Basic Information

Type: gene

Biological Identity

Species

malus_domestica

Chromosome

Chr10

Orthogroup ID

OG0006436

Physical Location & Seq

Genomic Coordinates Forward (+)

39423914 .. 39426319

Gene Structure 2406 bp

Loading structure...

UTR

Exon/CDS

Intron

Transcript / Protein ID

MD10G1309400.v1.1.491

Sequence Viewer

CDS Protein Promoter (2k)

Length: 1617 bp

ATGTTTGTTTTGCGCCCCCTTCAGGATTTAGGATCGAGGCGTACAATCCCGACAATCAAGGCACTTCCGCATCGGCATCTTCGAGTCCTCTTGGACTTGGCTACGGGGAAGATGATTGGATCGGGTACGCAACGTGATGGTCTTTATTATATGTCGCCGTTGCAACGGATGCCCATCTCCTGTCAAGTTTCCCACTCCACCAATTTATGGCATATGCGACTTGGCCATCCTTCGCCTACTCGCCTTAAATTAGTATTTCCCTCGTTATTCTCGAATAATATTTCTTTTGATAATAATTGTAACATTTGTCCCATAGCCAAACAAACTAGACTTCCGTTTCCTTCAAGTTTTATATCCACTCATAATCCATTTGATTTACTTCATTATGATATTTGGGGACCTCATAAAATTCCCACGCATTCAGGAGCTCGATTCTTTCTCACCATTGTGGATGATTTTACTAGATGCACATGGATATTTTTGATGAAATATAAATCTGAAACGCAAGACCTTTTAAAATCGTTTATTACCTTTGCTCATACTCAATTTCATGCCAAAATTAAAGCCATACGAGTCGACAATGGGTCTGAATTTTTGTCCATGAAAGTTTTTTTCCAAACCAATGACATTGAATATCAACGCACCTGTGTCTACACCCCGCAACAAAATGGGGTTGTCGAACGTAAGCATAGACACATCCTCACCATTGCACGTAGCTTACTATTTCAATCTCACTTACCCCTTTCTTTTTGGGGCGAATGTGTTTCCACTGCTGTCTACCTCATTAATCGATTACCATCCCCTTTGTTATCCAATAAATCTCCTTTCGAATCATTATACAAGTGTTCACCATCTTTTGATCACTTGAAAAATTTTGGTTGTTTGTGCTTCTCCACTATTGTTCATCCCACATACAAATTTGACCCTCGTGCTAGGCGTTGTATTTTTGTTGGTTACCCAACTGGTCAGAAGTGTTACAAACTTTATGATTTGGAGTCTAAAACCTTCTTTGTCAGTCGTGATGTTAAATTTTTTGAACACACATTTCCTTTCCACTCTATGTCCCCGTCACCCCCTGAGGATATCCCTGCCATACCGTCCATTCCCATCTCAACTGACACACTTGACCTCTCCCACATGGCCCCCCATAACCCTTCCATTCCACCACTCACGGACCCTACCCACATTCCTATTTCACCTCCCATCACTTCTTCCACCCCATCTCATCCTGAAGCCATCCCATCTTCTCCTGGACCCCACCTCTCCATCAATCATCCTTCACCCCTCCATCACATTTCTAACCCCCCATCAGACTCTCTCCTTCCCTACACCGAACCTACCCTCCATTCCCACCCCATTCCGTCCGATACTTCTTCTCCTCTCGCCACATCATCCTCTCCACCCCCATGCCAGTCCCATCGTCCTAAGCAACCTCCGATTTGGCATAAAAACTATCACGTTACTAATCAAGTCAGTCATTTTCCTTTGCAGCCTCGTGTTCCCTCAGGTACTCGGTATCCTCTTTCTAATTTTCTTTCCTACTCACGTCTTTCTCCTACCCACTGTGCTTTTCTAGCTACCATTACAAGTTCTATCGAGCCTACTTCATATGCTTAG

