Rh2DG609500

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr2D
OG0001845
Physical Location & Seq
Reverse (-)
84243195 .. 84254661
11467 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh2DG609500.1

Sequence Viewer

Length: 528 bp
ATGCGAGTTCCTGTAATACGGGCACATGCTGAGAGTGTAAATTGTGAATTTGAGAATCTTGATGAGGACACCGCAAGGGATATTCGGAAGAAGGCTCCTGGTGTGGTGGTTATTGATGACCATGCAGCTAATAACTTCCCTACACCTTTGGAGGTGTCAACCAAAGATGATGTTGCAGTTGGCAGAATCAGCCATGATGTGTCCCAGGAGGGGAACTATGGCAATTGCCATTATCAACTAGTCAGCATGGTCAAGACAGTTTACTTGTTTGGATTTCCCACTGTGGAGTCTCCAGAAGCAGTGACAAAATTTCTGGAGGAGTATACTGGAGAAGGAACTGTTATCTCTGTGAATGTTCTTCCTCCAAAAGATGGCGCATCAAGATCATCTGCCATAGTTGAATTCACAACTGCAGAATGTGCTGAAATAATAATTCCATTAGCCGATAATCGATGCCTGTGGTATGGAGAGTCTTATCTGAAAGCTCGAGAATGGAAGCGTGACTTGGCACCGAAATCAAAAGTCTAG
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 Retrotran_gag_3

Protein Analysis

175

Amino Acids

19.4

Weight (kDa)

5.03

Isoelectric Point (pI)

