AT1G21280

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
1
OG0006436
Physical Location & Seq
Reverse (-)
7447490 .. 7448483
994 bp
Loading structure...
UTR
Exon/CDS
Intron
AT1G21280.1

Sequence Viewer

Length: 714 bp
ATGGCGGAAACTATCAAGAGCGTATCTCCAACATCAGACCCCGATTCACCGTATTATCTCCCTCCCGATATTCATCATCCCTCCGATTTCTCTATCCAAAAACTCAGCAAAGACGAAGACAACTACGTCGCCTGGAAAATTCGATTTCGCTCTTTCCTCCGAGTCACGAAAAAATTCGGGTTTATCGACGGTACTCTCCCGAAGCCAGACCCTTTCTCTCCGCTCTATCAGCCATGGGAACAATGCAACGCAATGGTTATGTATTGGCTGATGAATTCGATGACCGATAAGCTTCTAGAATCTGTTATGTACGCGGAGACTGCTCATAAAATGTGGGAAGATCTCAGACGTGTATTCGTTCCTTGTGTTGATTTGAAGATTTATCAGCTTCGTCGGAGACTCGCGACGCTCAGGCAAGGTGGTGACTCTGTTGAGGAGTATTTTGGGAAATTGAGTAAAGTTTGGATGGAGTTGTCGGAGTATGCTCCTATACCGGAGTGTAAATGCGGTGGTTGCAATTGCGAGTGTACTAAACGAGCTGAAGAGGCGAGAGAGAAGGAGCAGCGTTACGAGTTTTTGATGGGGTTGAAGTTGAACCAAGGCTTCGAGGCTGTGACGACAAAAATCATGTTCCAGAAACCTCCTCCGTCACTTCACGAAGCTTTCGCTATGGTCAAAGATGCAGAATCGATGATGAAGTGGTACAGTAGATGA
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_3

Protein Analysis

237

Amino Acids

27.76

Weight (kDa)

6.9

Isoelectric Point (pI)

