RchiOBHm_Chr5g0017791

GAG-pre-integrase domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0016252
Physical Location & Seq
Reverse (-)
12391973 .. 12394946
2974 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 2028 bp
ATGGCAACCTCAGGTCAACATTGCAATACAGTCTCTGTTCATCTTGATGATACAAATTACCCCACTTGGCATTTTTTGATGCAGCACTACCTTCGTGGTCATGGATTGCTCAAGTTTGTAGATGGTTCTTATCCATGCCCTCCACAATGTCAGAAGGCCGATTATGATTCTCCCTCTGTTAATAACACTGGAGCTTGTGAAAAATGGCTGCAACAAGATAGTTTTGTTATCTCTATGATTACCAATACTCTCTCAGCTGAGGCTCTTACATTGGTAATTGGCTGTGAAACTTCAATGGAGGTATGGATCACTCTCAAACGACATTATGCAGCAAATTCTGAATTTCACATTATGCGATTAAAGTCTGCTTTGCAAAATATCAGAAAAGGTGCAGATTCGATAGACAAGTATTTGTTGCGCTTCAAAACTGTTAGAGATCATTTAGCTGTTGTTGGTATTAGAATATCAGATCAAGAGGTTAAAAGTTTGATTCTTGCTGGTCTCCCTTGTGAGTATGGTCACACTAGACAAATTATAAGAGAAAAAAATCCTATAAGCATGGAGGAATTAAGGTCCTTACTTCTTTCTGCTGAATTTGAACTTGAATTGAAGCATAAAACTCATCCAGTGACACCCTTAACTACAGTGGTTGCAAATAATAGCTCTATGTCATTCCCTGACTCTCATTTTAGTTCATTTGTTATACCCTCTACTACTGTGCCCCAACGTGGCAAAAATCATATTGATTATAATAACACTTCTACATGTCATGTACCTGTTGTGGCCAAGTCCAGTATCAGTGCTCTTACTAGTACTCATACAAGTCCAGTTACTCAAATTGCTTGTACACCACAGTCGGCTATTTTGTCAAATAATGTCAACATTGCTACTGCATACATGAGTAATACTATGGCATCGAATGGGAACTTTGGTATGCAATCTATGCCAAATAACGGATGCATGATAGATTTTGTTTCTACACCTAGTGGTCTCCTGATTCCCAACTCTGGCTCAAATTTTGTTACTCCATACACATCTACTGGTGCAACACAACAGCTTGGTGACTTTCATCATTCCCATGCAACTTATGCACAGCCACAAGTCAATTCTAATGGAAGAATCCAGTATAATTGGGGATTTTCTCAACCCAACAGTAACTTCATTCTACAAAGTGGTAGGCTTCAGCAAAGCAATGGATTTCAATCTGGTATGGGTACTTCTAATGGTTATCAAGCTTCATTTAATACTAATGCAATGATGAATGGTGGAAATTGCTTTCCTCGTACTGGTTTGGTTAGGAATAGCGTTGTATCTCCTTCATTAGCTCAATACAATGGTGTGATGAAGATGGATAACTCAGTTTTGGAGGTAGTACCTACTGATGAAAAATTCGACAATGAAGGTGCTAATCTTAATTCTGCTCGAGTAACTGAATTTAGTGTGAAATATTTGAAGGAAGCTGGCAATGGTCAGGATATAAAGGAGAATACCTTGAGTACAGAGAATCAGGTTGATGAGACTCTGGATGTGGTAGATACTTCTGTTGTTGTTACCTTGAAGCCTGAAGATGACGAGGGTGTGGACTTGCAAGAGAGAAATATGGATCCAGAGGATACTGAATGTGAGAGTACCAACTCAAAAGATGCTATGTCTATCACTGAAGCAAGGCAAGTGGTTAATAAAAGTTCTGCAAATGAGGACACGAAGAAGATTCAGGTTGGTGCATCACCTAAAGCGTTGTCTGCTTCCATCTGCACTCAACCAAAGCCACCCTCCACTGCTACTGAGCCAAATAACAACTCTTTTCAATCACAAGTTGTCAAGCCTCTAACAATTACATCTGCATACCCATTATCAGTTCCTCCTCACCCTCATTTGCAGCAAGCTCCACTCAAGAAAATTGAAGTTTTGCGAACACCAGGAACTTGGCTACTTCCTTCCACTCCGGACAGAAATCTAATGCATTGCAGGCATGCTTGTGAGTCTACGAGTTTATGGCAATCACTTCCTCTCATTCCTCCTGGCTGA
