MD12G1205500.v1.1

RNA polymerase II-associated protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr12
OG0005138
Physical Location & Seq
Forward (+)
28599791 .. 28603759
3969 bp
Loading structure...
UTR
Exon/CDS
Intron
MD12G1205500.v1.1.491

Sequence Viewer

Length: 1236 bp
ATGGCTAGACCTCCGAACAAGCACGGCCGCGACCAAGCTCTGGATTTCCAGGGGTTTTTGAGTGACTTGCAGGACTGGGAGCTTTCTCTCAAGGACAAGGACAAGAAAATGAGACCACAAGTTTCACAGCAGGAAAAGCTGACTAGAGATTCCGGGACCAGTTCTGGGAATTATGACTACTCAAGGAATTTTGATGCCATCAAAAGAATATCAAGTAGTTTGAGATCCGAAGATAGTCTTCCCGATGCTGCTTCAGAAAAAGAATTGGGTAATGAGTATTTTAAGCAGAAGAAGTTTAAGGAAGCTATCGACTGCTATTCAAGAAGCATCGCTTTGTCCCCATCTGCAGTAGCGTATGCAAATAGGGGAATGGCATATATCAAAATCAGAAGATTTCAGGAAGCTGAGGATGACTGTACAGAGGCCTTGAATTTGGATGATCGTTATATAAAAGCATACTCACGACGTGCAACAGCTAGAAAAGAACTTGGAAAGCTTAAAGAATCATTCGAGGATGCTGAGTTTGCCCTGAGGTTGGAGCCTCACAACCAAGAGATCAAGAAACAATACACGGAAGCCAAATCTTTGTATGACAAATCAAATCTTGAGAAGGCATCTGGAGCACTGAAAAATTCTGTACAAGAAGTGCAGAAAAGGGGAAAGTTGGATACCAAAGTAAATGGAAAAGGCATCCAGCCTGTCTCAAGCAGTGCTCAAATAACTGAAATAACTTCAGTTCAAGATCATACTAAGGGAGATAATACAAATAAGAAGCTAGAGGTGAAGGCATCGGTACAAGAGCTTGCTTCTCGAGCTGCTTCCAAAGCCAAGGTTGTAGCTGCAGAGAAAAACATCACCCCACCAACTACCGCATATCAATTTGAGGTTTCTTGGCGAGATCTCTCTGGAGATAGTGCTCTGCAGGCTAGTCTGTTGAAGTCTATATCTCCTAGTGCATTGCCACAGATATTCAAAAATGCTTTGACTGTTCCCATACTAATTGACATTATCAATTGCGTGGCGACCTTTTTTGTTGAAGAAATGGAACTGGCCGTCAATTATTTGGAGAACTTGACCAAGGTTCCAAGATTTGACACACTCATCATTTTTCTTTCATCCTCAAACAAGGCCGATCTTGATAAGATATGGGATGAAGTGTTCTACAATGAGGCAACTCCAATCGAGTATGCGGAGAAGCTTGGTAACCTGCGTGCAAAGTACTGCCTCAAGCGATGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0005575 GO:0005622 GO:0005623 GO:0005737 GO:0005829 GO:0032991 GO:0044424 GO:0044444 GO:0044464 GO:0097255
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
RPAP3_C TPR_1 TPR_8

Protein Analysis

412

Amino Acids

46.35

Weight (kDa)

8.55

Isoelectric Point (pI)

