) 72, 75, 389, 671
TfiI GAWTC 4 cut(s) 369, 912, 925, 1046
Tru1I TTAA 1 cut(s) 816
Tru9I TTAA 1 cut(s) 816
TscAI CASTG 3 cut(s) 68, 443, 875
TseFI GTSAC 3 cut(s) 207, 241, 461
Tsp45I GTSAC 3 cut(s) 207, 241, 461
TspDTI ATGAA 1 cut(s) 245
TspRI CASTG 3 cut(s) 68, 443, 875
VpaK11BI GGWCC 1 cut(s) 34
XapI RAATTY 2 cut(s) 744, 806
XceI RCATGY 1 cut(s) 717
XmaJI CCTAGG 1 cut(s) 557
XspI CTAG 4 cut(s) 273, 558, 936, 1054
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.