MD10G1250300.v1.1

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr10
OG0000278
Physical Location & Seq
Forward (+)
34282547 .. 34284685
2139 bp
Loading structure...
UTR
Exon/CDS
Intron
MD10G1250300.v1.1.491

Sequence Viewer

Length: 822 bp
ATGGAAAATGAAACTACTGCAGCTGGTTTGTGGCTTAAGTTGGAGAGTATATACATGACCAAATCCCTCACCAATCGTTTGTATTTGAAGCAACGTTTGTACACTCTCCGTATGACTGAAGGTACACCTATTCAAAACCATCTTGATGAGTTTAATAAGGTTATTATGGATTTGAAAAGTATGGATAATAAAATTGATGATGAGGATCAATCTTTGATTTTGTTGTGTTCTTTACCTCCTTCGTATGCGAATTTTGTTGAAACTTTGTTATATGGGAGAGATTATATTTGTATGGAGAATGTAAAAGCCGCTTTGAATTCAAGAGAGTTAAAGAACAAAGTATTTGGAAATTTGAATGATTCTCATTCTGAGGCTTTTATAGCAAGAGGCAGAGATAGGGAATATGGTTCAGGTAGTAATAAAGGAAATTTGAGATCGAAGTCTAAGACCAGAAACAACACATGCAACTATTGTCGCAAGGAAGGGCATTGGAAAGTTGATTGCCCAAAACTGAAAGATAATGTTGGTTTGAGGTGGAGTTCGTTGTGTGTCCAACTTTGGTATGGTGTGCTTGATCTTTTGTTGGTGATATTGAAGAATTTCAGTTCTTCGTTTGAATCACCTTTTGTTTTGATCAAGGCACTTATGGTTTGCAAATTTGGAGACGACGGTAGAGAAATGGTCTACTTTTGTTGGCTTTGGTACAATTTGAGTCGAGTGGAATTTCCCCGCCGTATCGGAACTGGACGTAAGCTTACGCCGAACCAGTATAAATCCTTGTGTCATTTGGATTATTTGTCTTATCATATTTTGCCGTTGTAG
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

274

Amino Acids

31.76

Weight (kDa)

8.94

Isoelectric Point (pI)

39.33

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 2 - 109 1.7e-26 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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Publication-ready
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Orthologous Genes (Group: OG0000278)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G29785
fragaria_vesca FvH4_1g10046 FvH4_1g17351 FvH4_1g18441 FvH4_1g24222 FvH4_2g00141 FvH4_2g05931 FvH4_2g06671 FvH4_2g14030 FvH4_2g15291 FvH4_2g22611 FvH4_2g22612 FvH4_2g26380 FvH4_2g39202 FvH4_2g39202 FvH4_3g06691 FvH4_3g08580 FvH4_3g20502 FvH4_3g20503 FvH4_3g22421 FvH4_3g42580 FvH4_4g02061 FvH4_4g06794 FvH4_4g08661 FvH4_4g11771 FvH4_4g14601 FvH4_4g14721 FvH4_4g20921 FvH4_4g33601 FvH4_4g33602 FvH4_5g07492 FvH4_5g20321 FvH4_5g21591 FvH4_5g30343 FvH4_5g37875 FvH4_6g04372 FvH4_6g04373 FvH4_6g04373 FvH4_6g21377 FvH4_6g23760 FvH4_6g29471 FvH4_6g43142 FvH4_7g14351 FvH4_7g14352 FvH4_7g22582 FvH4_7g22583 FvH4_7g22584
malus_domestica MD00G1179400.v1.1 MD01G1170500.v1.1 MD03G1286700.v1.1 MD04G1054600.v1.1 MD04G1071700.v1.1 MD04G1193900.v1.1 MD08G1054300.v1.1 MD08G1217500.v1.1 MD09G1034600.v1.1 MD09G1098100.v1.1 MD10G1018300.v1.1 MD10G1220000.v1.1 MD10G1250300.v1.1 MD12G1014400.v1.1 MD15G1021000.v1.1 MD16G1112200.v1.1
prunus_persica Prupe.1G188900_v2.0.a1 Prupe.1G258000_v2.0.a1 Prupe.4G233400_v2.0.a1
pyrus_communis pycom01g10100 pycom02g01340 pycom03g19700 pycom05g01320 pycom07g16000 pycom07g16520 pycom11g26500 pycom13g09380 pycom13g13960 pycom14g08180 pycom14g16810 pycom16g09590
rosa_chinensis RchiOBHm_Chr1g0319891 RchiOBHm_Chr1g0333711 RchiOBHm_Chr2g0115331 RchiOBHm_Chr2g0143411 RchiOBHm_Chr2g0167631 RchiOBHm_Chr3g0448581 RchiOBHm_Chr3g0494991 RchiOBHm_Chr4g0442471 RchiOBHm_Chr6g0262311 RchiOBHm_Chr6g0301831 RchiOBHm_Chr6g0301841 RchiOBHm_Chr7g0183451
rosa_roxburghii Rroxscaffold_1G00039280 Rroxscaffold_1G00047670 Rroxscaffold_1G00066330 Rroxscaffold_2G00107510 Rroxscaffold_3G00255410 Rroxscaffold_4G00301460 Rroxscaffold_5G00352730 Rroxscaffold_7G00166350 Rroxscaffold_7G00166360 Rroxscaffold_7G00203820
rosa_rugosa Rorug03G0240500 Rorug05G0191700 Rorug06G0310200
rosa_samantha Rh2BG287000 Rh4CG073500 Rh4CG176200 Rh4CG191400 Rh5BG356100 Rh5BG434100 Rh6AG110600 Rh6AG421900 Rh6AG422000 Rh6AG422100 Rh6BG428600 Rh6BG428700 Rh6BG428800 Rh6CG435200 Rh6CG435300 Rh6CG435400 Rh6DG422000 Rh6DG422100 Rh6DG422200 Rh7BG190500 Rh7CG172800 Rh7CG225200
rosa_wichuraiana Rw2G044060 Rw6G036540