54.36

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_3 PF14244 26 - 70 1.8e-15 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)
AasI GACNNNNNNGTC 1 cut(s) 125
AccBSI CCGCTC 1 cut(s) 223
AccII CGCG 2 cut(s) 314, 404
AciI CCGC 4 cut(s) 5, 221, 314, 507
AcsI RAATTY 3 cut(s) 138, 173, 274
AcuI CTGAAG 1 cut(s) 561
AfaI GTAC 4 cut(s) 193, 311, 529, 704
AflIII ACRYGT 1 cut(s) 349
AgsI TTSAA 3 cut(s) 376, 589, 595
AjiI CACGTC 1 cut(s) 350
AjnI CCWGG 1 cut(s) 131
AluBI AGCT 4 cut(s) 292, 388, 539, 662
AluI AGCT 4 cut(s) 292, 388, 539, 662
Alw26I GTCTC 2 cut(s) 311, 391
ApeKI GCWGC 1 cut(s) 562
ApoI RAATTY 3 cut(s) 138, 173, 274
Asp700I GAANNNNTTC 1 cut(s) 173
AsuHPI GGTGA 2 cut(s) 39, 434
BbsI GAAGAC 1 cut(s) 123
BbvI GCAGC 1 cut(s) 574
BccI CCATC 2 cut(s) 460, 574
BciT130I CCWGG 1 cut(s) 133
BcoDI GTCTC 2 cut(s) 311, 391
BfaI CTAG 1 cut(s) 296
BglII AGATCT 1 cut(s) 340
BisI GCNGC 1 cut(s) 563
BlsI GCNGC 1 cut(s) 564
Bme1390I CCNGG 1 cut(s) 133
BmgBI CACGTC 1 cut(s) 350
BmrFI CCNGG 1 cut(s) 133
BmsI GCATC 1 cut(s) 670
BpiI GAAGAC 1 cut(s) 123
BplI GAGNNNNNCTC 2 cut(s) 10, 42
Bpu10I CCTNAGC 1 cut(s) 410
Bsa29I ATCGAT 1 cut(s) 689
BsaBI GATNNNNATC 1 cut(s) 72
BsaJI CCNNGG 2 cut(s) 233, 598
BsaWI WCCGGW 1 cut(s) 493
Bse3DI GCAATG 1 cut(s) 258
Bse8I GATNNNNATC 1 cut(s) 72
BseBI CCWGG 1 cut(s) 133
BseCI ATCGAT 1 cut(s) 689
BseDI CCNNGG 2 cut(s) 233, 598
BseGI GGATG 2 cut(s) 76, 471
BseJI GATNNNNATC 1 cut(s) 72
BseMI GCAATG 1 cut(s) 258
BseMII CTCAG 3 cut(s) 118, 358, 424
BseRI GAGGAG 2 cut(s) 449, 633
BseXI GCAGC 1 cut(s) 574
Bsh1236I CGCG 2 cut(s) 314, 404
BshVI ATCGAT 1 cut(s) 689
BsiSI CCGG 1 cut(s) 494
BsmAI GTCTC 2 cut(s) 311, 391
Bsp143I GATC 1 cut(s) 340
Bsp19I CCATGG 1 cut(s) 233
Bsp68I TCGCGA 1 cut(s) 404
BspACI CCGC 4 cut(s) 5, 221, 314, 507
BspCNI CTCAG 3 cut(s) 117, 357, 423
BspDI ATCGAT 1 cut(s) 689
BspFNI CGCG 2 cut(s) 314, 404
BsrBI CCGCTC 1 cut(s) 223
BsrDI GCAATG 1 cut(s) 258
BssECI CCNNGG 2 cut(s) 233, 598
BssMI GATC 1 cut(s) 340
BssT1I CCWWGG 2 cut(s) 233, 598
Bst2UI CCWGG 1 cut(s) 133
Bst4CI ACNGT 3 cut(s) 51, 191, 707
Bst6I CTCTTC 1 cut(s) 537
BstDEI CTNAG 3 cut(s) 104, 344, 410
BstDSI CCRYGG 1 cut(s) 233
BstF5I GGATG 2 cut(s) 76, 471
BstFNI CGCG 2 cut(s) 314, 404
BstKTI GATC 1 cut(s) 343
BstMAI GTCTC 2 cut(s) 311, 391
BstMBI GATC 1 cut(s) 340
BstMWI GCNNNNNNNGC 4 cut(s) 229, 320, 513, 545
BstNI CCWGG 1 cut(s) 133
BstSCI CCNGG 1 cut(s) 131
BstUI CGCG 2 cut(s) 314, 404
BstV1I GCAGC 1 cut(s) 574
BstV2I GAAGAC 1 cut(s) 123
BstX2I RGATCY 1 cut(s) 340
BstYI RGATCY 1 cut(s) 340
Bsu15I ATCGAT 1 cut(s) 689
BsuTUI ATCGAT 1 cut(s) 689
BtgI CCRYGG 1 cut(s) 233
BtrI CACGTC 1 cut(s) 350
BtsCI GGATG 2 cut(s) 76, 471
BtuMI TCGCGA 1 cut(s) 404
ClaI ATCGAT 1 cut(s) 689
CseI GACGC 1 cut(s) 415
Csp6I GTAC 4 cut(s) 192, 310, 528, 703
CviAII CATG 2 cut(s) 234, 628
CviJI RGCY 9 cut(s) 205, 232, 268, 292, 388, 539, 603, 611, 662
CviKI_1 RGCY 9 cut(s) 205, 232, 268, 292, 388, 539, 603, 611, 662
CviQI GTAC 4 cut(s) 192, 310, 528, 703
DdeI CTNAG 3 cut(s) 104, 344, 410
DpnI GATC 1 cut(s) 342
DpnII GATC 1 cut(s) 340
DrdI GACNNNNNNGTC 1 cut(s) 125
DseDI GACNNNNNNGTC 1 cut(s) 125
Eam1104I CTCTTC 1 cut(s) 537
EarI CTCTTC 1 cut(s) 537
EciI GGCGGA 1 cut(s) 20
Eco130I CCWWGG 2 cut(s) 233, 598
Eco57I CTGAAG 1 cut(s) 561