45.61

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TPR_BSK1_C PF25575 78 - 151 1.5e-07 Serine/threonine-protein kinase BSK1-like, TPR repeats
TPR_1 PF00515 87 - 115 5e-08 Tetratricopeptide repeat
TPR_11 PF13414 90 - 127 1.7e-06 TPR repeat
TPR_1 PF00515 116 - 146 1.5e-06 Tetratricopeptide repeat
RPAP3_C PF13877 287 - 376 8.3e-26 Potential Monad-binding region of RPAP3
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 1215
AccB7I CCANNNNNTGG 1 cut(s) 40
AccII CGCG 1 cut(s) 30
AciI CCGC 3 cut(s) 28, 870, 1190
AclWI GGATC 1 cut(s) 219
AcoI YGGCCR 2 cut(s) 25, 1050
AcsI RAATTY 3 cut(s) 187, 430, 631
AcuI CTGAAG 2 cut(s) 237, 717
AdeI CACNNNGTG 1 cut(s) 467
AfaI GTAC 4 cut(s) 418, 639, 795, 1220
AfiI CCNNNNNNNGG 3 cut(s) 40, 165, 535
AgsI TTSAA 6 cut(s) 321, 430, 740, 937, 973, 1037
AjiI CACGTC 1 cut(s) 467
AjnI CCWGG 1 cut(s) 48
AloI GAACNNNNNNTCC 2 cut(s) 1142, 1174
Alw21I GWGCWC 3 cut(s) 625, 715, 919
Alw26I GTCTC 2 cut(s) 106, 706
AlwI GGATC 1 cut(s) 219
Ama87I CYCGRG 1 cut(s) 810
AoxI GGCC 4 cut(s) 25, 423, 1050, 1128
ApeKI GCWGC 3 cut(s) 248, 815, 839
ApoI RAATTY 3 cut(s) 187, 430, 631
AspS9I GGNCC 1 cut(s) 156
AsuC2I CCSGG 1 cut(s) 154
AsuHPI GGTGA 2 cut(s) 793, 847
AvaI CYCGRG 1 cut(s) 810
AvaII GGWCC 1 cut(s) 156
AxyI CCTNAGG 1 cut(s) 530
BaeI ACNNNNGTAYC 2 cut(s) 660, 693
BbsI GAAGAC 1 cut(s) 230
Bbv12I GWGCWC 3 cut(s) 625, 715, 919
BbvCI CCTCAGC 1 cut(s) 405
BbvI GCAGC 3 cut(s) 235, 802, 826
BccI CCATC 2 cut(s) 206, 349
BceAI ACGGC 2 cut(s) 40, 1037
BciT130I CCWGG 1 cut(s) 50
BciVI GTATCC 1 cut(s) 661
BcnI CCSGG 1 cut(s) 154
BcoDI GTCTC 2 cut(s) 106, 706
BfaI CTAG 6 cut(s) 6, 144, 477, 776, 927, 951
BfmI CTRYAG 3 cut(s) 345, 840, 920
BfuAI ACCTGC 1 cut(s) 1215
BfuI GTATCC 1 cut(s) 661
BglII AGATCT 1 cut(s) 898
BisI GCNGC 4 cut(s) 28, 249, 816, 840
BlsI GCNGC 4 cut(s) 29, 250, 817, 841
BmcAI AGTACT 1 cut(s) 1220
Bme1390I CCNGG 2 cut(s) 50, 154
Bme18I GGWCC 1 cut(s) 156
BmeT110I CYCGRG 1 cut(s) 810
BmgBI CACGTC 1 cut(s) 467
BmgT120I GGNCC 1 cut(s) 156
BmiI GGNNCC 3 cut(s) 157, 540, 1083
BmrFI CCNGG 2 cut(s) 50, 154
BmrI ACTGGG 1 cut(s) 85
BmsI GCATC 7 cut(s) 184, 235, 336, 505, 623, 699, 797
BmuI ACTGGG 1 cut(s) 85
BpiI GAAGAC 1 cut(s) 230
BpmI CTGGAG 2 cut(s) 639, 927
Bpu10I CCTNAGC 1 cut(s) 405
BpuEI CTTGAG 5 cut(s) 74, 166, 626, 688, 1211
BpuMI CCSGG 1 cut(s) 154
BsaI GGTCTC 1 cut(s) 106
BsaJI CCNNGG 3 cut(s) 49, 828, 1077
