Gene search

Sequence information

Select Gene Cds Cds_length GC_content Pep Pep_length
Cma16g01239 ATGCACCCGGGAATGAATTTTCACGACAAAGAGAAATCAAACTTCAACAATTCTTCAATAGATGAACAACATGACCACAGGAAAATTAAGAGAAATTTCTTCCGAACTTTGAAGATGGCGGAAGAGAGATTGACTGGAGTGGTTCAGTGGTTTAACGATTCCAAGGGGTTTGGCTTTATCAAGCCAGATGTGGAAGGCCCGGATCTGTTTGTTCATCAATCCTCCATTAAATCCGATGGCTACCGGAGCCTTGTCGTCGGAGATCATGTTGAGTTTCAGATCGCCCCTGGTGATGATGGGAAATCGAAAGCTATTGAGGTCGTTGCTCTCGATGGATCTTCGGGAAATCGGAGGGATAACTTTGGGGGTGGTGGTGGAAGGGGTGGCCGCGGCGGTGGCGGTGGAGGTTATGGGTTTGGTGGATGGAGGGGTGGCGATAGGCGTAATGGGAGCAGTGGAGCCGGTGGGGGTGGGTGTTATCAATGTGGTGAGCAAGGGCATTTGGCTAGAGATTGTACTCGTGCTAGTAACCGCGGCGGTGGTGGTGGTGGTGGTGGTGGCTGTTTTACTTGCGGTGAAGTCGGCCACTTAGCGAGGGATTGTCCACGAGGAAACAGCGGCGGCGGTGCCGGTGGTGGGGCTTGCTATAATTGTGGTGGTTTTGGGCATTTGGCTAGGGATTGCAATAGGGGTGGGGCTGGAGGTGGAAGTGGAGGTGGGGGTGGTAGTTGTTTTAATTGTGGAGAATATGGGCATTTAGCCAGAGATTGCCAGAATGAAAGCCGTGGCAGCGGCGGCGGCGGCGGAAGATTTGGTGGCGGTGGTGCAAACACTTGCTTCAATTGTGGGAAATCTGGGCATTTTGCTAGGGAGTGTCCTGATGTAAGGAGTGAGACAGAGTAA 903 52.05 MHPGMNFHDKEKSNFNNSSIDEQHDHRKIKRNFFRTLKMAEERLTGVVQWFNDSKGFGFIKPDVEGPDLFVHQSSIKSDGYRSLVVGDHVEFQIAPGDDGKSKAIEVVALDGSSGNRRDNFGGGGGRGGRGGGGGGYGFGGWRGGDRRNGSSGAGGGGCYQCGEQGHLARDCTRASNRGGGGGGGGGCFTCGEVGHLARDCPRGNSGGGAGGGACYNCGGFGHLARDCNRGGAGGGSGGGGGSCFNCGEYGHLARDCQNESRGSGGGGGRFGGGGANTCFNCGKSGHFARECPDVRSETE 300
       

Gff information

Chromosome Start End Strand Old_gene Gene Num
16 9367876 9370147 + CmaCh16G012390.1 Cma16g01239 311837