35.5

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Semialdhyde_dhC PF02774 2 - 69 1.2e-11 Semialdehyde dehydrogenase, dimerisation domain
RRM_RdRP1_2 PF26250 86 - 166 1.8e-13 RdRP1/2, RRM domain
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)
AccB1I GGYRCC 1 cut(s) 508
AccB7I CCANNNNNTGG 1 cut(s) 371
AccI GTMKAC 1 cut(s) 323
AciI CCGC 1 cut(s) 72
AcsI RAATTY 3 cut(s) 47, 308, 401
AfiI CCNNNNNNNGG 2 cut(s) 210, 371
AgsI TTSAA 1 cut(s) 401
AhlI ACTAGT 1 cut(s) 238
AjnI CCWGG 2 cut(s) 97, 204
AjuI GAANNNNNNNTTGG 2 cut(s) 488, 520
AluBI AGCT 2 cut(s) 128, 485
AluI AGCT 2 cut(s) 128, 485
Alw26I GTCTC 1 cut(s) 294
Ama87I CYCGRG 1 cut(s) 486
ApeKI GCWGC 1 cut(s) 125
ApoI RAATTY 3 cut(s) 47, 308, 401
AspLEI GCGC 1 cut(s) 377
AvaI CYCGRG 1 cut(s) 486
BaeGI GKGCMC 1 cut(s) 25
BanI GGYRCC 1 cut(s) 508
BbvI GCAGC 1 cut(s) 137
BccI CCATC 1 cut(s) 365
BciT130I CCWGG 2 cut(s) 99, 206
BcoDI GTCTC 1 cut(s) 294
BcuI ACTAGT 1 cut(s) 238
BfaI CTAG 2 cut(s) 239, 526
BfmI CTRYAG 1 cut(s) 411
BisI GCNGC 1 cut(s) 126
BlsI GCNGC 1 cut(s) 127
Bme1390I CCNGG 2 cut(s) 99, 206
BmeT110I CYCGRG 1 cut(s) 486
BmiI GGNNCC 2 cut(s) 96, 510
BmrFI CCNGG 2 cut(s) 99, 206
BmsI GCATC 2 cut(s) 386, 443
BpmI CTGGAG 3 cut(s) 276, 335, 348
Bsa29I ATCGAT 1 cut(s) 451
BsaJI CCNNGG 1 cut(s) 204
Bsc4I CCNNNNNNNGG 2 cut(s) 210, 371
Bse1I ACTGG 1 cut(s) 331
BseBI CCWGG 2 cut(s) 99, 206
BseCI ATCGAT 1 cut(s) 451
BseDI CCNNGG 1 cut(s) 204
BseLI CCNNNNNNNGG 2 cut(s) 210, 371
BseMII CTCAG 1 cut(s) 21
BseNI ACTGG 1 cut(s) 331
BseRI GAGGAG 1 cut(s) 332
BseSI GKGCMC 1 cut(s) 25
BseXI GCAGC 1 cut(s) 137
BshNI GGYRCC 1 cut(s) 508
BshVI ATCGAT 1 cut(s) 451
BsiHKCI CYCGRG 1 cut(s) 486
BslFI GGGAC 1 cut(s) 187
BslI CCNNNNNNNGG 2 cut(s) 210, 371
BsmAI GTCTC 1 cut(s) 294
BsmFI GGGAC 1 cut(s) 187
BsoBI CYCGRG 1 cut(s) 486
Bsp1286I GDGCHC 1 cut(s) 25
Bsp143I GATC 1 cut(s) 383
BspACI CCGC 1 cut(s) 72
BspCNI CTCAG 1 cut(s) 22
BspDI ATCGAT 1 cut(s) 451
BspLI GGNNCC 2 cut(s) 96, 510
BspMAI CTGCAG 1 cut(s) 415
BspT107I GGYRCC 1 cut(s) 508
BsrI ACTGG 1 cut(s) 331
BssECI CCNNGG 1 cut(s) 204
BssMI GATC 1 cut(s) 383
BssNAI GTATAC 1 cut(s) 324
Bst1107I GTATAC 1 cut(s) 324
Bst2UI CCWGG 2 cut(s) 99, 206
Bst4CI ACNGT 3 cut(s) 259, 283, 340
BstAPI GCANNNNNTGC 1 cut(s) 419
BstDEI CTNAG 1 cut(s) 30
BstHHI GCGC 1 cut(s) 377
BstKTI GATC 1 cut(s) 386
BstMAI GTCTC 1 cut(s) 294
BstMBI GATC 1 cut(s) 383
BstMWI GCNNNNNNNGC 2 cut(s) 189, 419
BstNI CCWGG 2 cut(s) 99, 206
BstNSI RCATGY 1 cut(s) 29
BstSCI CCNGG 2 cut(s) 97, 204
BstSFI CTRYAG 1 cut(s) 411
BstSLI GKGCMC 1 cut(s) 25
BstV1I GCAGC 1 cut(s) 137
BstZ17I GTATAC 1 cut(s) 324
Bsu15I ATCGAT 1 cut(s) 451
BsuTUI ATCGAT 1 cut(s) 451
BtsI GCAGTG 1 cut(s) 306
BtsIMutI CAGTG 2 cut(s) 279, 306
CfoI GCGC 1 cut(s) 377
ClaI ATCGAT 1 cut(s) 451
CviAII CATG 4 cut(s) 26, 122, 194, 247
CviJI RGCY 5 cut(s) 95, 128, 192, 443, 485
CviKI_1 RGCY 5 cut(s) 95, 128, 192, 443, 485
DdeI CTNAG 1 cut(s) 30
DpnI GATC 1 cut(s) 385
DpnII GATC 1 cut(s) 383
Eco88I CYCGRG 1 cut(s) 486
EcoRI GAATTC 1 cut(s) 401
