AT3G12990

polyadenylation-dependent mRNA catabolic process

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
3
OG0003830
Physical Location & Seq
Forward (+)
4156054 .. 4158004
1951 bp
Loading structure...
UTR
Exon/CDS
Intron
AT3G12990.1

Sequence Viewer

Length: 924 bp
ATGGAGGGGAGGTTGAATAATATGTGGAGGTTGACTGTGAATGAGAGCAAATTCGTTGAATCTGCGTTGCAATCTGAGCTCAGAGTCGATGGTCGTGGCCTTTATGATTACCGCAAGCTTACTATTAAGTTTGGCAAGGAATATGGCAGCTCACAAGTTCAACTGGGTCAGACTCATGTAATGGCTTTTGTGACTGCTCAGCTAGTACAACCTTACAAAGACAGACCTAGTGAAGGCTCCTTCTCTATCTTCACCGAGTTTTCTCCAATGGCTGATCCATCGTTTGAGCCAGGGCATCCTGGTGAATCTGCTGTTGAGCTTGGCCGTATTATAGACCGTGCTCTACGAGAAAGCCGTGCAGTAGATACAGAGTCGCTTTGTGTTCTAGCCGGAAAGCTGGTTTGGTCTGTTCGCATTGATCTTCACATTTTGGACAATGGAGGGAACTTGGTTGATGCTGCTAATGTTGCTGCCTTAGCCGCACTCATGACTTTCAGGAGACCTGATTGCACTGTAGGAGGGGACAACAGTCAAGACGTGATCATACATCCACCCGAAGAAAGGGAACCACTTCCTTTGATAATACATCATCTCCCAATAGCCTTCACGTTTGGATTTTTTAATAAAGGCAGTATCTTGGTGATGGACCCAACTTACGTTGAAGAAGCTGTTATGTGTGGGAGAATGACTGTGACAGTCAATGCCAATGGCGATATATGCGCAATCCAAAAACCAGGAGAAGAAGGCGTGAACCAGAGTGTAATCCTTCATTGCCTGCGTCTTGCTTCTTCAAGAGCTTCTGCAACAACAAAGATAATTAGAGATGCAGTTGAAGCATACAACCGTGAGAGGAGCTCACAGAAGGTGAAGCGGCATCATACTTTGGCTAAGTCTGAAGTTTTGGGACCTATTGTAGTTGTGTAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0000175 GO:0000176 GO:0000177 GO:0000178 GO:0000184 GO:0000288 GO:0000291 GO:0000459 GO:0000460 GO:0000466 GO:0000467 GO:0000469 GO:0000956 GO:0003674 GO:0003676 GO:0003723 GO:0003824 GO:0004518 GO:0004527 GO:0004532 GO:0004540 GO:0005488 GO:0005575 GO:0005622 GO:0005623 GO:0005634 GO:0005737 GO:0006139 GO:0006364 GO:0006396 GO:0006399 GO:0006401 GO:0006402 GO:0006725 GO:0006807 GO:0008150 GO:0008152 GO:0008408 GO:0009056 GO:0009057 GO:0009892 GO:0009987 GO:0010467 GO:0010468 GO:0010605 GO:0010629 GO:0016070 GO:0016071 GO:0016072 GO:0016073 GO:0016075 GO:0016078 GO:0016180 GO:0016787 GO:0016788 GO:0016796 GO:0016896 GO:0017091 GO:0019222 GO:0019439 GO:0022613 GO:0031123 GO:0031125 GO:0031974 GO:0031981 GO:0032991 GO:0034427 GO:0034470 GO:0034472 GO:0034473 GO:0034475 GO:0034476 GO:0034641 GO:0034655 GO:0034660 GO:0034661 GO:0042254 GO:0043170 GO:0043226 GO:0043227 GO:0043229 GO:0043231 GO:0043233 GO:0043628 GO:0043632 GO:0043633 GO:0043634 GO:0043928 GO:0044085 GO:0044237 GO:0044238 GO:0044248 GO:0044260 GO:0044265 GO:0044270 GO:0044422 GO:0044424 GO:0044428 GO:0044444 GO:0044446 GO:0044464 GO:0046483 GO:0046700 GO:0048519 GO:0050789 GO:0060255 GO:0065007 GO:0070013 GO:0070478 GO:0070481 GO:0070651 GO:0071025 GO:0071027 GO:0071028 GO:0071029 GO:0071035 GO:0071038 GO:0071042 GO:0071046 GO:0071047 GO:0071704 GO:0071840 GO:0090304 GO:0090305 GO:0090501 GO:0090503 GO:0097159 GO:0140098 GO:1901360 GO:1901361 GO:1901363 GO:1901575 GO:1902494 GO:1905354
KEGG Pathways
Metabolic & Signaling
ko03018 map03018
Pfam Domains
Protein Families
RNase_PH RNase_PH_C