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
RVT_2 gag_pre-integrs rve

Protein Analysis

675

Amino Acids

73.98

Weight (kDa)

6.05

Isoelectric Point (pI)

44.74

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 27 - 198 3.4e-23 gag-polypeptide of LTR copia-type
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 2 cut(s) 536, 750
AccI GTMKAC 1 cut(s) 1985
AccIII TCCGGA 1 cut(s) 1945
AclWI GGATC 3 cut(s) 314, 1598, 1611
AcoI YGGCCR 1 cut(s) 783
AcsI RAATTY 6 cut(s) 334, 341, 593, 1015, 1388, 1433
AcuI CTGAAG 3 cut(s) 1166, 1584, 1680
AdeI CACNNNGTG 1 cut(s) 986
AfaI GTAC 8 cut(s) 774, 814, 847, 1216, 1285, 1374, 1498, 1630
AfiI CCNNNNNNNGG 4 cut(s) 728, 953, 1007, 1286
AflIII ACRYGT 1 cut(s) 764
AhlI ACTAGT 1 cut(s) 809
AjnI CCWGG 2 cut(s) 1918, 2020
AjuI GAANNNNNNNTTGG 2 cut(s) 1142, 1174
AluBI AGCT 9 cut(s) 194, 257, 446, 663, 1057, 1235, 1325, 1460, 1886
AluI AGCT 9 cut(s) 194, 257, 446, 663, 1057, 1235, 1325, 1460, 1886
Alw21I GWGCWC 1 cut(s) 805
Alw26I GTCTC 4 cut(s) 37, 506, 995, 1511
AlwI GGATC 3 cut(s) 314, 1598, 1611
AlwNI CAGNNNCTG 1 cut(s) 35
Ama87I CYCGRG 1 cut(s) 1422
Aor13HI TCCGGA 1 cut(s) 1945
AoxI GGCC 2 cut(s) 156, 783
ApeKI GCWGC 4 cut(s) 82, 208, 329, 1879
ApoI RAATTY 6 cut(s) 334, 341, 593, 1015, 1388, 1433
AspLEI GCGC 1 cut(s) 420
AspS9I GGNCC 1 cut(s) 573
AsuHPI GGTGA 3 cut(s) 1073, 1719, 1859
AvaI CYCGRG 1 cut(s) 1422
AvaII GGWCC 1 cut(s) 573
AxyI CCTNAGG 1 cut(s) 10
BaeGI GKGCMC 1 cut(s) 723
BaeI ACNNNNGTAYC 2 cut(s) 1527, 1560
BalI TGGCCA 1 cut(s) 785
BamHI GGATCC 1 cut(s) 1603
BarI GAAGNNNNNNTAC 2 cut(s) 1201, 1233
Bbv12I GWGCWC 1 cut(s) 805
BbvCI CCTCAGC 1 cut(s) 258
BbvI GCAGC 4 cut(s) 94, 195, 341, 1891
BccI CCATC 3 cut(s) 116, 1342, 1757
BcgI CGANNNNNNTGC 2 cut(s) 74, 108
BciT130I CCWGG 2 cut(s) 1920, 2022
BciVI GTATCC 1 cut(s) 1606
BcoDI GTCTC 4 cut(s) 37, 506, 995, 1511
BcuI ACTAGT 1 cut(s) 809
BfaI CTAG 3 cut(s) 525, 810, 984
BfmI CTRYAG 1 cut(s) 642
BfuI GTATCC 1 cut(s) 1606
BisI GCNGC 4 cut(s) 83, 209, 330, 1880
