RchiOBHm_Chr4g0422781

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0001357
Physical Location & Seq
Forward (+)
48368499 .. 48370471
1973 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ39222

Sequence Viewer

Length: 1539 bp
ATGAAAATCACACGTGCAAGGAACCAATTAGATGCTTTGGGAGTAAGGATGGAAGACCAGGATATTGTTGTGGTTTTACTCAATGGTTTGCCTGCAGAATTTAATCTCATAAAAGCAATTATTCGGGCAAGGAAAACCCCAATTACAATGCAAGAATTGAGGATTCAATTACTAGCTGCTGAAAGAGATATTGCAAATAGGGCTATTCTGAATATAATGCCAGCCTTCTCTGTTAGGAGAACTAAGAAGAATGTGTCTCAGAGGTGTCTAAATGGCAATAGGAATGACATTGGCAGCATGTTTGAAAATGGTGGAGGCTACTGGAATAATTTTGGGTTGTCTCCAGAGTGTCAAATCTGTAGGAAGAGAGGCCACACTGCTGCATATTGCTTCTACAGGAATGACATCCCTCCTGATAATCTCTCTAACTCTGTGATCATTTGTCAAATCTGTGGTCTGAAGGGACATGCAGCCTTGGACTGCCATCACAAGTCAAACTTTGCATTACAAGGAGCTGAACCATCTTCTACTCTTGCTGCAATGACTGTGCATAATACCAATGGAGCTAGTACTTCTGGTGCTTCTATTACTGCACAGGGTTTCTCATATGCAGTCTCTCTTGTTGTGGTTGATGGGGGAGATCAGAATGTGATAAATAATGATCAAGTTGATGCACAGTTGAAGTTACCTCGTGAACAATTTGATCAAAGAAGAAGTCAGATTTATGAGAAATCCATGCTTACCAAAGCCAAAGGTTTGAGTATCAAGAAGAAGACATTTCGGGATTTTTCTGCTTATTCCTACATTGCTCAACAAAAATTGTTTGATGAGTTTGCATACTTCAGTGGCTTTACTTCTGCATTGGATATCCATGATGCTATAGAACCAAAGACGTTCAAAACTGTTGTTGGAAAATCAAAGTGGGATTCTGCTATGAATGGAGAAACTAATGCCCTTAAGAAGCAAGAGATCAGTTACAGACATAATGGAGTGTTCATCTATCAAGAAAGATATGCAAAGGATTTTATTAATGGTCAAGCATTAATTAAAACTGGAATTGAAAAAGACAAAGGCAGTAAACTGGAGGTGCTTTCAAGGGTTGAACTTTCTCCAAACACAATTGGTAAAGGTGGCTCCAAGAAGCAAAAGTCCTCTAATCGCGTGGCTACTAGAACTGAGCAAGTCCAGGCACAGCCTCAATTGAATTATGGTCAAGAAACCATGGATCAAGTATATAATCAGCATTCCATGCTTACCAGAGCCAAACATGTAACTGTCAATAAGCTGACATTTCAACCATTTCAAGATTTTTGTGCATTAATTGATAAAACTAGTATGGATACATCAACAGCTAGCACGCAAAGCATTTTCACGTTGTTAGAGAAAGAGGGTAAATGTATGATTTGTTACTTCATTATGTTTCTACTTCTGAGCATTCTCCAACTTCTGAGCATACTGAAGATATTCTTACTAAAAGGTTACACAAGCTCAATAGTCAGTACACATAGATCCAATCTCAGTTTGGTTAACCATAACTGA
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
No domains found.