Bsc4I CCNNNNNNNGG 3 cut(s) 40, 165, 535
Bse1I ACTGG 3 cut(s) 80, 159, 1053
Bse21I CCTNAGG 1 cut(s) 530
Bse3DI GCAATG 1 cut(s) 956
BseBI CCWGG 1 cut(s) 50
BseDI CCNNGG 3 cut(s) 49, 828, 1077
BseGI GGATG 6 cut(s) 415, 442, 520, 690, 1115, 1156
BseLI CCNNNNNNNGG 3 cut(s) 40, 165, 535
BseMI GCAATG 1 cut(s) 956
BseMII CTCAG 3 cut(s) 396, 510, 521
BseNI ACTGG 3 cut(s) 80, 159, 1053
BseX3I CGGCCG 1 cut(s) 25
BseXI GCAGC 3 cut(s) 235, 802, 826
BsgI GTGCAG 1 cut(s) 668
Bsh1236I CGCG 1 cut(s) 30
Bsh1285I CGRYCG 1 cut(s) 28
BshFI GGCC 4 cut(s) 27, 425, 1052, 1130
BsiEI CGRYCG 1 cut(s) 28
BsiHKAI GWGCWC 3 cut(s) 625, 715, 919
BsiHKCI CYCGRG 1 cut(s) 810
BsiSI CCGG 1 cut(s) 153
BslFI GGGAC 2 cut(s) 169, 322
BslI CCNNNNNNNGG 3 cut(s) 40, 165, 535
BsmAI GTCTC 2 cut(s) 106, 706
BsmFI GGGAC 2 cut(s) 169, 322
BsnI GGCC 4 cut(s) 27, 425, 1052, 1130
Bso31I GGTCTC 1 cut(s) 106
BsoBI CYCGRG 1 cut(s) 810
Bsp1286I GDGCHC 3 cut(s) 625, 715, 919
Bsp1407I TGTACA 2 cut(s) 416, 637
Bsp143I GATC 6 cut(s) 224, 439, 555, 742, 898, 1132
BspACI CCGC 3 cut(s) 28, 870, 1190
BspANI GGCC 4 cut(s) 27, 425, 1052, 1130
BspCNI CTCAG 3 cut(s) 397, 511, 522
BspFNI CGCG 1 cut(s) 30
BspLI GGNNCC 3 cut(s) 157, 540, 1083
BspMAI CTGCAG 3 cut(s) 349, 844, 924
BspMI ACCTGC 1 cut(s) 1215
BspPI GGATC 1 cut(s) 219
BspTNI GGTCTC 1 cut(s) 106
BsrDI GCAATG 1 cut(s) 956
BsrGI TGTACA 2 cut(s) 416, 637
BsrI ACTGG 3 cut(s) 80, 159, 1053
BssECI CCNNGG 3 cut(s) 49, 828, 1077
BssMI GATC 6 cut(s) 224, 439, 555, 742, 898, 1132
BssT1I CCWWGG 2 cut(s) 828, 1077
Bst2UI CCWGG 1 cut(s) 50
Bst4CI ACNGT 2 cut(s) 416, 988
BstAUI TGTACA 2 cut(s) 416, 637
BstC8I GCNNGC 3 cut(s) 804, 924, 1212
BstDEI CTNAG 4 cut(s) 405, 519, 530, 750
BstEII GGTNACC 1 cut(s) 1202
BstF5I GGATG 6 cut(s) 415, 442, 520, 690, 1115, 1156
BstFNI CGCG 1 cut(s) 30
BstKTI GATC 6 cut(s) 227, 442, 558, 745, 901, 1135
BstMAI GTCTC 2 cut(s) 106, 706
BstMBI GATC 6 cut(s) 224, 439, 555, 742, 898, 1132
BstMCI CGRYCG 1 cut(s) 28
BstMWI GCNNNNNNNGC 6 cut(s) 136, 524, 620, 812, 824, 923
BstNI CCWGG 1 cut(s) 50
BstPI GGTNACC 1 cut(s) 1202
BstSCI CCNGG 2 cut(s) 48, 152
BstSFI CTRYAG 3 cut(s) 345, 840, 920
BstUI CGCG 1 cut(s) 30
BstV1I GCAGC 3 cut(s) 235, 802, 826
BstV2I GAAGAC 1 cut(s) 230
BstX2I RGATCY 2 cut(s) 224, 898
BstYI RGATCY 2 cut(s) 224, 898
BstZI CGGCCG 1 cut(s) 25
Bsu36I CCTNAGG 1 cut(s) 530
BsuI GTATCC 1 cut(s) 661
BsuRI GGCC 4 cut(s) 27, 425, 1052, 1130