BlsI GCNGC 4 cut(s) 84, 210, 331, 1881
BmcAI AGTACT 1 cut(s) 814
Bme1390I CCNGG 2 cut(s) 1920, 2022
Bme18I GGWCC 1 cut(s) 573
BmeT110I CYCGRG 1 cut(s) 1422
BmgT120I GGNCC 1 cut(s) 573
BmiI GGNNCC 1 cut(s) 1605
BmrFI CCNGG 2 cut(s) 1920, 2022
BmsI GCATC 5 cut(s) 69, 923, 947, 1633, 1733
BpmI CTGGAG 1 cut(s) 210
Bpu10I CCTNAGC 1 cut(s) 258
BpuEI CTTGAG 3 cut(s) 95, 1513, 1877
BsaBI GATNNNNATC 1 cut(s) 1201
BsaI GGTCTC 2 cut(s) 506, 995
BsaWI WCCGGW 1 cut(s) 1945
Bsc4I CCNNNNNNNGG 4 cut(s) 728, 953, 1007, 1286
Bse1I ACTGG 7 cut(s) 193, 626, 792, 827, 1045, 1123, 1291
Bse21I CCTNAGG 1 cut(s) 10
Bse3DI GCAATG 6 cut(s) 19, 882, 1198, 1260, 1471, 1963
Bse8I GATNNNNATC 1 cut(s) 1201
BseAI TCCGGA 1 cut(s) 1945
BseBI CCWGG 2 cut(s) 1920, 2022
BseGI GGATG 3 cut(s) 622, 962, 1531
BseJI GATNNNNATC 1 cut(s) 1201
BseLI CCNNNNNNNGG 4 cut(s) 728, 953, 1007, 1286
BseMI GCAATG 6 cut(s) 19, 882, 1198, 1260, 1471, 1963
BseMII CTCAG 5 cut(s) 24, 249, 267, 1371, 1776
BseNI ACTGG 7 cut(s) 193, 626, 792, 827, 1045, 1123, 1291
BseRI GAGGAG 1 cut(s) 1854
BseSI GKGCMC 1 cut(s) 723
BseXI GCAGC 4 cut(s) 94, 195, 341, 1891
BsgI GTGCAG 2 cut(s) 411, 1738
BshFI GGCC 2 cut(s) 158, 785
BsiHKAI GWGCWC 1 cut(s) 805
BsiHKCI CYCGRG 1 cut(s) 1422
BsiSI CCGG 1 cut(s) 1946
BslI CCNNNNNNNGG 4 cut(s) 728, 953, 1007, 1286
BsmAI GTCTC 4 cut(s) 37, 506, 995, 1511
BsnI GGCC 2 cut(s) 158, 785
Bso31I GGTCTC 2 cut(s) 506, 995
BsoBI CYCGRG 1 cut(s) 1422
Bsp1286I GDGCHC 2 cut(s) 723, 805
Bsp13I TCCGGA 1 cut(s) 1945
Bsp1407I TGTACA 1 cut(s) 845
Bsp143I GATC 4 cut(s) 306, 436, 469, 1603
BspANI GGCC 2 cut(s) 158, 785
BspCNI CTCAG 5 cut(s) 23, 250, 266, 1370, 1777
BspEI TCCGGA 1 cut(s) 1945
BspLI GGNNCC 1 cut(s) 1605
BspPI GGATC 3 cut(s) 314, 1598, 1611
BspTNI GGTCTC 2 cut(s) 506, 995
BsrDI GCAATG 6 cut(s) 19, 882, 1198, 1260, 1471, 1963
BsrGI TGTACA 1 cut(s) 845
BsrI ACTGG 7 cut(s) 193, 626, 792, 827, 1045, 1123, 1291
BssMI GATC 4 cut(s) 306, 436, 469, 1603
Bst2UI CCWGG 2 cut(s) 1920, 2022
Bst4CI ACNGT 6 cut(s) 31, 430, 646, 718, 855, 1154
BstAPI GCANNNNNTGC 2 cut(s) 943, 1088
BstAUI TGTACA 1 cut(s) 845
BstC8I GCNNGC 4 cut(s) 1462, 1884, 1970, 1974