Protein Analysis

307

Amino Acids

33.87

Weight (kDa)

6.16

Isoelectric Point (pI)

42.81

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RNase_PH PF01138 37 - 168 9.1e-29 3' exoribonuclease family, domain 1
RNase_PH_C PF03725 197 - 264 7e-16 3' exoribonuclease family, domain 2
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)
Acc16I TGCGCA 1 cut(s) 721
AciI CCGC 3 cut(s) 112, 480, 871
AclWI GGATC 1 cut(s) 269
AcoI YGGCCR 1 cut(s) 322
AcsI RAATTY 1 cut(s) 50
AcuI CTGAAG 1 cut(s) 915
AfaI GTAC 1 cut(s) 207
AfiI CCNNNNNNNGG 2 cut(s) 233, 561
AgsI TTSAA 6 cut(s) 16, 59, 161, 662, 792, 833
AjiI CACGTC 1 cut(s) 538
AjnI CCWGG 3 cut(s) 289, 298, 733
AjuI GAANNNNNNNTTGG 2 cut(s) 385, 417
AluBI AGCT 9 cut(s) 79, 118, 150, 202, 319, 397, 668, 797, 855
AluI AGCT 9 cut(s) 79, 118, 150, 202, 319, 397, 668, 797, 855
Alw21I GWGCWC 3 cut(s) 81, 343, 857
Alw26I GTCTC 1 cut(s) 493
AlwI GGATC 1 cut(s) 269
AoxI GGCC 2 cut(s) 97, 322
ApeKI GCWGC 3 cut(s) 147, 458, 470
ApoI RAATTY 1 cut(s) 50
Asp700I GAANNNNTTC 1 cut(s) 570
AspLEI GCGC 1 cut(s) 722
AspS9I GGNCC 2 cut(s) 646, 905
AsuHPI GGTGA 4 cut(s) 244, 314, 652, 877
AvaII GGWCC 2 cut(s) 646, 905
BanII GRGCYC 2 cut(s) 81, 857
Bbv12I GWGCWC 3 cut(s) 81, 343, 857
BbvI GCAGC 3 cut(s) 159, 445, 457
BccI CCATC 3 cut(s) 83, 286, 637
BceAI ACGGC 2 cut(s) 309, 339
BciT130I CCWGG 3 cut(s) 291, 300, 735
BclI TGATCA 1 cut(s) 540
BcoDI GTCTC 1 cut(s) 493
BfaI CTAG 3 cut(s) 203, 228, 386
BfmI CTRYAG 1 cut(s) 513
BisI GCNGC 5 cut(s) 148, 459, 471, 480, 872
BlpI GCTNAGC 1 cut(s) 198
BlsI GCNGC 5 cut(s) 149, 460, 472, 481, 873
Bme1390I CCNGG 3 cut(s) 291, 300, 735
Bme18I GGWCC 2 cut(s) 646, 905
BmgBI CACGTC 1 cut(s) 538
BmgT120I GGNCC 2 cut(s) 646, 905
BmiI GGNNCC 4 cut(s) 238, 567, 648, 906
BmrFI CCNGG 3 cut(s) 291, 300, 735
BmrI ACTGGG 1 cut(s) 173
BmsI GCATC 4 cut(s) 304, 445, 814, 883
BmuI ACTGGG 1 cut(s) 173
BoxI GACNNNNGTC 1 cut(s) 528
BplI GAGNNNNNCTC 2 cut(s) 839, 871
Bpu10I CCTNAGC 1 cut(s) 475
Bpu1102I GCTNAGC 1 cut(s) 198
BsaI GGTCTC 1 cut(s) 493
BsaJI CCNNGG 1 cut(s) 290
BsaXI ACNNNNNCTCC 3 cut(s) 26, 576, 606
Bsc4I CCNNNNNNNGG 2 cut(s) 233, 561
Bse1I ACTGG 1 cut(s) 168
