Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Bma03g00602 ATGAGCAGCACGGGCAGAGTCAGTGGCAACGTCAAATGGTTTAACGACGTCAAGGGCTATGGCTTCATAACCCCTCGCGATGGCGGCGAGGATGTCTTTGTTCACCAGTCTTCGATCCGATCTGAAGGCTTTCGCAGTCTCGGTGAAGGCGAGGAGGTCGAATTCATGCTCGAAGCCGACACTGATGGTCGCTCCAAGGCCGTTGATGTCACTGGACCTGGTGAGGCACCAGTTCAAGGCACCCGTGGCGGCGGTGGCGGAGGCGGCGGCGGCGGTGGCGGAAGAGGTCGGCGTGAAGGTGGCGGAGGCGGATATGGATTTAGTGGTGGACGCGGAGGAGGAGGCGGTGGTGGACGAGGAGGATACGGCGGTGGAGGGGGTGGGTACGGCGGCGGCGGTGGTGGTTATGGTGGTGGAGGCGGCAGGGGTAATGGTTGCTTTAAGTGCGGTGAATCGGGGCATATGGCTAGGGACTGCTACCAGGGCGGTGGTGGTGGCGCTGGCGGTGGCGGAGGAAGGTATGGTGGTGGCGGTGGTGGTGGTGGTGGGAGCTGCTACAACTGTGGGGAGTCTGGGCATTTTGCCAGAGACTGTACGACTGGCGGGGGCCGTTGA 615 62.6 MSSTGRVSGNVKWFNDVKGYGFITPRDGGEDVFVHQSSIRSEGFRSLGEGEEVEFMLEADTDGRSKAVDVTGPGEAPVQGTRGGGGGGGGGGGGRGRREGGGGGYGFSGGRGGGGGGGRGGYGGGGGGYGGGGGGYGGGGGRGNGCFKCGESGHMARDCYQGGGGGAGGGGGRYGGGGGGGGGSCYNCGESGHFARDCTTGGGR 204
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
3 4953951 4954565 + Bma016893.1 Bma03g00602 79275

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Bma03g00602 204 Pfam Zinc knuckle 184 199 IPR001878 GO:0003676|GO:0008270
Bma03g00602 204 Pfam Zinc knuckle 145 159 IPR001878 GO:0003676|GO:0008270
Bma03g00602 204 ProSitePatterns Cold-shock (CSD) domain signature. 20 39 IPR019844 -
Bma03g00602 204 SMART csp_8 8 73 IPR011129 GO:0003676
Bma03g00602 204 Gene3D - 2 83 IPR012340 -
Bma03g00602 204 PANTHER COLD SHOCK PROTEIN 1 3 200 - -
Bma03g00602 204 MobiDBLite consensus disorder prediction 71 107 - -
Bma03g00602 204 Pfam 'Cold-shock' DNA-binding domain 8 72 IPR002059 GO:0003676
Bma03g00602 204 PRINTS Cold shock protein signature 30 39 IPR002059 GO:0003676
Bma03g00602 204 PRINTS Cold shock protein signature 45 63 IPR002059 GO:0003676
Bma03g00602 204 PRINTS Cold shock protein signature 9 24 IPR002059 GO:0003676
Bma03g00602 204 SUPERFAMILY Retrovirus zinc finger-like domains 139 201 IPR036875 GO:0003676|GO:0008270
Bma03g00602 204 ProSiteProfiles Zinc finger CCHC-type profile. 146 159 IPR001878 GO:0003676|GO:0008270
Bma03g00602 204 SUPERFAMILY Nucleic acid-binding proteins 6 72 IPR012340 -
Bma03g00602 204 Gene3D - 180 204 - -
Bma03g00602 204 Gene3D - 141 168 - -
Bma03g00602 204 CDD CSP_CDS 7 72 IPR002059 GO:0003676
Bma03g00602 204 PANTHER COLD SHOCK DOMAIN PROTEIN 2 3 200 - -
Bma03g00602 204 ProSiteProfiles Zinc finger CCHC-type profile. 185 198 IPR001878 GO:0003676|GO:0008270
Bma03g00602 204 SMART c2hcfinal6 184 200 IPR001878 GO:0003676|GO:0008270
Bma03g00602 204 SMART c2hcfinal6 145 161 IPR001878 GO:0003676|GO:0008270
Bma03g00602 204 ProSiteProfiles Cold-shock (CSD) domain profile. 6 72 IPR002059 GO:0003676
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Bma03g00602 - - - qsu:111995957 163.696
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Bma03g00602 Bma-Chr3:4953951 Bma06g00094 Bma-Chr6:1428808 5.59E-31 dispersed
Bma03g00602 Bma-Chr3:4953951 Bma01g00831 Bma-Chr1:7819151 1.22E-38 transposed
       

Deco-Alignment

Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi3g135 . . . . . Bpe12g00116 . . Cmo19g00739 . . . . . Sed01g3135 . Cpe15g00585 Bhi05g01731 Tan02g0700 Cmetu01g0199 . Hepe02g0435 . . Cla02g00437 Cam02g0446 Cec02g0444 Cco02g0462 Clacu02g0448 Cmu02g0442 Cre02g0776 Cone12ag1224 Cone8ag1275 . . . . . Cme01g01275 Blo04g00561 Blo13g00516 Bda15g01039 Bda14g00610 Bpe15g00819 . Bma03g00602 . . . . . Cma19g00731 . Car19g00560 . . . . . . . . . . . . . . . . Lsi11g01191 . Chy01g00689 .
       

Syn-Orthogroups

Select Orthogroup Bda Bhi Blo Bma Bpe Cam Car Cco Cec Chy Cla Clacu Cma Cme Cmetu Cmo Cmu Cone Cpe Cre Csa HCH Hepe Lac Lcy Lsi Mch Sed Tan Vvi Total
OG0001587 3 2 3 3 4 2 3 2 2 2 2 2 2 2 2 3 2 4 4 2 2 2 2 0 1 3 2 3 2 2 70
       

Regulatory proteins

Select Gene Hmm_acc Hmm_name Score E-value Regulatory Factors Family
57006 PF00313 CSD 6.10E-25 CL0021 Bma TF
       

Transcriptome

Select Gene Chr Type da1 da2 da3 da4 da5 da6 da7 da8 da9 da10
Bma03g00602 Bma_Chr03 FPKM 3.228758 5.143811 2.974444 2.632191 1.679206 1.452989 0.785838 1.630808 0.848555 1.012739