BstDEI CTNAG 5 cut(s) 10, 253, 258, 1357, 1785
BstF5I GGATG 3 cut(s) 622, 962, 1531
BstHHI GCGC 1 cut(s) 420
BstKTI GATC 4 cut(s) 309, 439, 472, 1606
BstMAI GTCTC 4 cut(s) 37, 506, 995, 1511
BstMBI GATC 4 cut(s) 306, 436, 469, 1603
BstMWI GCNNNNNNNGC 4 cut(s) 943, 1088, 1742, 1969
BstNI CCWGG 2 cut(s) 1920, 2022
BstNSI RCATGY 2 cut(s) 768, 1976
BstSCI CCNGG 2 cut(s) 1918, 2020
BstSFI CTRYAG 1 cut(s) 642
BstSLI GKGCMC 1 cut(s) 723
BstV1I GCAGC 4 cut(s) 94, 195, 341, 1891
BstX2I RGATCY 1 cut(s) 1603
BstXI CCANNNNNNTGG 1 cut(s) 1926
BstYI RGATCY 1 cut(s) 1603
Bsu36I CCTNAGG 1 cut(s) 10
BsuI GTATCC 1 cut(s) 1606
BsuRI GGCC 2 cut(s) 158, 785
BtsCI GGATG 3 cut(s) 622, 962, 1531
BtsI GCAGTG 1 cut(s) 1776
BtsIMutI CAGTG 6 cut(s) 186, 633, 651, 805, 1656, 1776
Cac8I GCNNGC 4 cut(s) 1462, 1884, 1970, 1974
CaiI CAGNNNCTG 1 cut(s) 35
CfoI GCGC 1 cut(s) 420
Cfr13I GGNCC 1 cut(s) 573
Csp6I GTAC 8 cut(s) 773, 813, 846, 1215, 1284, 1373, 1497, 1629
CspCI CAANNNNNGTGG 2 cut(s) 1653, 1688
CviAII CATG 9 cut(s) 101, 135, 559, 765, 770, 898, 961, 1079, 1973
CviQI GTAC 8 cut(s) 773, 813, 846, 1215, 1284, 1373, 1497, 1629
DdeI CTNAG 5 cut(s) 10, 253, 258, 1357, 1785
DpnI GATC 4 cut(s) 308, 438, 471, 1605
DpnII GATC 4 cut(s) 306, 436, 469, 1603
DraIII CACNNNGTG 1 cut(s) 986
EaeI YGGCCR 1 cut(s) 783
Eco31I GGTCTC 2 cut(s) 506, 995
Eco47I GGWCC 1 cut(s) 573
Eco57I CTGAAG 3 cut(s) 1166, 1584, 1680
Eco81I CCTNAGG 1 cut(s) 10
Eco88I CYCGRG 1 cut(s) 1422
EcoO109I RGGNCCY 1 cut(s) 573
EcoRII CCWGG 2 cut(s) 1918, 2020
EcoT22I ATGCAT 2 cut(s) 962, 1965
FaeI CATG 9 cut(s) 104, 138, 562, 768, 773, 901, 964, 1082, 1976
FatI CATG 9 cut(s) 100, 134, 558, 764, 769, 897, 960, 1078, 1972
FblI GTMKAC 1 cut(s) 1985
Fnu4HI GCNGC 4 cut(s) 83, 209, 330, 1880
FokI GGATG 3 cut(s) 609, 969, 1538
Fsp4HI GCNGC 4 cut(s) 83, 209, 330, 1880
FspBI CTAG 3 cut(s) 525, 810, 984
GlaI GCGC 1 cut(s) 419
GluI GCNGC 4 cut(s) 83, 209, 330, 1880
GsuI CTGGAG 1 cut(s) 210
HaeIII GGCC 2 cut(s) 158, 785
HapII CCGG 1 cut(s) 1946
HhaI GCGC 1 cut(s) 420
Hin1II CATG 9 cut(s) 104, 138, 562, 768, 773, 901, 964, 1082, 1976
Hin6I GCGC 1 cut(s) 418
HinP1I GCGC 1 cut(s) 418
HincII GTYRAC 2 cut(s) 17, 880