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

RVT_2 Retrotran_gag_3 Retrotrans_gag gag_pre-integrs rve

Protein Analysis

539

Amino Acids

60.92

Weight (kDa)

9.24

Isoelectric Point (pI)

62.01

Instability Index

Protein Domains (Pfam)

Domain Name	Pfam ID	Position	E-value	Description
gag_pre-integrs	PF13976	47 - 108	2.2e-11	GAG-pre-integrase domain
rve	PF00665	121 - 220	2e-09	Integrase core domain
SH3_retrovirus	PF25597	294 - 354	7.5e-21	Retroviral polymerase SH3-like domain

Hydrophobicity Profile (Kyte-Doolittle)

AI Structure Prediction Report

Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter

Style Settings

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Align Labels (Cladogram)

Image

Tree File

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Publication-ready

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Orthologous Genes (Group: OG0006436)

Species	Orthologous Gene IDs
arabidopsis_thaliana	AT1G21280
fragaria_vesca	FvH4_3g37931 FvH4_3g37931 FvH4_3g37931
malus_domestica	MD01G1094300.v1.1 MD02G1156200.v1.1 MD10G1309400.v1.1 MD14G1005300.v1.1
pyrus_communis	pycom02g16670 pycom03g10030 pycom04g21390 pycom05g29420 pycom07g08570 pycom08g06430 pycom15g03080 pycom15g21690
rosa_chinensis	RchiOBHm_Chr4g0394011 RchiOBHm_Chr4g0436631
rosa_multiflora	Rmu_sc0002646.1_g000018 Rmu_sc0004135.1_g000007
rosa_roxburghii	Rroxscaffold_2G00099130
rosa_samantha	Rh1AG086000 Rh2BG003200 Rh5DG450100 Rh7AG095400
rosa_wichuraiana	Rw1G012660