Protein Analysis

512

Amino Acids

57.28

Weight (kDa)

9.41

Isoelectric Point (pI)

31.29

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 3 - 63 5.1e-09 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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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 1161
AclWI GGATC 2 cut(s) 1233, 1503
AcsI RAATTY 1 cut(s) 98
AcuI CTGAAG 3 cut(s) 479, 826, 1478
AcvI CACGTG 1 cut(s) 14
AfaI GTAC 2 cut(s) 571, 1501
AflII CTTAAG 1 cut(s) 956
AflIII ACRYGT 2 cut(s) 11, 1267
AhlI ACTAGT 1 cut(s) 1331
AjnI CCWGG 2 cut(s) 57, 1185
AluBI AGCT 6 cut(s) 176, 515, 566, 1285, 1352, 1488
AluI AGCT 6 cut(s) 176, 515, 566, 1285, 1352, 1488
Alw26I GTCTC 3 cut(s) 261, 345, 619
AlwI GGATC 2 cut(s) 1233, 1503
AoxI GGCC 1 cut(s) 370
ApeKI GCWGC 5 cut(s) 176, 294, 380, 470, 536
ApoI RAATTY 1 cut(s) 98
ArsI GACNNNNNNTTYG 4 cut(s) 439, 471, 700, 732
AseI ATTAAT 3 cut(s) 1029, 1043, 1319
Asp700I GAANNNNTTC 1 cut(s) 1463
AsuNHI GCTAGC 1 cut(s) 1352
BauI CACGAG 1 cut(s) 690
BbrPI CACGTG 1 cut(s) 14
BbsI GAAGAC 2 cut(s) 60, 779
BbvI GCAGC 5 cut(s) 163, 306, 367, 482, 523
BccI CCATC 4 cut(s) 43, 492, 529, 626
BciT130I CCWGG 2 cut(s) 59, 1187
BciVI GTATCC 1 cut(s) 1333
BclI TGATCA 3 cut(s) 435, 661, 703
BcoDI GTCTC 3 cut(s) 261, 345, 619
BcuI ACTAGT 1 cut(s) 1331
BfaI CTAG 5 cut(s) 173, 567, 1170, 1332, 1353
BfmI CTRYAG 4 cut(s) 93, 358, 394, 879
BfrI CTTAAG 1 cut(s) 956
BfuI GTATCC 1 cut(s) 1333
BisI GCNGC 5 cut(s) 177, 295, 381, 471, 537
BlsI GCNGC 5 cut(s) 178, 296, 382, 472, 538
BmcAI AGTACT 1 cut(s) 571
Bme1390I CCNGG 2 cut(s) 59, 1187
BmiI GGNNCC 2 cut(s) 23, 1135
BmrFI CCNGG 2 cut(s) 59, 1187
BmsI GCATC 3 cut(s) 22, 661, 865
BmtI GCTAGC 1 cut(s) 1356
BpiI GAAGAC 2 cut(s) 60, 779
BpmI CTGGAG 2 cut(s) 327, 1103
BsaAI YACGTR 1 cut(s) 14
BsaJI CCNNGG 2 cut(s) 474, 1221
Bse1I ACTGG 3 cut(s) 326, 1057, 1086
Bse3DI GCAATG 2 cut(s) 546, 804
BseBI CCWGG 2 cut(s) 59, 1187
BseDI CCNNGG 2 cut(s) 474, 1221
BseGI GGATG 2 cut(s) 54, 405
BseMI GCAATG 2 cut(s) 546, 804
BseMII CTCAG 5 cut(s) 272, 1167, 1421, 1439, 1531
BseNI ACTGG 3 cut(s) 326, 1057, 1086
BseXI GCAGC 5 cut(s) 163, 306, 367, 482, 523
BsgI GTGCAG 1 cut(s) 576