HindII GTYRAC 2 cut(s) 17, 880
HindIII AAGCTT 1 cut(s) 1233
HpaII CCGG 1 cut(s) 1946
HphI GGTGA 3 cut(s) 1073, 1719, 1859
Hpy166II GTNNAC 5 cut(s) 17, 848, 880, 1582, 1986
Hpy188I TCNGA 4 cut(s) 153, 340, 383, 469
Hpy188III TCNNGA 8 cut(s) 44, 473, 994, 1472, 1523, 1607, 1894, 1946
Hpy8I GTNNAC 5 cut(s) 17, 848, 880, 1582, 1986
HpyAV CCTTC 6 cut(s) 101, 148, 1326, 1394, 1447, 1947
HpyCH4III ACNGT 6 cut(s) 31, 430, 646, 718, 855, 1154
HpyCH4IV ACGT 1 cut(s) 727
HpyF10VI GCNNNNNNNGC 4 cut(s) 943, 1088, 1742, 1969
HpyF3I CTNAG 5 cut(s) 10, 253, 258, 1357, 1785
HpySE526I ACGT 1 cut(s) 727
Hsp92II CATG 9 cut(s) 104, 138, 562, 768, 773, 901, 964, 1082, 1976
HspAI GCGC 1 cut(s) 418
Kpn2I TCCGGA 1 cut(s) 1945
Kzo9I GATC 4 cut(s) 306, 436, 469, 1603
LmnI GCTCC 2 cut(s) 191, 1891
Lsp1109I GCAGC 4 cut(s) 94, 195, 341, 1891
LweI GCATC 5 cut(s) 69, 923, 947, 1633, 1733
MaeI CTAG 3 cut(s) 525, 810, 984
MaeII ACGT 1 cut(s) 727
MaeIII GTNAC 8 cut(s) 518, 628, 829, 1021, 1061, 1154, 1426, 1549
MalI GATC 4 cut(s) 308, 438, 471, 1605
MboI GATC 4 cut(s) 306, 436, 469, 1603
MboII GAAGA 5 cut(s) 1128, 1357, 1577, 1717, 1720
MflI RGATCY 1 cut(s) 1603
MhlI GDGCHC 2 cut(s) 723, 805
MlsI TGGCCA 1 cut(s) 785
MluNI TGGCCA 1 cut(s) 785
MlyI GAGTC 3 cut(s) 674, 1513, 1991
Mox20I TGGCCA 1 cut(s) 785
Mph1103I ATGCAT 2 cut(s) 962, 1965
MroI TCCGGA 1 cut(s) 1945
MscI TGGCCA 1 cut(s) 785
MseI TTAA 8 cut(s) 180, 359, 480, 569, 638, 1242, 1413, 1677
MslI CAYNNNNRTG 3 cut(s) 45, 1077, 1977
Msp20I TGGCCA 1 cut(s) 785
MspA1I CMGCKG 1 cut(s) 257
MspI CCGG 1 cut(s) 1946
MspR9I CCNGG 2 cut(s) 1920, 2022
MvaI CCWGG 2 cut(s) 1920, 2022
MwoI GCNNNNNNNGC 4 cut(s) 943, 1088, 1742, 1969
NdeII GATC 4 cut(s) 306, 436, 469, 1603
NlaIII CATG 9 cut(s) 104, 138, 562, 768, 773, 901, 964, 1082, 1976
NlaIV GGNNCC 1 cut(s) 1605
NmuCI GTSAC 3 cut(s) 518, 628, 1061
NsiI ATGCAT 2 cut(s) 962, 1965
NspI RCATGY 2 cut(s) 768, 1976
PaeI GCATGC 1 cut(s) 1976
PaeR7I CTCGAG 1 cut(s) 1422
PciI ACATGT 1 cut(s) 764
PfeI GAWTC 7 cut(s) 167, 395, 490, 997, 1119, 1504, 1711
PkrI GCNGC 4 cut(s) 84, 210, 331, 1881
PleI GAGTC 3 cut(s) 674, 1513, 1990
PpsI GAGTC 3 cut(s) 674, 1513, 1990