Restriction Enzyme Sites

1 / 10

Enzyme	Recognition Site	Cut Count	Positions (bp)
AccB7I	CCANNNNNTGG	1 cut(s)	207
AccI	GTMKAC	3 cut(s)	576, 651, 777
AciI	CCGC	2 cut(s)	68, 659
AclWI	GGATC	2 cut(s)	40, 127
AcoI	YGGCCR	1 cut(s)	223
AcsI	RAATTY	5 cut(s)	408, 590, 871, 917, 1028
AcuI	CTGAAG	2 cut(s)	5, 1251
AfaI	GTAC	3 cut(s)	43, 127, 1510
AfiI	CCNNNNNNNGG	2 cut(s)	22, 207
AgsI	TTSAA	5 cut(s)	345, 632, 728, 868, 1037
AhdI	GACNNNNNGTC	1 cut(s)	583
AjiI	CACGTC	1 cut(s)	1547
AjnI	CCWGG	1 cut(s)	1249
AleI	CACNNNNGTG	1 cut(s)	446
AloI	GAACNNNNNNTCC	2 cut(s)	1326, 1358
AluBI	AGCT	3 cut(s)	428, 717, 1577
AluI	AGCT	3 cut(s)	428, 717, 1577
Alw21I	GWGCWC	1 cut(s)	430
AlwI	GGATC	2 cut(s)	40, 127
AoxI	GGCC	2 cut(s)	223, 1140
ApeKI	GCWGC	1 cut(s)	1489
ApoI	RAATTY	5 cut(s)	408, 590, 871, 917, 1028
AseI	ATTAAT	1 cut(s)	786
AspLEI	GCGC	1 cut(s)	15
AspS9I	GGNCC	4 cut(s)	398, 1141, 1174, 1253
AsuHPI	GGTGA	6 cut(s)	433, 694, 840, 1062, 1188, 1272
AsuII	TTCGAA	1 cut(s)	828
AvaII	GGWCC	3 cut(s)	398, 1174, 1253
AxyI	CCTNAGG	2 cut(s)	1077, 1504
BalI	TGGCCA	1 cut(s)	225
BanII	GRGCYC	1 cut(s)	430
BauI	CACGAG	2 cut(s)	927, 1494
Bbv12I	GWGCWC	1 cut(s)	430
BbvI	GCAGC	1 cut(s)	1501
BceAI	ACGGC	1 cut(s)	142
BciT130I	CCWGG	1 cut(s)	1251
BciVI	GTATCC	1 cut(s)	1527
BclI	TGATCA	1 cut(s)	859
BfaI	CTAG	4 cut(s)	327, 462, 933, 1574
BfuI	GTATCC	1 cut(s)	1527
BisI	GCNGC	1 cut(s)	1490
BlsI	GCNGC	1 cut(s)	1491
Bme1390I	CCNGG	1 cut(s)	1251
Bme18I	GGWCC	3 cut(s)	398, 1174, 1253
BmeRI	GACNNNNNGTC	1 cut(s)	583
BmgBI	CACGTC	1 cut(s)	1547
BmgT120I	GGNCC	4 cut(s)	398, 1141, 1174, 1253
BmiI	GGNNCC	4 cut(s)	399, 1143, 1176, 1255
BmrFI	CCNGG	1 cut(s)	1251
BmsI	GCATC	4 cut(s)	79, 85, 159, 455
Bpu10I	CCTNAGC	1 cut(s)	1425
Bpu14I	TTCGAA	1 cut(s)	828
Bsa29I	ATCGAT	1 cut(s)	790
BsaAI	YACGTR	1 cut(s)	713
BsaBI	GATNNNNATC	2 cut(s)	173, 796
BsaXI	ACNNNNNCTCC	4 cut(s)	1326, 1356, 1360, 1390
Bsc4I	CCNNNNNNNGG	2 cut(s)	22, 207
Bse1I	ACTGG	2 cut(s)	967, 1411
Bse21I	CCTNAGG	2 cut(s)	1077, 1504
Bse3DI	GCAATG	1 cut(s)	705
Bse8I	GATNNNNATC	2 cut(s)	173, 796
BseBI	CCWGG	1 cut(s)	1251
BseCI	ATCGAT	1 cut(s)	790
BseJI	GATNNNNATC	2 cut(s)	173, 796
BseLI	CCNNNNNNNGG	2 cut(s)	22, 207
BseMI	GCAATG	1 cut(s)	705
BseMII	CTCAG	2 cut(s)	1068, 1518
BseNI	ACTGG	2 cut(s)	967, 1411