EcoRI GAATTC 1 cut(s) 274
EcoRII CCWGG 1 cut(s) 131
EcoT14I CCWWGG 2 cut(s) 233, 598
ErhI CCWWGG 2 cut(s) 233, 598
FaeI CATG 2 cut(s) 237, 631
FaiI YATR 8 cut(s) 235, 260, 308, 327, 483, 491, 629, 671
FatI CATG 2 cut(s) 233, 627
Fnu4HI GCNGC 1 cut(s) 563
FokI GGATG 2 cut(s) 63, 478
Fsp4HI GCNGC 1 cut(s) 563
FspBI CTAG 1 cut(s) 296
GluI GCNGC 1 cut(s) 563
HapII CCGG 1 cut(s) 494
HgaI GACGC 1 cut(s) 415
Hin1II CATG 2 cut(s) 237, 631
HindIII AAGCTT 2 cut(s) 290, 660
HinfI GANTC 6 cut(s) 44, 162, 299, 399, 425, 686
HpaII CCGG 1 cut(s) 494
HphI GGTGA 2 cut(s) 39, 434
Hpy166II GTNNAC 1 cut(s) 528
Hpy188I TCNGA 6 cut(s) 37, 85, 161, 347, 396, 478
Hpy188III TCNNGA 8 cut(s) 16, 65, 166, 199, 296, 403, 634, 656
Hpy8I GTNNAC 1 cut(s) 528
Hpy99I CGWCG 4 cut(s) 131, 191, 396, 409
HpyAV CCTTC 1 cut(s) 550
HpyCH4III ACNGT 3 cut(s) 51, 191, 707
HpyCH4IV ACGT 2 cut(s) 126, 349
HpyCH4V TGCA 3 cut(s) 246, 516, 683
HpyF10VI GCNNNNNNNGC 4 cut(s) 229, 320, 513, 545
HpyF3I CTNAG 3 cut(s) 104, 344, 410
HpySE526I ACGT 2 cut(s) 126, 349
Hsp92II CATG 2 cut(s) 237, 631
Kzo9I GATC 1 cut(s) 340
LmnI GCTCC 2 cut(s) 490, 559
LpnPI CCDG 6 cut(s) 118, 145, 219, 397, 507, 647
Lsp1109I GCAGC 1 cut(s) 574
LweI GCATC 1 cut(s) 670
MaeI CTAG 1 cut(s) 296
MaeII ACGT 2 cut(s) 126, 349
MaeIII GTNAC 5 cut(s) 163, 422, 566, 613, 648
MalI GATC 1 cut(s) 342
MbiI CCGCTC 1 cut(s) 223
MboI GATC 1 cut(s) 340
MboII GAAGA 4 cut(s) 128, 350, 388, 554
MfeI CAATTG 1 cut(s) 517
MflI RGATCY 1 cut(s) 340
MluCI AATT 5 cut(s) 138, 173, 274, 449, 517
MlyI GAGTC 3 cut(s) 171, 393, 419
MmeI TCCRAC 3 cut(s) 53, 374, 456
MnlI CCTC 8 cut(s) 72, 91, 167, 427, 538, 601, 651, 654
MroXI GAANNNNTTC 1 cut(s) 173
MspI CCGG 1 cut(s) 494
MspR9I CCNGG 1 cut(s) 133
MunI CAATTG 1 cut(s) 517
MvaI CCWGG 1 cut(s) 133
MvnI CGCG 2 cut(s) 314, 404
MwoI GCNNNNNNNGC 4 cut(s) 229, 320, 513, 545
NcoI CCATGG 1 cut(s) 233
NdeII GATC 1 cut(s) 340
NlaIII CATG 2 cut(s) 237, 631
NmuCI GTSAC 4 cut(s) 163, 422, 613, 648
NruI TCGCGA 1 cut(s) 404
PcsI WCGNNNNNNNCGW 1 cut(s) 183
PdmI GAANNNNTTC 1 cut(s) 173
PfeI GAWTC 3 cut(s) 44, 299, 686
PkrI GCNGC 1 cut(s) 564
PleI GAGTC 3 cut(s) 170, 393, 419
PpsI GAGTC 3 cut(s) 170, 393, 419
Psp6I CCWGG 1 cut(s) 131
PspGI CCWGG 1 cut(s) 131
PsuI RGATCY 1 cut(s) 340
RruI TCGCGA 1 cut(s) 404
RsaI GTAC 4 cut(s) 193, 311, 529, 704
RsaNI GTAC 4 cut(s) 192, 310, 528, 703
SatI GCNGC 1 cut(s) 563
Sau3AI GATC 1 cut(s) 340
SchI GAGTC 3 cut(s) 171, 393, 419
ScrFI CCNGG 1 cut(s) 133
SetI ASST 8 cut(s) 129, 294, 352, 390, 421, 541, 643, 664
SfaNI GCATC 1 cut(s) 670
Sse9I AATT 5 cut(s) 138, 173, 274, 449, 517
SsiI CCGC 4 cut(s) 5, 221, 314, 507
SspMI CTAG 1 cut(s) 296
StyD4I CCNGG 1 cut(s) 131
StyI CCWWGG 2 cut(s) 233, 598
TaaI ACNGT 3 cut(s) 51, 191, 707
TaiI ACGT 2 cut(s) 129, 352
TaqI TCGA 5 cut(s) 142, 186, 278, 606, 689
TaqII GACCGA 1 cut(s) 299
TasI AATT 5 cut(s) 138, 173, 274, 449, 517
TatI WGTACW 1 cut(s) 527
TfiI GAWTC 3 cut(s) 44, 299, 686
TseFI GTSAC 4 cut(s) 163, 422, 613, 648
TseI GCWGC 1 cut(s) 562
Tsp45I GTSAC 4 cut(s) 163, 422, 613, 648
TspDTI ATGAA 3 cut(s) 62, 287, 710
TspGWI ACGGA 1 cut(s) 636
XapI RAATTY 3 cut(s) 138, 173, 274
XbaI TCTAGA 1 cut(s) 295
XmnI GAANNNNTTC 1 cut(s) 173
XspI CTAG 1 cut(s) 296
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.