EcoRII CCWGG 2 cut(s) 97, 204
FaeI CATG 4 cut(s) 29, 125, 197, 250
FaiI YATR 8 cut(s) 27, 123, 195, 219, 248, 324, 395, 465
FalI AAGNNNNNCTT 2 cut(s) 488, 520
FaqI GGGAC 1 cut(s) 187
FatI CATG 4 cut(s) 25, 121, 193, 246
FblI GTMKAC 1 cut(s) 323
Fnu4HI GCNGC 1 cut(s) 126
Fsp4HI GCNGC 1 cut(s) 126
FspBI CTAG 2 cut(s) 239, 526
GlaI GCGC 1 cut(s) 376
GluI GCNGC 1 cut(s) 126
GsuI CTGGAG 3 cut(s) 276, 335, 348
HhaI GCGC 1 cut(s) 377
Hin1II CATG 4 cut(s) 29, 125, 197, 250
Hin6I GCGC 1 cut(s) 375
HinP1I GCGC 1 cut(s) 375
HincII GTYRAC 1 cut(s) 159
HindII GTYRAC 1 cut(s) 159
HinfI GANTC 4 cut(s) 55, 186, 287, 470
Hpy166II GTNNAC 3 cut(s) 159, 262, 324
Hpy188I TCNGA 2 cut(s) 87, 480
Hpy188III TCNNGA 6 cut(s) 59, 253, 293, 314, 381, 488
Hpy8I GTNNAC 3 cut(s) 159, 262, 324
HpyAV CCTTC 2 cut(s) 85, 326
HpyCH4III ACNGT 3 cut(s) 259, 283, 340
HpyCH4V TGCA 3 cut(s) 125, 176, 413
HpyF10VI GCNNNNNNNGC 2 cut(s) 189, 419
HpyF3I CTNAG 1 cut(s) 30
Hsp92II CATG 4 cut(s) 29, 125, 197, 250
HspAI GCGC 1 cut(s) 375
Kzo9I GATC 1 cut(s) 383
LmnI GCTCC 1 cut(s) 100
LpnPI CCDG 9 cut(s) 24, 84, 111, 191, 218, 299, 306, 312, 470
Lsp1109I GCAGC 1 cut(s) 137
LweI GCATC 2 cut(s) 386, 443
MaeI CTAG 2 cut(s) 239, 526
MaeIII GTNAC 2 cut(s) 301, 500
MalI GATC 1 cut(s) 385
MboI GATC 1 cut(s) 383
MboII GAAGA 2 cut(s) 100, 350
MfeI CAATTG 1 cut(s) 223
MhlI GDGCHC 1 cut(s) 25
MluCI AATT 6 cut(s) 40, 47, 223, 308, 401, 432
MlyI GAGTC 2 cut(s) 296, 479
MnlI CCTC 5 cut(s) 58, 145, 202, 310, 372
MspR9I CCNGG 2 cut(s) 99, 206
MunI CAATTG 1 cut(s) 223
MvaI CCWGG 2 cut(s) 99, 206
MwoI GCNNNNNNNGC 2 cut(s) 189, 419
NdeII GATC 1 cut(s) 383
NlaIII CATG 4 cut(s) 29, 125, 197, 250
NlaIV GGNNCC 2 cut(s) 96, 510
NmuCI GTSAC 2 cut(s) 301, 500
NspI RCATGY 1 cut(s) 29
PaeR7I CTCGAG 1 cut(s) 486
PfeI GAWTC 2 cut(s) 55, 186
PflMI CCANNNNNTGG 1 cut(s) 371
PkrI GCNGC 1 cut(s) 127
PleI GAGTC 2 cut(s) 295, 478
PpsI GAGTC 2 cut(s) 295, 478
Psp6I CCWGG 2 cut(s) 97, 204
PspGI CCWGG 2 cut(s) 97, 204
PspN4I GGNNCC 2 cut(s) 96, 510
PstI CTGCAG 1 cut(s) 415
SatI GCNGC 1 cut(s) 126
Sau3AI GATC 1 cut(s) 383
SchI GAGTC 2 cut(s) 296, 479
ScrFI CCNGG 2 cut(s) 99, 206
SduI GDGCHC 1 cut(s) 25
SetI ASST 4 cut(s) 130, 148, 156, 487
SfaNI GCATC 2 cut(s) 386, 443
SfcI CTRYAG 1 cut(s) 411
Sfr274I CTCGAG 1 cut(s) 486
SlaI CTCGAG 1 cut(s) 486
SmlI CTYRAG 1 cut(s) 486
SmoI CTYRAG 1 cut(s) 486
SpeI ACTAGT 1 cut(s) 238
Sse9I AATT 6 cut(s) 40, 47, 223, 308, 401, 432
SsiI CCGC 1 cut(s) 72
SspMI CTAG 2 cut(s) 239, 526
StyD4I CCNGG 2 cut(s) 97, 204
TaaI ACNGT 3 cut(s) 259, 283, 340
TaqI TCGA 2 cut(s) 451, 487
TasI AATT 6 cut(s) 40, 47, 223, 308, 401, 432
TfiI GAWTC 2 cut(s) 55, 186
TscAI CASTG 2 cut(s) 286, 306
TseFI GTSAC 2 cut(s) 301, 500
TseI GCWGC 1 cut(s) 125
Tsp45I GTSAC 2 cut(s) 301, 500
TspRI CASTG 2 cut(s) 286, 306
Van91I CCANNNNNTGG 1 cut(s) 371
XapI RAATTY 3 cut(s) 47, 308, 401
XceI RCATGY 1 cut(s) 29
XhoI CTCGAG 1 cut(s) 486
XmiI GTMKAC 1 cut(s) 323
XspI CTAG 2 cut(s) 239, 526
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.