BseRI	GAGGAG	1 cut(s)	1368
BseXI	GCAGC	1 cut(s)	1501
BshFI	GGCC	2 cut(s)	225, 1142
BshVI	ATCGAT	1 cut(s)	790
BsiHKAI	GWGCWC	1 cut(s)	430
BslFI	GGGAC	4 cut(s)	294, 411, 1048, 1399
BslI	CCNNNNNNNGG	2 cut(s)	22, 207
BsmFI	GGGAC	4 cut(s)	294, 411, 1048, 1399
BsmI	GAATGC	1 cut(s)	418
BsnI	GGCC	2 cut(s)	225, 1142
Bsp119I	TTCGAA	1 cut(s)	828
Bsp1286I	GDGCHC	1 cut(s)	430
Bsp143I	GATC	3 cut(s)	32, 119, 859
BspACI	CCGC	2 cut(s)	68, 659
BspANI	GGCC	2 cut(s)	225, 1142
BspCNI	CTCAG	2 cut(s)	1069, 1517
BspDI	ATCGAT	1 cut(s)	790
BspLI	GGNNCC	4 cut(s)	399, 1143, 1176, 1255
BspPI	GGATC	2 cut(s)	40, 127
BspT104I	TTCGAA	1 cut(s)	828
BsrDI	GCAATG	1 cut(s)	705
BsrI	ACTGG	2 cut(s)	967, 1411
BssMI	GATC	3 cut(s)	32, 119, 859
BssSI	CACGAG	2 cut(s)	927, 1494
Bst2BI	CACGAG	2 cut(s)	927, 1494
Bst2UI	CCWGG	1 cut(s)	1251
Bst4CI	ACNGT	2 cut(s)	1098, 1565
BstAPI	GCANNNNNTGC	1 cut(s)	169
BstBAI	YACGTR	1 cut(s)	713
BstBI	TTCGAA	1 cut(s)	828
BstDEI	CTNAG	4 cut(s)	1077, 1425, 1504, 1614
BstEII	GGTNACC	1 cut(s)	953
BstHHI	GCGC	1 cut(s)	15
BstKTI	GATC	3 cut(s)	35, 122, 862
BstMBI	GATC	3 cut(s)	32, 119, 859
BstMWI	GCNNNNNNNGC	2 cut(s)	169, 1574
BstNI	CCWGG	1 cut(s)	1251
BstPI	GGTNACC	1 cut(s)	953
BstSCI	CCNGG	1 cut(s)	1249
BstV1I	GCAGC	1 cut(s)	1501
Bsu15I	ATCGAT	1 cut(s)	790
Bsu36I	CCTNAGG	2 cut(s)	1077, 1504
BsuI	GTATCC	1 cut(s)	1527
BsuRI	GGCC	2 cut(s)	225, 1142
BsuTUI	ATCGAT	1 cut(s)	790
BtrI	CACGTC	1 cut(s)	1547
BtsI	GCAGTG	1 cut(s)	768
BtsIMutI	CAGTG	2 cut(s)	768, 1561
CfoI	GCGC	1 cut(s)	15
Cfr13I	GGNCC	4 cut(s)	398, 1141, 1174, 1253
ClaI	ATCGAT	1 cut(s)	790
Csp6I	GTAC	3 cut(s)	42, 126, 1509
CviAII	CATG	5 cut(s)	471, 551, 601, 1138, 1407
CviQI	GTAC	3 cut(s)	42, 126, 1509
DdeI	CTNAG	4 cut(s)	1077, 1425, 1504, 1614
DpnI	GATC	3 cut(s)	34, 121, 861
DpnII	GATC	3 cut(s)	32, 119, 859
DraI	TTTAAA	1 cut(s)	516
DriI	GACNNNNNGTC	1 cut(s)	583
EaeI	YGGCCR	1 cut(s)	223
Eam1105I	GACNNNNNGTC	1 cut(s)	583
Ecl136II	GAGCTC	1 cut(s)	428
Eco24I	GRGCYC	1 cut(s)	430
Eco32I	GATATC	1 cut(s)	1084
Eco47I	GGWCC	3 cut(s)	398, 1174, 1253
Eco53kI	GAGCTC	1 cut(s)	428
Eco57I	CTGAAG	2 cut(s)	5, 1251
Eco81I	CCTNAGG	2 cut(s)	1077, 1504
Eco91I	GGTNACC	1 cut(s)	953
EcoICRI	GAGCTC	1 cut(s)	428
EcoO109I	RGGNCCY	1 cut(s)	398
EcoO65I	GGTNACC	1 cut(s)	953
