Gene loci information

Transcript annotation

  • This transcript has been annotated as Calmodulin.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g11432 g11432.t4 isoform g11432.t4 16196196 16200849
chr_1 g11432 g11432.t4 exon g11432.t4.exon1 16196196 16196205
chr_1 g11432 g11432.t4 exon g11432.t4.exon2 16197311 16197948
chr_1 g11432 g11432.t4 cds g11432.t4.CDS1 16197920 16197948
chr_1 g11432 g11432.t4 exon g11432.t4.exon3 16198111 16198353
chr_1 g11432 g11432.t4 cds g11432.t4.CDS2 16198111 16198353
chr_1 g11432 g11432.t4 exon g11432.t4.exon4 16199164 16199299
chr_1 g11432 g11432.t4 cds g11432.t4.CDS3 16199164 16199299
chr_1 g11432 g11432.t4 exon g11432.t4.exon5 16199438 16199476
chr_1 g11432 g11432.t4 cds g11432.t4.CDS4 16199438 16199476
chr_1 g11432 g11432.t4 exon g11432.t4.exon6 16200847 16200849
chr_1 g11432 g11432.t4 cds g11432.t4.CDS5 16200847 16200849
chr_1 g11432 g11432.t4 TSS g11432.t4 16201105 16201105
chr_1 g11432 g11432.t4 TTS g11432.t4 NA NA

Sequences

>g11432.t4 Gene=g11432 Length=1069
ATGGCTGATCAATTAACAGAGGAGCAAATCGCTGAGTTCAAAGAAGCATTCTCATTGTTC
GACAAAGACGGTGATGGCACAATTACCACAAAAGAATTGGGCACTGTGATGAGATCACTT
GGTCAAAACCCGACAGAAGCTGAACTTCAGGATATGATTAACGAAGTTGATGCTGACGGC
AATGGTACCATAGATTTCCCTGAATTCTTAACTATGATGGCTCGCAAAATGAAAGATACT
GATAGTGAAGAAGAAATTCGGGAAGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTC
ATCTCTGCAGCTGAATTGCGCCACGTGATGACAAATTTGGGAGAAAAATTAACAGATGAA
GAAGTCGATGAAATGATTCGTGAGGCAGATATTGATGGTGACGGACAAGTTAATTACGAA
GAATTTGTCACCATGATGACATCAAAGTGAGCTCCTGTTTTAAGTGTACGTCAGCCTTTG
AATACACAACACTATTACAATTATAAAAAAACTATAATAAAAAACTGTAATATGATCTTC
TATCAATATTTTGTTTTGTAAAGAAAAGAAGCTACGGAGAATGCTGCATATTTACCATCA
TGTAGCATTTTCTGCATTTTTCTAAATAAGCTTCTAATACAACAAGTGAAAAAAGAGAAA
AAATAACATTTTAAAAAGCGTATATTCGCACCGTAATTTTTTTTATAATTTTTTTAAAAG
TTTTTTCAGTTAATTCAAAAAGATGATGAAGAGAGGAAAAAAGAGATAAAACATTAAAAA
ACATTGTCCTAAAGAAATTTGTTGAAAAATTTTCAGAGAATGAATAATAAGAAAAATTTG
CAAAAATACTTATTTAAAATGAATAACAGAAAAAAAAACTATCGCTAAAAGTTTAAATAT
AAAAGTAATAGTAAAGTAAGAGAAAAAAATTGAGAGAAAATTTTAAAATCCACTGTACTT
TTTGAAAAATTGCAATTTAATCAAGCTTATCACACACTTCTCACACAATTCTGTACTATT
CAAAATTCAAAAAATAAATATATGATTTCATTTAAAATAAAAATATTGA

>g11432.t4 Gene=g11432 Length=149
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYEEFVTMMTSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11432.t4 CDD cd00051 EFh 12 74 5.45279E-22
10 g11432.t4 CDD cd00051 EFh 85 147 2.23407E-23
8 g11432.t4 Gene3D G3DSA:1.10.238.10 - 1 75 1.8E-34
6 g11432.t4 Gene3D G3DSA:1.10.238.10 - 76 123 1.0E-27
7 g11432.t4 Gene3D G3DSA:1.10.238.10 - 124 149 3.3E-7
3 g11432.t4 PANTHER PTHR23050:SF401 CALMODULIN 3 149 1.3E-95
4 g11432.t4 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 3 149 1.3E-95
2 g11432.t4 Pfam PF13499 EF-hand domain pair 12 73 1.2E-15
1 g11432.t4 Pfam PF13499 EF-hand domain pair 83 146 7.9E-19
14 g11432.t4 ProSitePatterns PS00018 EF-hand calcium-binding domain. 21 33 -
11 g11432.t4 ProSitePatterns PS00018 EF-hand calcium-binding domain. 57 69 -
13 g11432.t4 ProSitePatterns PS00018 EF-hand calcium-binding domain. 94 106 -
12 g11432.t4 ProSitePatterns PS00018 EF-hand calcium-binding domain. 130 142 -
19 g11432.t4 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 8 43 17.303
21 g11432.t4 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 44 79 14.792
22 g11432.t4 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 81 116 17.972
20 g11432.t4 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 117 149 15.155
18 g11432.t4 SMART SM00054 efh_1 12 40 8.5E-9
17 g11432.t4 SMART SM00054 efh_1 48 76 7.2E-9
16 g11432.t4 SMART SM00054 efh_1 85 113 5.8E-9
15 g11432.t4 SMART SM00054 efh_1 121 149 1.3E-9
5 g11432.t4 SUPERFAMILY SSF47473 EF-hand 2 148 1.01E-58

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0005509 calcium ion binding MF
GO:0019722 calcium-mediated signaling BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values