BtgZI GCGATG 1 cut(s) 313
BtrI CACGTC 1 cut(s) 467
BtsCI GGATG 6 cut(s) 415, 442, 520, 690, 1115, 1156
BtsI GCAGTG 1 cut(s) 715
BtsIMutI CAGTG 2 cut(s) 623, 715
BveI ACCTGC 1 cut(s) 1215
Cac8I GCNNGC 3 cut(s) 804, 924, 1212
Cfr13I GGNCC 1 cut(s) 156
Csp6I GTAC 4 cut(s) 417, 638, 794, 1219
CviQI GTAC 4 cut(s) 417, 638, 794, 1219
DdeI CTNAG 4 cut(s) 405, 519, 530, 750
DpnI GATC 6 cut(s) 226, 441, 557, 744, 900, 1134
DpnII GATC 6 cut(s) 224, 439, 555, 742, 898, 1132
DraIII CACNNNGTG 1 cut(s) 467
EaeI YGGCCR 2 cut(s) 25, 1050
EagI CGGCCG 1 cut(s) 25
EclXI CGGCCG 1 cut(s) 25
Eco130I CCWWGG 2 cut(s) 828, 1077
Eco147I AGGCCT 1 cut(s) 425
Eco31I GGTCTC 1 cut(s) 106
Eco47I GGWCC 1 cut(s) 156
Eco52I CGGCCG 1 cut(s) 25
Eco57I CTGAAG 2 cut(s) 237, 717
Eco81I CCTNAGG 1 cut(s) 530
Eco88I CYCGRG 1 cut(s) 810
Eco91I GGTNACC 1 cut(s) 1202
EcoO65I GGTNACC 1 cut(s) 1202
EcoRII CCWGG 1 cut(s) 48
EcoT14I CCWWGG 2 cut(s) 828, 1077
ErhI CCWWGG 2 cut(s) 828, 1077
FalI AAGNNNNNCTT 4 cut(s) 222, 254, 316, 348
FaqI GGGAC 2 cut(s) 169, 322
Fnu4HI GCNGC 4 cut(s) 28, 249, 816, 840
FokI GGATG 6 cut(s) 422, 449, 527, 677, 1102, 1163
Fsp4HI GCNGC 4 cut(s) 28, 249, 816, 840
FspBI CTAG 6 cut(s) 6, 144, 477, 776, 927, 951
GluI GCNGC 4 cut(s) 28, 249, 816, 840
GsuI CTGGAG 2 cut(s) 639, 927
HaeIII GGCC 4 cut(s) 27, 425, 1052, 1130
HapII CCGG 1 cut(s) 153
HindIII AAGCTT 2 cut(s) 494, 1196
HinfI GANTC 2 cut(s) 149, 503
HpaII CCGG 1 cut(s) 153
HphI GGTGA 2 cut(s) 793, 847
Hpy188I TCNGA 4 cut(s) 15, 229, 256, 389
Hpy99I CGWCG 1 cut(s) 468
HpyAV CCTTC 2 cut(s) 604, 778
HpyCH4III ACNGT 2 cut(s) 416, 988
HpyCH4IV ACGT 1 cut(s) 466
HpyCH4V TGCA 9 cut(s) 70, 347, 359, 470, 649, 842, 922, 956, 1214
HpyF10VI GCNNNNNNNGC 6 cut(s) 136, 524, 620, 812, 824, 923
HpyF3I CTNAG 4 cut(s) 405, 519, 530, 750
HpySE526I ACGT 1 cut(s) 466
Kzo9I GATC 6 cut(s) 224, 439, 555, 742, 898, 1132
LmnI GCTCC 3 cut(s) 79, 538, 620
Lsp1109I GCAGC 3 cut(s) 235, 802, 826
LweI GCATC 7 cut(s) 184, 235, 336, 505, 623, 699, 797
MaeI CTAG 6 cut(s) 6, 144, 477, 776, 927, 951
MaeII ACGT 1 cut(s) 466
MaeIII GTNAC 2 cut(s) 62, 1202
MalI GATC 6 cut(s) 226, 441, 557, 744, 900, 1134
MboI GATC 6 cut(s) 224, 439, 555, 742, 898, 1132
MboII GAAGA 5 cut(s) 230, 242, 301, 402, 1049
MfeI CAATTG 1 cut(s) 1012
MflI RGATCY 2 cut(s) 224, 898
MhlI GDGCHC 3 cut(s) 625, 715, 919
MluCI AATT 9 cut(s) 169, 187, 263, 430, 631, 878, 999, 1012, 1057