EcoRII	CCWGG	1 cut(s)	1249
EcoRV	GATATC	1 cut(s)	1084
EcoT38I	GRGCYC	1 cut(s)	430
FaeI	CATG	5 cut(s)	474, 554, 604, 1141, 1410
FaqI	GGGAC	4 cut(s)	294, 411, 1048, 1399
FatI	CATG	5 cut(s)	470, 550, 600, 1137, 1406
FauI	CCCGC	1 cut(s)	666
FauNDI	CATATG	2 cut(s)	213, 1609
FbaI	TGATCA	1 cut(s)	859
FblI	GTMKAC	3 cut(s)	576, 651, 777
Fnu4HI	GCNGC	1 cut(s)	1490
FriOI	GRGCYC	1 cut(s)	430
Fsp4HI	GCNGC	1 cut(s)	1490
FspBI	CTAG	4 cut(s)	327, 462, 933, 1574
GlaI	GCGC	1 cut(s)	14
GluI	GCNGC	1 cut(s)	1490
HaeIII	GGCC	2 cut(s)	225, 1142
HhaI	GCGC	1 cut(s)	15
Hin1II	CATG	5 cut(s)	474, 554, 604, 1141, 1410
Hin6I	GCGC	1 cut(s)	13
HinP1I	GCGC	1 cut(s)	13
HincII	GTYRAC	1 cut(s)	577
HindII	GTYRAC	1 cut(s)	577
HinfI	GANTC	6 cut(s)	84, 432, 573, 830, 995, 1313
HphI	GGTGA	6 cut(s)	433, 694, 840, 1062, 1188, 1272
Hpy166II	GTNNAC	4 cut(s)	577, 652, 778, 848
Hpy188I	TCNGA	6 cut(s)	499, 589, 969, 1312, 1366, 1437
Hpy188III	TCNNGA	6 cut(s)	23, 49, 271, 423, 1019, 1229
Hpy8I	GTNNAC	4 cut(s)	577, 652, 778, 848
HpyAV	CCTTC	7 cut(s)	29, 240, 351, 1015, 1164, 1287, 1331
HpyCH4III	ACNGT	2 cut(s)	1098, 1565
HpyCH4IV	ACGT	5 cut(s)	133, 682, 712, 1458, 1546
HpyCH4V	TGCA	4 cut(s)	163, 468, 710, 1489
HpyF10VI	GCNNNNNNNGC	2 cut(s)	169, 1574
HpyF3I	CTNAG	4 cut(s)	1077, 1425, 1504, 1614
HpySE526I	ACGT	5 cut(s)	133, 682, 712, 1458, 1546
Hsp92II	CATG	5 cut(s)	474, 554, 604, 1141, 1410
HspAI	GCGC	1 cut(s)	13
Ksp22I	TGATCA	1 cut(s)	859
Kzo9I	GATC	3 cut(s)	32, 119, 859
LmnI	GCTCC	1 cut(s)	425
Lsp1109I	GCAGC	1 cut(s)	1501
LweI	GCATC	4 cut(s)	79, 85, 159, 455
MaeI	CTAG	4 cut(s)	327, 462, 933, 1574
MaeII	ACGT	5 cut(s)	133, 682, 712, 1458, 1546
MaeIII	GTNAC	5 cut(s)	299, 953, 974, 1068, 1459
MalI	GATC	3 cut(s)	34, 121, 861
MboI	GATC	3 cut(s)	32, 119, 859
MboII	GAAGA	5 cut(s)	71, 121, 1203, 1236, 1365
MhlI	GDGCHC	1 cut(s)	430
MlsI	TGGCCA	1 cut(s)	225
MluNI	TGGCCA	1 cut(s)	225
MlyI	GAGTC	4 cut(s)	93, 582, 1004, 1307
Mox20I	TGGCCA	1 cut(s)	225
MscI	TGGCCA	1 cut(s)	225
MseI	TTAA	5 cut(s)	246, 515, 561, 786, 1026
MslI	CAYNNNNRTG	2 cut(s)	446, 1405
Msp20I	TGGCCA	1 cut(s)	225
MspR9I	CCNGG	1 cut(s)	1251
Mva1269I	GAATGC	1 cut(s)	418
MvaI	CCWGG	1 cut(s)	1251
MwoI	GCNNNNNNNGC	2 cut(s)	169, 1574
NdeI	CATATG	2 cut(s)	213, 1609