Bsh1236I CGCG 1 cut(s) 1161
BshFI GGCC 1 cut(s) 372
BslFI GGGAC 1 cut(s) 477
BsmAI GTCTC 3 cut(s) 261, 345, 619
BsmFI GGGAC 1 cut(s) 477
BsmI GAATGC 2 cut(s) 1243, 1434
BsnI GGCC 1 cut(s) 372
Bsp143I GATC 7 cut(s) 435, 640, 661, 703, 969, 1225, 1508
Bsp19I CCATGG 1 cut(s) 1221
BspANI GGCC 1 cut(s) 372
BspCNI CTCAG 5 cut(s) 271, 1168, 1422, 1440, 1530
BspFNI CGCG 1 cut(s) 1161
BspLI GGNNCC 2 cut(s) 23, 1135
BspMAI CTGCAG 1 cut(s) 97
BspOI GCTAGC 1 cut(s) 1356
BspPI GGATC 2 cut(s) 1233, 1503
BspTI CTTAAG 1 cut(s) 956
BsrDI GCAATG 2 cut(s) 546, 804
BsrI ACTGG 3 cut(s) 326, 1057, 1086
BssECI CCNNGG 2 cut(s) 474, 1221
BssMI GATC 7 cut(s) 435, 640, 661, 703, 969, 1225, 1508
BssSI CACGAG 1 cut(s) 690
BssT1I CCWWGG 2 cut(s) 474, 1221
Bst2BI CACGAG 1 cut(s) 690
Bst2UI CCWGG 2 cut(s) 59, 1187
Bst4CI ACNGT 4 cut(s) 547, 678, 904, 1276
Bst6I CTCTTC 1 cut(s) 359
BstAFI CTTAAG 1 cut(s) 956
BstAPI GCANNNNNTGC 1 cut(s) 1249
BstBAI YACGTR 1 cut(s) 14
BstC8I GCNNGC 4 cut(s) 93, 222, 1354, 1358
BstDEI CTNAG 6 cut(s) 243, 258, 1176, 1430, 1448, 1517
BstDSI CCRYGG 1 cut(s) 1221
BstF5I GGATG 2 cut(s) 54, 405
BstFNI CGCG 1 cut(s) 1161
BstKTI GATC 7 cut(s) 438, 643, 664, 706, 972, 1228, 1511
BstMAI GTCTC 3 cut(s) 261, 345, 619
BstMBI GATC 7 cut(s) 435, 640, 661, 703, 969, 1225, 1508
BstMWI GCNNNNNNNGC 3 cut(s) 200, 1249, 1362
BstNI CCWGG 2 cut(s) 59, 1187
BstNSI RCATGY 3 cut(s) 301, 470, 1271
BstSCI CCNGG 2 cut(s) 57, 1185
BstSFI CTRYAG 4 cut(s) 93, 358, 394, 879
BstUI CGCG 1 cut(s) 1161
BstV1I GCAGC 5 cut(s) 163, 306, 367, 482, 523
BstV2I GAAGAC 2 cut(s) 60, 779
BstX2I RGATCY 1 cut(s) 1508
BstYI RGATCY 1 cut(s) 1508
BsuI GTATCC 1 cut(s) 1333
BsuRI GGCC 1 cut(s) 372
BtgI CCRYGG 1 cut(s) 1221
BtsCI GGATG 2 cut(s) 54, 405
BtsI GCAGTG 1 cut(s) 375
BtsIMutI CAGTG 2 cut(s) 375, 850
Cac8I GCNNGC 4 cut(s) 93, 222, 1354, 1358
Csp6I GTAC 2 cut(s) 570, 1500
CviAII CATG 7 cut(s) 298, 467, 736, 872, 1222, 1249, 1268
CviQI GTAC 2 cut(s) 570, 1500
DdeI CTNAG 6 cut(s) 243, 258, 1176, 1430, 1448, 1517
DpnI GATC 7 cut(s) 437, 642, 663, 705, 971, 1227, 1510
DpnII GATC 7 cut(s) 435, 640, 661, 703, 969, 1225, 1508
Eam1104I CTCTTC 1 cut(s) 359
EarI CTCTTC 1 cut(s) 359
Eco130I CCWWGG 2 cut(s) 474, 1221