Annotation

Select Seq ID Length Analysis Description Start End IPR GO
Cma16g01239 300 CDD CSP_CDS 45 107 IPR002059 GO:0003676
Cma16g01239 300 ProSitePatterns Cold-shock (CSD) domain signature. 57 76 IPR019844 -
Cma16g01239 300 SUPERFAMILY Retrovirus zinc finger-like domains 204 260 IPR036875 GO:0003676|GO:0008270
Cma16g01239 300 SMART c2hcfinal6 278 294 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 SMART c2hcfinal6 243 259 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 SMART c2hcfinal6 158 174 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 SMART c2hcfinal6 214 230 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 SMART c2hcfinal6 187 203 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 ProSiteProfiles Zinc finger CCHC-type profile. 188 203 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 SUPERFAMILY Nucleic acid-binding proteins 38 112 IPR012340 -
Cma16g01239 300 Gene3D - 138 182 - -
Cma16g01239 300 Pfam Zinc knuckle 243 258 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 Pfam Zinc knuckle 214 228 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 Pfam Zinc knuckle 187 202 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 Pfam Zinc knuckle 277 293 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 Pfam Zinc knuckle 158 173 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 MobiDBLite consensus disorder prediction 1 23 - -
Cma16g01239 300 PANTHER COLD SHOCK DOMAIN PROTEIN 2 175 295 - -
Cma16g01239 300 PANTHER COLD SHOCK DOMAIN PROTEIN 2 149 181 - -
Cma16g01239 300 PANTHER COLD SHOCK DOMAIN PROTEIN 2 39 149 - -
Cma16g01239 300 PANTHER COLD SHOCK PROTEIN 2 175 295 - -
Cma16g01239 300 PANTHER COLD SHOCK PROTEIN 2 149 181 - -
Cma16g01239 300 ProSiteProfiles Zinc finger CCHC-type profile. 215 228 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 Gene3D - 183 209 - -
Cma16g01239 300 Gene3D - 274 299 - -
Cma16g01239 300 Gene3D - 210 236 - -
Cma16g01239 300 Gene3D - 237 266 - -
Cma16g01239 300 Pfam 'Cold-shock' DNA-binding domain 45 108 IPR002059 GO:0003676
Cma16g01239 300 ProSiteProfiles Zinc finger CCHC-type profile. 244 259 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 SMART csp_8 45 110 IPR011129 GO:0003676
Cma16g01239 300 ProSiteProfiles Zinc finger CCHC-type profile. 279 294 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 PANTHER COLD SHOCK PROTEIN 2 39 149 - -
Cma16g01239 300 ProSiteProfiles Zinc finger CCHC-type profile. 159 174 IPR001878 GO:0003676|GO:0008270
Cma16g01239 300 SUPERFAMILY Retrovirus zinc finger-like domains 150 205 IPR036875 GO:0003676|GO:0008270
Cma16g01239 300 SUPERFAMILY Retrovirus zinc finger-like domains 261 297 IPR036875 GO:0003676|GO:0008270
Cma16g01239 300 ProSiteProfiles Cold-shock (CSD) domain profile. 43 109 IPR002059 GO:0003676
Cma16g01239 300 Gene3D - 26 108 IPR012340 -
Cma16g01239 300 PRINTS Cold shock protein signature 67 76 IPR002059 GO:0003676
Cma16g01239 300 PRINTS Cold shock protein signature 46 61 IPR002059 GO:0003676
Cma16g01239 300 PRINTS Cold shock protein signature 82 100 IPR002059 GO:0003676
       

Pathway

Select Query KO Definition Second KO KEGG Genes ID GHOSTX Score
Cma16g01239 K09250 CNBP; cellular nucleic acid-binding protein - csv:101216334 335.495
       

Dupl-types

Select Gene1 Location1 Gene2 Location2 E-value Duplicated-type
Cma11g00324 Cma-Chr11:1617572 Cma16g01239 Cma-Chr16:9367876 4.53E-09 dispersed
Cma16g00124 Cma-Chr16:569503 Cma16g01239 Cma-Chr16:9367876 1.48E-07 dispersed
Cma16g01239 Cma-Chr16:9367876 Cma18g01248 Cma-Chr18:9739710 1.26E-08 dispersed
Cma11g01386 Cma-Chr11:9134828 Cma16g01239 Cma-Chr16:9367876 6.18E-08 transposed
Cma19g00731 Cma-Chr19:7348385 Cma16g01239 Cma-Chr16:9367876 3.55E-29 transposed
Cma16g01239 Cma-Chr16:9367876 Cma06g00577 Cma-Chr6:2781837 1.89E-100 wgd
       

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
Vvi4g1119 Blo04g00883 . . . Bpe15g00473 Bpe13g00413 . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag0853 Cone12ag0714 Cone6ag1686 . . . . . . . Bda11g01834 . . . Bma03g00959 Bma06g00094 . . . Cma16g01239 . . . . . . . . . . . . . . . . . . . Lsi07g01102 . . .
       

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
OG0006925 2 0 0 2 2 1 2 1 1 1 1 1 2 1 1 2 1 3 2 1 1 1 1 1 1 1 1 1 1 0 36
       

Regulatory proteins

Select Gene Hmm_acc Hmm_name Score E-value Regulatory Factors Family
36610 PF00313 CSD 1.40E-22 CL0021 Cma TF
       

Transcriptome

Select Gene Chr Type da1 da2 da3 da4 da5 da6 da7 da8 da9 da10
Cma16g01239 Cma_Chr16 FPKM 16.013288 18.489849 19.000292 19.272882 15.14307 17.922169 16.60368 28.342421 28.954517 29.292437