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 684
AciI CCGC 2 cut(s) 309, 730
AclI AACGTT 1 cut(s) 94
AclWI GGATC 1 cut(s) 213
AcsI RAATTY 7 cut(s) 250, 316, 349, 427, 598, 656, 722
AcuI CTGAAG 1 cut(s) 138
AfaI GTAC 3 cut(s) 101, 124, 704
AflII CTTAAG 1 cut(s) 35
AgsI TTSAA 9 cut(s) 88, 134, 175, 260, 316, 321, 355, 595, 617
AluBI AGCT 2 cut(s) 23, 754
AluI AGCT 2 cut(s) 23, 754
Alw26I GTCTC 1 cut(s) 657
AlwI GGATC 1 cut(s) 213
ApeKI GCWGC 1 cut(s) 20
ApoI RAATTY 7 cut(s) 250, 316, 349, 427, 598, 656, 722
Asp700I GAANNNNTTC 1 cut(s) 599
AsuHPI GGTGA 3 cut(s) 61, 598, 612
BbvI GCAGC 1 cut(s) 32
BccI CCATC 1 cut(s) 147
BceAI ACGGC 2 cut(s) 717, 799
BclI TGATCA 1 cut(s) 633
BcoDI GTCTC 1 cut(s) 657
BfmI CTRYAG 1 cut(s) 18
BfrI CTTAAG 1 cut(s) 35
BisI GCNGC 2 cut(s) 21, 309
BlsI GCNGC 2 cut(s) 22, 310
BsaBI GATNNNNATC 1 cut(s) 204
Bse1I ACTGG 2 cut(s) 748, 766
Bse8I GATNNNNATC 1 cut(s) 204
BseJI GATNNNNATC 1 cut(s) 204
BseMII CTCAG 1 cut(s) 360
BseNI ACTGG 2 cut(s) 748, 766
BseXI GCAGC 1 cut(s) 32
BsmAI GTCTC 1 cut(s) 657
BsmBI CGTCTC 1 cut(s) 657
Bsp1407I TGTACA 1 cut(s) 99
Bsp143I GATC 4 cut(s) 205, 434, 574, 633
BspACI CCGC 2 cut(s) 309, 730
BspCNI CTCAG 1 cut(s) 361
BspMAI CTGCAG 1 cut(s) 22
BspPI GGATC 1 cut(s) 213
BspTI CTTAAG 1 cut(s) 35
BsrGI TGTACA 1 cut(s) 99
BsrI ACTGG 2 cut(s) 748, 766
BssMI GATC 4 cut(s) 205, 434, 574, 633
Bst4CI ACNGT 1 cut(s) 671
BstAFI CTTAAG 1 cut(s) 35
BstAUI TGTACA 1 cut(s) 99
BstDEI CTNAG 2 cut(s) 369, 444
BstKTI GATC 4 cut(s) 208, 437, 577, 636
BstMAI GTCTC 1 cut(s) 657
BstMBI GATC 4 cut(s) 205, 434, 574, 633
BstMWI GCNNNNNNNGC 1 cut(s) 380
BstNSI RCATGY 1 cut(s) 465
BstSFI CTRYAG 1 cut(s) 18
BstV1I GCAGC 1 cut(s) 32
Csp6I GTAC 3 cut(s) 100, 123, 703
CviAII CATG 2 cut(s) 55, 462
CviJI RGCY 6 cut(s) 23, 34, 308, 374, 697, 754
CviKI_1 RGCY 6 cut(s) 23, 34, 308, 374, 697, 754
CviQI GTAC 3 cut(s) 100, 123, 703
DdeI CTNAG 2 cut(s) 369, 444
DpnI GATC 4 cut(s) 207, 436, 576, 635
DpnII GATC 4 cut(s) 205, 434, 574, 633
Eco57I CTGAAG 1 cut(s) 138
EcoRI GAATTC 1 cut(s) 316
Esp3I CGTCTC 1 cut(s) 657
FaeI CATG 2 cut(s) 58, 465
FatI CATG 2 cut(s) 54, 461
FauI CCCGC 1 cut(s) 737
FbaI TGATCA 1 cut(s) 633
FblI GTMKAC 1 cut(s) 684
Fnu4HI GCNGC 2 cut(s) 21, 309
Fsp4HI GCNGC 2 cut(s) 21, 309
GluI GCNGC 2 cut(s) 21, 309
Hin1II CATG 2 cut(s) 58, 465
HindIII AAGCTT 1 cut(s) 752
HinfI GANTC 3 cut(s) 359, 617, 712