Bse3DI GCAATG 1 cut(s) 769
BseBI CCWGG 3 cut(s) 291, 300, 735
BseDI CCNNGG 1 cut(s) 290
BseGI GGATG 2 cut(s) 295, 547
BseLI CCNNNNNNNGG 2 cut(s) 233, 561
BseMI GCAATG 1 cut(s) 769
BseMII CTCAG 3 cut(s) 66, 94, 212
BseNI ACTGG 1 cut(s) 168
BseRI GAGGAG 1 cut(s) 865
BseXI GCAGC 3 cut(s) 159, 445, 457
BsgI GTGCAG 1 cut(s) 378
BshFI GGCC 2 cut(s) 99, 324
BsiHKAI GWGCWC 3 cut(s) 81, 343, 857
BsiSI CCGG 1 cut(s) 390
BslFI GGGAC 2 cut(s) 536, 918
BslI CCNNNNNNNGG 2 cut(s) 233, 561
BsmAI GTCTC 1 cut(s) 493
BsmFI GGGAC 2 cut(s) 536, 918
BsnI GGCC 2 cut(s) 99, 324
Bso31I GGTCTC 1 cut(s) 493
Bsp1286I GDGCHC 3 cut(s) 81, 343, 857
Bsp143I GATC 3 cut(s) 274, 418, 540
Bsp1720I GCTNAGC 1 cut(s) 198
BspACI CCGC 3 cut(s) 112, 480, 871
BspANI GGCC 2 cut(s) 99, 324
BspCNI CTCAG 3 cut(s) 67, 93, 211
BspHI TCATGA 1 cut(s) 486
BspLI GGNNCC 4 cut(s) 238, 567, 648, 906
BspPI GGATC 1 cut(s) 269
BspTNI GGTCTC 1 cut(s) 493
BsrDI GCAATG 1 cut(s) 769
BsrI ACTGG 1 cut(s) 168
BssECI CCNNGG 1 cut(s) 290
BssMI GATC 3 cut(s) 274, 418, 540
Bst2UI CCWGG 3 cut(s) 291, 300, 735
Bst4CI ACNGT 7 cut(s) 37, 338, 514, 530, 691, 697, 845
BstC8I GCNNGC 2 cut(s) 116, 776
BstDEI CTNAG 5 cut(s) 75, 80, 198, 475, 888
BstENI CCTNNNNNAGG 1 cut(s) 231
BstF5I GGATG 2 cut(s) 295, 547
BstHHI GCGC 1 cut(s) 722
BstKTI GATC 3 cut(s) 277, 421, 543
BstMAI GTCTC 1 cut(s) 493
BstMBI GATC 3 cut(s) 274, 418, 540
BstMWI GCNNNNNNNGC 6 cut(s) 76, 467, 476, 479, 717, 833
BstNI CCWGG 3 cut(s) 291, 300, 735
BstPAI GACNNNNGTC 1 cut(s) 528
BstSCI CCNGG 3 cut(s) 289, 298, 733
BstSFI CTRYAG 1 cut(s) 513
BstV1I GCAGC 3 cut(s) 159, 445, 457
BsuRI GGCC 2 cut(s) 99, 324
BtrI CACGTC 1 cut(s) 538
BtsCI GGATG 2 cut(s) 295, 547
BtsIMutI CAGTG 1 cut(s) 510
Cac8I GCNNGC 2 cut(s) 116, 776
CciI TCATGA 1 cut(s) 486
CfoI GCGC 1 cut(s) 722
Cfr13I GGNCC 2 cut(s) 646, 905
CseI GACGC 1 cut(s) 767
Csp6I GTAC 1 cut(s) 206
CspCI CAANNNNNGTGG 2 cut(s) 558, 593
CviAII CATG 2 cut(s) 176, 487
CviQI GTAC 1 cut(s) 206
DdeI CTNAG 5 cut(s) 75, 80, 198, 475, 888
DpnI GATC 3 cut(s) 276, 420, 542
DpnII GATC 3 cut(s) 274, 418, 540
EaeI YGGCCR 1 cut(s) 322
Ecl136II GAGCTC 2 cut(s) 79, 855