Eco32I GATATC 1 cut(s) 868
Eco57I CTGAAG 3 cut(s) 479, 826, 1478
Eco72I CACGTG 1 cut(s) 14
EcoRII CCWGG 2 cut(s) 57, 1185
EcoRV GATATC 1 cut(s) 868
EcoT14I CCWWGG 2 cut(s) 474, 1221
ErhI CCWWGG 2 cut(s) 474, 1221
FaeI CATG 7 cut(s) 301, 470, 739, 875, 1225, 1252, 1271
FalI AAGNNNNNCTT 4 cut(s) 482, 514, 1451, 1483
FaqI GGGAC 1 cut(s) 477
FatI CATG 7 cut(s) 297, 466, 735, 871, 1221, 1248, 1267
FauNDI CATATG 1 cut(s) 607
FbaI TGATCA 3 cut(s) 435, 661, 703
Fnu4HI GCNGC 5 cut(s) 177, 295, 381, 471, 537
FokI GGATG 2 cut(s) 61, 392
Fsp4HI GCNGC 5 cut(s) 177, 295, 381, 471, 537
FspBI CTAG 5 cut(s) 173, 567, 1170, 1332, 1353
GluI GCNGC 5 cut(s) 177, 295, 381, 471, 537
GsuI CTGGAG 2 cut(s) 327, 1103
HaeIII GGCC 1 cut(s) 372
Hin1II CATG 7 cut(s) 301, 470, 739, 875, 1225, 1252, 1271
HincII GTYRAC 1 cut(s) 1528
HindII GTYRAC 1 cut(s) 1528
HinfI GANTC 2 cut(s) 163, 926
HpaI GTTAAC 1 cut(s) 1528
Hpy166II GTNNAC 4 cut(s) 695, 1079, 1502, 1528
Hpy188I TCNGA 7 cut(s) 210, 261, 459, 645, 720, 1431, 1449
Hpy188III TCNNGA 8 cut(s) 344, 413, 692, 766, 782, 1004, 1214, 1304
Hpy8I GTNNAC 4 cut(s) 695, 1079, 1502, 1528
HpyAV CCTTC 2 cut(s) 235, 454
HpyCH4III ACNGT 4 cut(s) 547, 678, 904, 1276
HpyCH4IV ACGT 3 cut(s) 13, 893, 1373
HpyF10VI GCNNNNNNNGC 3 cut(s) 200, 1249, 1362
HpyF3I CTNAG 6 cut(s) 243, 258, 1176, 1430, 1448, 1517
HpySE526I ACGT 3 cut(s) 13, 893, 1373
Hsp92II CATG 7 cut(s) 301, 470, 739, 875, 1225, 1252, 1271
Ksp22I TGATCA 3 cut(s) 435, 661, 703
KspAI GTTAAC 1 cut(s) 1528
Kzo9I GATC 7 cut(s) 435, 640, 661, 703, 969, 1225, 1508
LmnI GCTCC 3 cut(s) 512, 563, 1139
Lsp1109I GCAGC 5 cut(s) 163, 306, 367, 482, 523
LweI GCATC 3 cut(s) 22, 661, 865
MaeI CTAG 5 cut(s) 173, 567, 1170, 1332, 1353
MaeII ACGT 3 cut(s) 13, 893, 1373
MaeIII GTNAC 5 cut(s) 684, 974, 1270, 1406, 1478
MalI GATC 7 cut(s) 437, 642, 663, 705, 971, 1227, 1510
MboI GATC 7 cut(s) 435, 640, 661, 703, 969, 1225, 1508
MboII GAAGA 8 cut(s) 65, 259, 376, 516, 723, 781, 784, 1471
MfeI CAATTG 2 cut(s) 1119, 1199
MflI RGATCY 1 cut(s) 1508
MmeI TCCRAC 2 cut(s) 889, 1465
MroXI GAANNNNTTC 1 cut(s) 1463
MseI TTAA 7 cut(s) 102, 957, 1029, 1043, 1047, 1319, 1527
MspCI CTTAAG 1 cut(s) 956