HphI GGTGA 3 cut(s) 61, 598, 612
Hpy166II GTNNAC 3 cut(s) 102, 125, 685
Hpy188I TCNGA 2 cut(s) 370, 740
Hpy188III TCNNGA 2 cut(s) 143, 321
Hpy8I GTNNAC 3 cut(s) 102, 125, 685
Hpy99I CGWCG 1 cut(s) 671
HpyAV CCTTC 3 cut(s) 113, 249, 476
HpyCH4III ACNGT 1 cut(s) 671
HpyCH4IV ACGT 2 cut(s) 94, 748
HpyCH4V TGCA 3 cut(s) 20, 465, 654
HpyF10VI GCNNNNNNNGC 1 cut(s) 380
HpyF3I CTNAG 2 cut(s) 369, 444
HpySE526I ACGT 2 cut(s) 94, 748
Hsp92II CATG 2 cut(s) 58, 465
Ksp22I TGATCA 1 cut(s) 633
Kzo9I GATC 4 cut(s) 205, 434, 574, 633
LpnPI CCDG 5 cut(s) 9, 396, 463, 729, 779
Lsp1109I GCAGC 1 cut(s) 32
MaeII ACGT 2 cut(s) 94, 748
MalI GATC 4 cut(s) 207, 436, 576, 635
MboI GATC 4 cut(s) 205, 434, 574, 633
MboII GAAGA 2 cut(s) 600, 607
MluCI AATT 9 cut(s) 192, 250, 316, 349, 427, 598, 656, 706, 722
MlyI GAGTC 1 cut(s) 721
MmeI TCCRAC 2 cut(s) 21, 577
MnlI CCTC 6 cut(s) 77, 196, 246, 364, 380, 525
MroXI GAANNNNTTC 1 cut(s) 599
MseI TTAA 3 cut(s) 36, 153, 329
MslI CAYNNNNRTG 1 cut(s) 144
MspA1I CMGCKG 1 cut(s) 23
MspCI CTTAAG 1 cut(s) 35
MwoI GCNNNNNNNGC 1 cut(s) 380
NdeII GATC 4 cut(s) 205, 434, 574, 633
NlaIII CATG 2 cut(s) 58, 465
NspI RCATGY 1 cut(s) 465
PdmI GAANNNNTTC 1 cut(s) 599
PfeI GAWTC 2 cut(s) 359, 617
PkrI GCNGC 2 cut(s) 22, 310
PleI GAGTC 1 cut(s) 720
PpsI GAGTC 1 cut(s) 720
Psp1406I AACGTT 1 cut(s) 94
PstI CTGCAG 1 cut(s) 22
PvuII CAGCTG 1 cut(s) 23
RsaI GTAC 3 cut(s) 101, 124, 704
RsaNI GTAC 3 cut(s) 100, 123, 703
RseI CAYNNNNRTG 1 cut(s) 144
SaqAI TTAA 3 cut(s) 36, 153, 329
SatI GCNGC 2 cut(s) 21, 309
Sau3AI GATC 4 cut(s) 205, 434, 574, 633
SchI GAGTC 1 cut(s) 721
SfcI CTRYAG 1 cut(s) 18
SmiMI CAYNNNNRTG 1 cut(s) 144
SmlI CTYRAG 1 cut(s) 35
SmoI CTYRAG 1 cut(s) 35
Sse9I AATT 9 cut(s) 192, 250, 316, 349, 427, 598, 656, 706, 722
SsiI CCGC 2 cut(s) 309, 730
TaaI ACNGT 1 cut(s) 671
TaiI ACGT 2 cut(s) 97, 751
TaqI TCGA 2 cut(s) 437, 715
TasI AATT 9 cut(s) 192, 250, 316, 349, 427, 598, 656, 706, 722
TatI WGTACW 1 cut(s) 99
TauI GCSGC 1 cut(s) 311
TfiI GAWTC 2 cut(s) 359, 617
Tru1I TTAA 3 cut(s) 36, 153, 329
Tru9I TTAA 3 cut(s) 36, 153, 329
TseI GCWGC 1 cut(s) 20
TspDTI ATGAA 1 cut(s) 24
TspGWI ACGGA 1 cut(s) 98
Vha464I CTTAAG 1 cut(s) 35
XapI RAATTY 7 cut(s) 250, 316, 349, 427, 598, 656, 722
XceI RCATGY 1 cut(s) 465
XcmI CCANNNNNNNNNTGG 1 cut(s) 560
XmiI GTMKAC 1 cut(s) 684
XmnI GAANNNNTTC 1 cut(s) 599
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.