Eco24I GRGCYC 2 cut(s) 81, 857
Eco31I GGTCTC 1 cut(s) 493
Eco47I GGWCC 2 cut(s) 646, 905
Eco53kI GAGCTC 2 cut(s) 79, 855
Eco57I CTGAAG 1 cut(s) 915
EcoICRI GAGCTC 2 cut(s) 79, 855
EcoNI CCTNNNNNAGG 1 cut(s) 231
EcoO109I RGGNCCY 1 cut(s) 905
EcoRII CCWGG 3 cut(s) 289, 298, 733
EcoT38I GRGCYC 2 cut(s) 81, 857
FaeI CATG 2 cut(s) 179, 490
FaqI GGGAC 2 cut(s) 536, 918
FatI CATG 2 cut(s) 175, 486
FbaI TGATCA 1 cut(s) 540
Fnu4HI GCNGC 5 cut(s) 148, 459, 471, 480, 872
FokI GGATG 2 cut(s) 282, 534
FriOI GRGCYC 2 cut(s) 81, 857
Fsp4HI GCNGC 5 cut(s) 148, 459, 471, 480, 872
FspBI CTAG 3 cut(s) 203, 228, 386
FspI TGCGCA 1 cut(s) 721
GlaI GCGC 1 cut(s) 721
GluI GCNGC 5 cut(s) 148, 459, 471, 480, 872
HaeIII GGCC 2 cut(s) 99, 324
HapII CCGG 1 cut(s) 390
HgaI GACGC 1 cut(s) 767
HhaI GCGC 1 cut(s) 722
Hin1II CATG 2 cut(s) 179, 490
Hin6I GCGC 1 cut(s) 720
HinP1I GCGC 1 cut(s) 720
HincII GTYRAC 1 cut(s) 33
HindII GTYRAC 1 cut(s) 33
HindIII AAGCTT 1 cut(s) 116
HinfI GANTC 5 cut(s) 59, 84, 172, 305, 371
HpaII CCGG 1 cut(s) 390
HphI GGTGA 4 cut(s) 244, 314, 652, 877
Hpy166II GTNNAC 2 cut(s) 33, 751
Hpy188I TCNGA 4 cut(s) 76, 83, 171, 895
Hpy188III TCNNGA 4 cut(s) 487, 496, 533, 792
Hpy8I GTNNAC 2 cut(s) 33, 751
HpyAV CCTTC 6 cut(s) 227, 250, 613, 737, 776, 856
HpyCH4III ACNGT 7 cut(s) 37, 338, 514, 530, 691, 697, 845
HpyCH4IV ACGT 3 cut(s) 537, 608, 657
HpyCH4V TGCA 5 cut(s) 70, 359, 510, 803, 827
HpyF10VI GCNNNNNNNGC 6 cut(s) 76, 467, 476, 479, 717, 833
HpyF3I CTNAG 5 cut(s) 75, 80, 198, 475, 888
HpySE526I ACGT 3 cut(s) 537, 608, 657
Hsp92II CATG 2 cut(s) 179, 490
HspAI GCGC 1 cut(s) 720
Ksp22I TGATCA 1 cut(s) 540
Kzo9I GATC 3 cut(s) 274, 418, 540
LmnI GCTCC 2 cut(s) 242, 852
Lsp1109I GCAGC 3 cut(s) 159, 445, 457
LweI GCATC 4 cut(s) 304, 445, 814, 883
MaeI CTAG 3 cut(s) 203, 228, 386
MaeII ACGT 3 cut(s) 537, 608, 657
MaeIII GTNAC 2 cut(s) 190, 691
MalI GATC 3 cut(s) 276, 420, 542
MboI GATC 3 cut(s) 274, 418, 540
MboII GAAGA 6 cut(s) 241, 413, 569, 674, 752, 780
MhlI GDGCHC 3 cut(s) 81, 343, 857
MluCI AATT 2 cut(s) 50, 816
MlyI GAGTC 3 cut(s) 93, 166, 380
MnlI CCTC 5 cut(s) 3, 21, 434, 512, 843
MroXI GAANNNNTTC 1 cut(s) 570
MseI TTAA 2 cut(s) 126, 621
