RchiOBHm_Chr1g0376911

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
1
OG0002402
Physical Location & Seq
Forward (+)
64065504 .. 64066314
811 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ60051

Sequence Viewer

Length: 762 bp
ATGTCAGGACACCCTATCACCAAAATTCTCAATGAAAATCGTCTTGAGGGCCCAAACTTCAATGACTGGCTCCGCAATTTGAAAATTGTATTGACATTCGATAAGATCGCTTATGTCTTACAAAATGCACCCCCTCACACTCTTTTGGCTCAAGATGCAACCGATGAGCAACGTGTTGCTTATCAAAAGCATAAGGATGATGACACTCAAGCTAAATGTGTTATGCTTGCATCCATGAACTCACAACTTCAGAAGCAACATGAGAATATGGATAGCGCCAATTCTATGTTACTTCATCTCACTGAATTGTTTGGTGAGAGAAATAGAAATGTGCGCTTCACAGTAGTCAATGAGCTTGTTAAGACAAAGCATGTGAGGGGTGCACCTGTTCATCAACATGGTCTAAAAATGATAGGCCTTATTGAGCAAATTCAAGACCTTGGATTTGCACTTGATGCGGAGCTAGCTCAAGATCTTCTTCTTTCCTCCCTAGATGATTCATTTTCTCAGTTCATAATGAACTATAATATGCAACAAATGGATCATACTCTTTCTGATCTTCTCAATATGCTGGTAACAGCTGAGAAACAAATCAAGAAAGAGAGTGGGAGTGCGGCCATTATCGCTTCTTCTTCATCCAGTAAGTCCAAAGGCAAAGGGAAGAAGAAACAAGTGATAAAGCCTAAGGGAGCAGTCCAAAAGAAGAAGAAGAAGGAACAAAAGGAACCAAAAGGAATTGCAAAGCTTATCTTGCATCCTTGA
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

253

Amino Acids

28.46

Weight (kDa)

9.39

Isoelectric Point (pI)