PpuMI RGGWCCY 1 cut(s) 573
PscI ACATGT 1 cut(s) 764
PsiI TTATAA 2 cut(s) 536, 750
Psp5II RGGWCCY 1 cut(s) 573
Psp6I CCWGG 2 cut(s) 1918, 2020
PspGI CCWGG 2 cut(s) 1918, 2020
PspN4I GGNNCC 1 cut(s) 1605
PspPI GGNCC 1 cut(s) 573
PspPPI RGGWCCY 1 cut(s) 573
PspXI VCTCGAGB 1 cut(s) 1422
PstNI CAGNNNCTG 1 cut(s) 35
PsuI RGATCY 1 cut(s) 1603
PvuII CAGCTG 1 cut(s) 257
RsaI GTAC 8 cut(s) 774, 814, 847, 1216, 1285, 1374, 1498, 1630
RsaNI GTAC 8 cut(s) 773, 813, 846, 1215, 1284, 1373, 1497, 1629
RseI CAYNNNNRTG 3 cut(s) 45, 1077, 1977
SaqAI TTAA 8 cut(s) 180, 359, 480, 569, 638, 1242, 1413, 1677
SatI GCNGC 4 cut(s) 83, 209, 330, 1880
Sau3AI GATC 4 cut(s) 306, 436, 469, 1603
Sau96I GGNCC 1 cut(s) 573
ScaI AGTACT 1 cut(s) 814
SchI GAGTC 3 cut(s) 674, 1513, 1991
ScrFI CCNGG 2 cut(s) 1920, 2022
SduI GDGCHC 2 cut(s) 723, 805
SfaNI GCATC 5 cut(s) 69, 923, 947, 1633, 1733
SfcI CTRYAG 1 cut(s) 642
Sfr274I CTCGAG 1 cut(s) 1422
SinI GGWCC 1 cut(s) 573
SlaI CTCGAG 1 cut(s) 1422
SmiMI CAYNNNNRTG 3 cut(s) 45, 1077, 1977
SmlI CTYRAG 4 cut(s) 110, 1422, 1492, 1892
SmoI CTYRAG 4 cut(s) 110, 1422, 1492, 1892
SpeI ACTAGT 1 cut(s) 809
SphI GCATGC 1 cut(s) 1976
SspI AATATT 1 cut(s) 1448
SspMI CTAG 3 cut(s) 525, 810, 984
StyD4I CCNGG 2 cut(s) 1918, 2020
TaaI ACNGT 6 cut(s) 31, 430, 646, 718, 855, 1154
TaiI ACGT 1 cut(s) 730
TaqI TCGA 4 cut(s) 398, 917, 1392, 1423
TatI WGTACW 3 cut(s) 812, 845, 1496
TfiI GAWTC 7 cut(s) 167, 395, 490, 997, 1119, 1504, 1711
Tru1I TTAA 8 cut(s) 180, 359, 480, 569, 638, 1242, 1413, 1677
Tru9I TTAA 8 cut(s) 180, 359, 480, 569, 638, 1242, 1413, 1677
TscAI CASTG 6 cut(s) 193, 633, 651, 805, 1663, 1783
TseFI GTSAC 3 cut(s) 518, 628, 1061
TseI GCWGC 4 cut(s) 82, 208, 329, 1879
Tsp45I GTSAC 3 cut(s) 518, 628, 1061
TspGWI ACGGA 1 cut(s) 969
TspRI CASTG 6 cut(s) 193, 633, 651, 805, 1663, 1783
VpaK11BI GGWCC 1 cut(s) 573
XapI RAATTY 6 cut(s) 334, 341, 593, 1015, 1388, 1433
XceI RCATGY 2 cut(s) 768, 1976
XhoI CTCGAG 1 cut(s) 1422
XmiI GTMKAC 1 cut(s) 1985
XspI CTAG 3 cut(s) 525, 810, 984
ZrmI AGTACT 1 cut(s) 814
Zsp2I ATGCAT 2 cut(s) 962, 1965
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.