MslI CAYNNNNRTG 1 cut(s) 300
MspI CCGG 1 cut(s) 390
MspR9I CCNGG 3 cut(s) 291, 300, 735
MvaI CCWGG 3 cut(s) 291, 300, 735
MwoI GCNNNNNNNGC 6 cut(s) 76, 467, 476, 479, 717, 833
NdeII GATC 3 cut(s) 274, 418, 540
NlaIII CATG 2 cut(s) 179, 490
NlaIV GGNNCC 4 cut(s) 238, 567, 648, 906
NmuCI GTSAC 2 cut(s) 190, 691
NsbI TGCGCA 1 cut(s) 721
PagI TCATGA 1 cut(s) 486
PcsI WCGNNNNNNNCGW 1 cut(s) 352
PdmI GAANNNNTTC 1 cut(s) 570
PfeI GAWTC 2 cut(s) 59, 305
PkrI GCNGC 5 cut(s) 149, 460, 472, 481, 873
PleI GAGTC 3 cut(s) 92, 166, 379
PpsI GAGTC 3 cut(s) 92, 166, 379
PpuMI RGGWCCY 1 cut(s) 905
PshAI GACNNNNGTC 1 cut(s) 528
Psp124BI GAGCTC 2 cut(s) 81, 857
Psp5II RGGWCCY 1 cut(s) 905
Psp6I CCWGG 3 cut(s) 289, 298, 733
PspGI CCWGG 3 cut(s) 289, 298, 733
PspN4I GGNNCC 4 cut(s) 238, 567, 648, 906
PspPI GGNCC 2 cut(s) 646, 905
PspPPI RGGWCCY 1 cut(s) 905
RsaI GTAC 1 cut(s) 207
RsaNI GTAC 1 cut(s) 206
RseI CAYNNNNRTG 1 cut(s) 300
SacI GAGCTC 2 cut(s) 81, 857
SaqAI TTAA 2 cut(s) 126, 621
SatI GCNGC 5 cut(s) 148, 459, 471, 480, 872
Sau3AI GATC 3 cut(s) 274, 418, 540
Sau96I GGNCC 2 cut(s) 646, 905
SchI GAGTC 3 cut(s) 93, 166, 380
ScrFI CCNGG 3 cut(s) 291, 300, 735
SduI GDGCHC 3 cut(s) 81, 343, 857
SfaNI GCATC 4 cut(s) 304, 445, 814, 883
SfcI CTRYAG 1 cut(s) 513
SinI GGWCC 2 cut(s) 646, 905
SmiMI CAYNNNNRTG 1 cut(s) 300
Sse9I AATT 2 cut(s) 50, 816
SsiI CCGC 3 cut(s) 112, 480, 871
SspMI CTAG 3 cut(s) 203, 228, 386
SstI GAGCTC 2 cut(s) 81, 857
StyD4I CCNGG 3 cut(s) 289, 298, 733
TaaI ACNGT 7 cut(s) 37, 338, 514, 530, 691, 697, 845
TaiI ACGT 3 cut(s) 540, 611, 660
TaqI TCGA 1 cut(s) 87
TasI AATT 2 cut(s) 50, 816
TatI WGTACW 1 cut(s) 205
TauI GCSGC 2 cut(s) 482, 874
TfiI GAWTC 2 cut(s) 59, 305
Tru1I TTAA 2 cut(s) 126, 621
Tru9I TTAA 2 cut(s) 126, 621
TscAI CASTG 1 cut(s) 517
TseFI GTSAC 2 cut(s) 190, 691
TseI GCWGC 3 cut(s) 147, 458, 470
Tsp45I GTSAC 2 cut(s) 190, 691
TspDTI ATGAA 1 cut(s) 758
TspRI CASTG 1 cut(s) 517
VpaK11BI GGWCC 2 cut(s) 646, 905
XagI CCTNNNNNAGG 1 cut(s) 231
XapI RAATTY 1 cut(s) 50
XmnI GAANNNNTTC 1 cut(s) 570
XspI CTAG 3 cut(s) 203, 228, 386
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.