MmeI TCCRAC 2 cut(s) 516, 645
MseI TTAA 3 cut(s) 282, 297, 498
MspI CCGG 1 cut(s) 153
MspR9I CCNGG 2 cut(s) 50, 154
MunI CAATTG 1 cut(s) 1012
MvaI CCWGG 1 cut(s) 50
MvnI CGCG 1 cut(s) 30
MwoI GCNNNNNNNGC 6 cut(s) 136, 524, 620, 812, 824, 923
NciI CCSGG 1 cut(s) 154
NdeII GATC 6 cut(s) 224, 439, 555, 742, 898, 1132
NlaIV GGNNCC 3 cut(s) 157, 540, 1083
NmuCI GTSAC 1 cut(s) 62
PaeR7I CTCGAG 1 cut(s) 810
PceI AGGCCT 1 cut(s) 425
PfeI GAWTC 2 cut(s) 149, 503
PflMI CCANNNNNTGG 1 cut(s) 40
PfoI TCCNGGA 1 cut(s) 152
PkrI GCNGC 4 cut(s) 29, 250, 817, 841
Psp6I CCWGG 1 cut(s) 48
PspEI GGTNACC 1 cut(s) 1202
PspGI CCWGG 1 cut(s) 48
PspN4I GGNNCC 3 cut(s) 157, 540, 1083
PspPI GGNCC 1 cut(s) 156
PstI CTGCAG 3 cut(s) 349, 844, 924
PsuI RGATCY 2 cut(s) 224, 898
RsaI GTAC 4 cut(s) 418, 639, 795, 1220
RsaNI GTAC 4 cut(s) 417, 638, 794, 1219
SaqAI TTAA 3 cut(s) 282, 297, 498
SatI GCNGC 4 cut(s) 28, 249, 816, 840
Sau3AI GATC 6 cut(s) 224, 439, 555, 742, 898, 1132
Sau96I GGNCC 1 cut(s) 156
ScaI AGTACT 1 cut(s) 1220
ScrFI CCNGG 2 cut(s) 50, 154
SduI GDGCHC 3 cut(s) 625, 715, 919
SfaNI GCATC 7 cut(s) 184, 235, 336, 505, 623, 699, 797
SfcI CTRYAG 3 cut(s) 345, 840, 920
Sfr274I CTCGAG 1 cut(s) 810
SinI GGWCC 1 cut(s) 156
SlaI CTCGAG 1 cut(s) 810
SmlI CTYRAG 6 cut(s) 89, 181, 605, 703, 810, 1226
SmoI CTYRAG 6 cut(s) 89, 181, 605, 703, 810, 1226
Sse9I AATT 9 cut(s) 169, 187, 263, 430, 631, 878, 999, 1012, 1057
SseBI AGGCCT 1 cut(s) 425
SsiI CCGC 3 cut(s) 28, 870, 1190
SspMI CTAG 6 cut(s) 6, 144, 477, 776, 927, 951
StuI AGGCCT 1 cut(s) 425
StyD4I CCNGG 2 cut(s) 48, 152
StyI CCWWGG 2 cut(s) 828, 1077
TaaI ACNGT 2 cut(s) 416, 988
TaiI ACGT 1 cut(s) 469
TaqI TCGA 4 cut(s) 309, 510, 811, 1182
TasI AATT 9 cut(s) 169, 187, 263, 430, 631, 878, 999, 1012, 1057
TatI WGTACW 3 cut(s) 416, 637, 1218
TauI GCSGC 1 cut(s) 30
TfiI GAWTC 2 cut(s) 149, 503
Tru1I TTAA 3 cut(s) 282, 297, 498
Tru9I TTAA 3 cut(s) 282, 297, 498
TscAI CASTG 2 cut(s) 630, 715
TseFI GTSAC 1 cut(s) 62
TseI GCWGC 3 cut(s) 248, 815, 839
Tsp45I GTSAC 1 cut(s) 62
TspDTI ATGAA 2 cut(s) 1104, 1167
TspGWI ACGGA 1 cut(s) 587
TspRI CASTG 2 cut(s) 630, 715
Van91I CCANNNNNTGG 1 cut(s) 40
VpaK11BI GGWCC 1 cut(s) 156
XapI RAATTY 3 cut(s) 187, 430, 631
XhoI CTCGAG 1 cut(s) 810
XspI CTAG 6 cut(s) 6, 144, 477, 776, 927, 951
ZrmI AGTACT 1 cut(s) 1220
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.