NdeII	GATC	3 cut(s)	32, 119, 859
NlaIII	CATG	5 cut(s)	474, 554, 604, 1141, 1410
NlaIV	GGNNCC	4 cut(s)	399, 1143, 1176, 1255
NmuCI	GTSAC	1 cut(s)	1068
NspV	TTCGAA	1 cut(s)	828
OliI	CACNNNNGTG	1 cut(s)	446
PcsI	WCGNNNNNNNCGW	3 cut(s)	79, 269, 934
PctI	GAATGC	1 cut(s)	418
PfeI	GAWTC	2 cut(s)	432, 830
PflMI	CCANNNNNTGG	1 cut(s)	207
PfoI	TCCNGGA	1 cut(s)	1249
PkrI	GCNGC	1 cut(s)	1491
PleI	GAGTC	4 cut(s)	92, 581, 1003, 1307
PpsI	GAGTC	4 cut(s)	92, 581, 1003, 1307
Ppu21I	YACGTR	1 cut(s)	713
PpuMI	RGGWCCY	1 cut(s)	398
PshBI	ATTAAT	1 cut(s)	786
Psp124BI	GAGCTC	1 cut(s)	430
Psp5II	RGGWCCY	1 cut(s)	398
Psp6I	CCWGG	1 cut(s)	1249
PspEI	GGTNACC	1 cut(s)	953
PspGI	CCWGG	1 cut(s)	1249
PspN4I	GGNNCC	4 cut(s)	399, 1143, 1176, 1255
PspPI	GGNCC	4 cut(s)	398, 1141, 1174, 1253
PspPPI	RGGWCCY	1 cut(s)	398
RsaI	GTAC	3 cut(s)	43, 127, 1510
RsaNI	GTAC	3 cut(s)	42, 126, 1509
RseI	CAYNNNNRTG	2 cut(s)	446, 1405
SacI	GAGCTC	1 cut(s)	430
SalI	GTCGAC	1 cut(s)	575
SaqAI	TTAA	5 cut(s)	246, 515, 561, 786, 1026
SatI	GCNGC	1 cut(s)	1490
Sau3AI	GATC	3 cut(s)	32, 119, 859
Sau96I	GGNCC	4 cut(s)	398, 1141, 1174, 1253
SchI	GAGTC	4 cut(s)	93, 582, 1004, 1307
ScrFI	CCNGG	1 cut(s)	1251
SduI	GDGCHC	1 cut(s)	430
SfaNI	GCATC	4 cut(s)	79, 85, 159, 455
SfuI	TTCGAA	1 cut(s)	828
SinI	GGWCC	3 cut(s)	398, 1174, 1253
SmiMI	CAYNNNNRTG	2 cut(s)	446, 1405
SsiI	CCGC	2 cut(s)	68, 659
SspI	AATATT	1 cut(s)	280
SspMI	CTAG	4 cut(s)	327, 462, 933, 1574
SstI	GAGCTC	1 cut(s)	430
StyD4I	CCNGG	1 cut(s)	1249
TaaI	ACNGT	2 cut(s)	1098, 1565
TaiI	ACGT	5 cut(s)	136, 685, 715, 1461, 1549
TaqI	TCGA	9 cut(s)	35, 82, 272, 430, 576, 678, 790, 828, 1596
TfiI	GAWTC	2 cut(s)	432, 830
Tru1I	TTAA	5 cut(s)	246, 515, 561, 786, 1026
Tru9I	TTAA	5 cut(s)	246, 515, 561, 786, 1026
TscAI	CASTG	2 cut(s)	775, 1568
TseFI	GTSAC	1 cut(s)	1068
TseI	GCWGC	1 cut(s)	1489
Tsp45I	GTSAC	1 cut(s)	1068
TspDTI	ATGAA	6 cut(s)	371, 500, 539, 617, 893, 1596
TspGWI	ACGGA	4 cut(s)	181, 324, 1187, 1350
TspRI	CASTG	2 cut(s)	775, 1568
Van91I	CCANNNNNTGG	1 cut(s)	207
VpaK11BI	GGWCC	3 cut(s)	398, 1174, 1253
VspI	ATTAAT	1 cut(s)	786
XapI	RAATTY	5 cut(s)	408, 590, 871, 917, 1028
XmiI	GTMKAC	3 cut(s)	576, 651, 777
XspI	CTAG	4 cut(s)	327, 462, 933, 1574

Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.