32.09

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 53 - 202 2e-13 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
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
AflIII ACRYGT 1 cut(s) 172
AgsI TTSAA 3 cut(s) 61, 82, 434
AluBI AGCT 6 cut(s) 212, 355, 463, 467, 581, 745
AluI AGCT 6 cut(s) 212, 355, 463, 467, 581, 745
Alw21I GWGCWC 1 cut(s) 385
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 2 cut(s) 278, 336
AspS9I GGNCC 2 cut(s) 49, 50
AsuHPI GGTGA 2 cut(s) 10, 326
AsuNHI GCTAGC 1 cut(s) 463
AxyI CCTNAGG 1 cut(s) 684
BaeGI GKGCMC 2 cut(s) 53, 385
BanII GRGCYC 1 cut(s) 53
Bbv12I GWGCWC 1 cut(s) 385
BfaI CTAG 2 cut(s) 464, 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, 726
BmsI GCATC 3 cut(s) 145, 239, 445
BmtI GCTAGC 1 cut(s) 467
BpuEI CTTGAG 4 cut(s) 65, 135, 192, 453
BsaJI CCNNGG 1 cut(s) 439
Bse1I ACTGG 2 cut(s) 71, 639
Bse21I CCTNAGG 1 cut(s) 684
BseDI CCNNGG 1 cut(s) 439
BseGI GGATG 4 cut(s) 202, 230, 635, 754
BseMII CTCAG 2 cut(s) 521, 573
BseNI ACTGG 2 cut(s) 71, 639
BseSI GKGCMC 2 cut(s) 53, 385
BshFI GGCC 3 cut(s) 51, 417, 617
BsiHKAI GWGCWC 1 cut(s) 385
BsnI GGCC 3 cut(s) 51, 417, 617
Bsp120I GGGCCC 1 cut(s) 49
Bsp1286I GDGCHC 2 cut(s) 53, 385
Bsp143I GATC 4 cut(s) 105, 472, 541, 556
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, 726
BspOI GCTAGC 1 cut(s) 467
BspPI GGATC 1 cut(s) 549
BsrI ACTGG 2 cut(s) 71, 639
BssECI CCNNGG 1 cut(s) 439
BssMI GATC 4 cut(s) 105, 472, 541, 556
BssT1I CCWWGG 1 cut(s) 439
Bst4CI ACNGT 1 cut(s) 343
BstAPI GCANNNNNTGC 1 cut(s) 455
BstC8I GCNNGC 2 cut(s) 228, 465
BstDEI CTNAG 3 cut(s) 507, 582, 684
BstF5I GGATG 4 cut(s) 202, 230, 635, 754
BstH2I RGCGCY 1 cut(s) 279
BstHHI GCGC 2 cut(s) 278, 336
BstKTI GATC 4 cut(s) 108, 475, 544, 559
BstMBI GATC 4 cut(s) 105, 472, 541, 556
BstMWI GCNNNNNNNGC 5 cut(s) 155, 455, 464, 623, 751
BstNSI RCATGY 1 cut(s) 374
BstSLI GKGCMC 2 cut(s) 53, 385
BstX2I RGATCY 1 cut(s) 472
BstYI RGATCY 1 cut(s) 472
Bsu36I CCTNAGG 1 cut(s) 684
BsuRI GGCC 3 cut(s) 51, 417, 617
BtsCI GGATG 4 cut(s) 202, 230, 635, 754
BtsIMutI CAGTG 1 cut(s) 300
Cac8I GCNNGC 2 cut(s) 228, 465
CfoI GCGC 2 cut(s) 278, 336
Cfr13I GGNCC 2 cut(s) 49, 50
CviAII CATG 4 cut(s) 235, 260, 371, 398
DdeI CTNAG 3 cut(s) 507, 582, 684
DpnI GATC 4 cut(s) 107, 474, 543, 558
DpnII GATC 4 cut(s) 105, 472, 541, 556
EaeI YGGCCR 1 cut(s) 615
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) 684
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 3 cut(s) 462, 494, 734
FatI CATG 4 cut(s) 234, 259, 370, 397
Fnu4HI GCNGC 1 cut(s) 615
FokI GGATG 4 cut(s) 209, 217, 622, 741
FriOI GRGCYC 1 cut(s) 53
Fsp4HI GCNGC 1 cut(s) 615
FspBI CTAG 2 cut(s) 464, 491
GlaI GCGC 2 cut(s) 277, 335
GluI GCNGC 1 cut(s) 615
HaeII RGCGCY 1 cut(s) 279
HaeIII GGCC 3 cut(s) 51, 417, 617
HhaI GCGC 2 cut(s) 278, 336
Hin1II CATG 4 cut(s) 238, 263, 374, 401
Hin6I GCGC 2 cut(s) 276, 334
HinP1I GCGC 2 cut(s) 276, 334
HindIII AAGCTT 1 cut(s) 743
HinfI GANTC 1 cut(s) 497
HphI GGTGA 2 cut(s) 10, 326
Hpy166II GTNNAC 1 cut(s) 383
Hpy188I TCNGA 2 cut(s) 252, 556
Hpy188III TCNNGA 6 cut(s) 6, 44, 152, 434, 470, 595
Hpy8I GTNNAC 1 cut(s) 383
HpyAV CCTTC 1 cut(s) 706
HpyCH4III ACNGT 1 cut(s) 343
HpyCH4IV ACGT 1 cut(s) 172
HpyCH4V TGCA 8 cut(s) 128, 158, 230, 383, 449, 532, 740, 754
HpyF10VI GCNNNNNNNGC 5 cut(s) 155, 455, 464, 623, 751
HpyF3I CTNAG 3 cut(s) 507, 582, 684
HpySE526I ACGT 1 cut(s) 172
Hsp92II CATG 4 cut(s) 238, 263, 374, 401
HspAI GCGC 2 cut(s) 276, 334
Kzo9I GATC 4 cut(s) 105, 472, 541, 556
LmnI GCTCC 3 cut(s) 75, 460, 689
LpnPI CCDG 4 cut(s) 52, 399, 557, 652
LweI GCATC 3 cut(s) 145, 239, 445
MaeI CTAG 2 cut(s) 464, 491
MaeII ACGT 1 cut(s) 172
MaeIII GTNAC 2 cut(s) 288, 574
MalI GATC 4 cut(s) 107, 474, 543, 558
MboI GATC 4 cut(s) 105, 472, 541, 556
MflI RGATCY 1 cut(s) 472
MhlI GDGCHC 2 cut(s) 53, 385
MluCI AATT 7 cut(s) 24, 76, 84, 280, 305, 429, 735
MnlI CCTC 4 cut(s) 40, 144, 369, 496
MseI TTAA 1 cut(s) 360
MslI CAYNNNNRTG 2 cut(s) 195, 396
MspA1I CMGCKG 1 cut(s) 581
MwoI GCNNNNNNNGC 5 cut(s) 155, 455, 464, 623, 751
NdeII GATC 4 cut(s) 105, 472, 541, 556
NheI GCTAGC 1 cut(s) 463
NlaIII CATG 4 cut(s) 238, 263, 374, 401
NlaIV GGNNCC 3 cut(s) 51, 71, 726
NspI RCATGY 1 cut(s) 374
PceI AGGCCT 1 cut(s) 417
PfeI GAWTC 1 cut(s) 497
PkrI GCNGC 1 cut(s) 616
PspN4I GGNNCC 3 cut(s) 51, 71, 726
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
RseI CAYNNNNRTG 2 cut(s) 195, 396
SaqAI TTAA 1 cut(s) 360
SatI GCNGC 1 cut(s) 615
Sau3AI GATC 4 cut(s) 105, 472, 541, 556
Sau96I GGNCC 2 cut(s) 49, 50
SduI GDGCHC 2 cut(s) 53, 385
SetI ASST 9 cut(s) 175, 214, 357, 388, 441, 465, 469, 583, 747
SfaNI GCATC 3 cut(s) 145, 239, 445
SmiMI CAYNNNNRTG 2 cut(s) 195, 396
SmlI CTYRAG 4 cut(s) 44, 150, 207, 468
SmoI CTYRAG 4 cut(s) 44, 150, 207, 468
Sse9I AATT 7 cut(s) 24, 76, 84, 280, 305, 429, 735
SseBI AGGCCT 1 cut(s) 417
SsiI CCGC 3 cut(s) 73, 458, 614
SspMI CTAG 2 cut(s) 464, 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 1 cut(s) 99
TasI AATT 7 cut(s) 24, 76, 84, 280, 305, 429, 735
TauI GCSGC 1 cut(s) 617
TfiI GAWTC 1 cut(s) 497
Tru1I TTAA 1 cut(s) 360
Tru9I TTAA 1 cut(s) 360
TscAI CASTG 1 cut(s) 307
TspDTI ATGAA 8 cut(s) 48, 251, 284, 380, 489, 502, 533, 624
TspRI CASTG 1 cut(s) 307
VneI GTGCAC 1 cut(s) 381
XapI RAATTY 2 cut(s) 24, 429
XceI RCATGY 1 cut(s) 374
XspI CTAG 2 cut(s) 464, 491
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.