MspR9I CCNGG 2 cut(s) 59, 1187
MunI CAATTG 2 cut(s) 1119, 1199
Mva1269I GAATGC 2 cut(s) 1243, 1434
MvaI CCWGG 2 cut(s) 59, 1187
MvnI CGCG 1 cut(s) 1161
MwoI GCNNNNNNNGC 3 cut(s) 200, 1249, 1362
NcoI CCATGG 1 cut(s) 1221
NdeI CATATG 1 cut(s) 607
NdeII GATC 7 cut(s) 435, 640, 661, 703, 969, 1225, 1508
NheI GCTAGC 1 cut(s) 1352
NlaIII CATG 7 cut(s) 301, 470, 739, 875, 1225, 1252, 1271
NlaIV GGNNCC 2 cut(s) 23, 1135
NspI RCATGY 3 cut(s) 301, 470, 1271
PacI TTAATTAA 1 cut(s) 1047
PciI ACATGT 1 cut(s) 1267
PctI GAATGC 2 cut(s) 1243, 1434
PdmI GAANNNNTTC 1 cut(s) 1463
PfeI GAWTC 2 cut(s) 163, 926
PkrI GCNGC 5 cut(s) 178, 296, 382, 472, 538
PmaCI CACGTG 1 cut(s) 14
PmlI CACGTG 1 cut(s) 14
Ppu21I YACGTR 1 cut(s) 14
PscI ACATGT 1 cut(s) 1267
PshBI ATTAAT 3 cut(s) 1029, 1043, 1319
Psp6I CCWGG 2 cut(s) 57, 1185
PspCI CACGTG 1 cut(s) 14
PspGI CCWGG 2 cut(s) 57, 1185
PspN4I GGNNCC 2 cut(s) 23, 1135
PstI CTGCAG 1 cut(s) 97
PsuI RGATCY 1 cut(s) 1508
RsaI GTAC 2 cut(s) 571, 1501
RsaNI GTAC 2 cut(s) 570, 1500
SaqAI TTAA 7 cut(s) 102, 957, 1029, 1043, 1047, 1319, 1527
SatI GCNGC 5 cut(s) 177, 295, 381, 471, 537
Sau3AI GATC 7 cut(s) 435, 640, 661, 703, 969, 1225, 1508
ScaI AGTACT 1 cut(s) 571
ScrFI CCNGG 2 cut(s) 59, 1187
SfaNI GCATC 3 cut(s) 22, 661, 865
SfcI CTRYAG 4 cut(s) 93, 358, 394, 879
SmlI CTYRAG 1 cut(s) 956
SmoI CTYRAG 1 cut(s) 956
SpeI ACTAGT 1 cut(s) 1331
SspMI CTAG 5 cut(s) 173, 567, 1170, 1332, 1353
StyD4I CCNGG 2 cut(s) 57, 1185
StyI CCWWGG 2 cut(s) 474, 1221
TaaI ACNGT 4 cut(s) 547, 678, 904, 1276
TaiI ACGT 3 cut(s) 16, 896, 1376
TatI WGTACW 2 cut(s) 569, 1499
TfiI GAWTC 2 cut(s) 163, 926
Tru1I TTAA 7 cut(s) 102, 957, 1029, 1043, 1047, 1319, 1527
Tru9I TTAA 7 cut(s) 102, 957, 1029, 1043, 1047, 1319, 1527
TscAI CASTG 2 cut(s) 382, 850
TseI GCWGC 5 cut(s) 176, 294, 380, 470, 536
TspDTI ATGAA 4 cut(s) 17, 950, 985, 1402
TspRI CASTG 2 cut(s) 382, 850
Vha464I CTTAAG 1 cut(s) 956
VspI ATTAAT 3 cut(s) 1029, 1043, 1319
XapI RAATTY 1 cut(s) 98
XceI RCATGY 3 cut(s) 301, 470, 1271
XcmI CCANNNNNNNNNTGG 1 cut(s) 1519
XmnI GAANNNNTTC 1 cut(s) 1463
XspI CTAG 5 cut(s) 173, 567, 1170, 1332, 1353
ZrmI AGTACT 1 cut(s) 571
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.