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.t15 isoform g11432.t15 16197311 16199198
chr_1 g11432 g11432.t15 exon g11432.t15.exon1 16197311 16197948
chr_1 g11432 g11432.t15 TTS g11432.t15 16197312 16197312
chr_1 g11432 g11432.t15 cds g11432.t15.CDS1 16197920 16197948
chr_1 g11432 g11432.t15 exon g11432.t15.exon2 16198111 16198353
chr_1 g11432 g11432.t15 cds g11432.t15.CDS2 16198111 16198353
chr_1 g11432 g11432.t15 exon g11432.t15.exon3 16199164 16199198
chr_1 g11432 g11432.t15 cds g11432.t15.CDS3 16199164 16199188
chr_1 g11432 g11432.t15 TSS g11432.t15 NA NA

Sequences

>g11432.t15 Gene=g11432 Length=916
ACTTCAGGATATGATTAACGAAGTTGATGCTGACGGCAATGGTACCATAGATTTCCCTGA
ATTCTTAACTATGATGGCTCGCAAAATGAAAGATACTGATAGTGAAGAAGAAATTCGGGA
AGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTCATCTCTGCAGCTGAATTGCGCCA
CGTGATGACAAATTTGGGAGAAAAATTAACAGATGAAGAAGTCGATGAAATGATTCGTGA
GGCAGATATTGATGGTGACGGACAAGTTAATTACGAAGAATTTGTCACCATGATGACATC
AAAGTGAGCTCCTGTTTTAAGTGTACGTCAGCCTTTGAATACACAACACTATTACAATTA
TAAAAAAACTATAATAAAAAACTGTAATATGATCTTCTATCAATATTTTGTTTTGTAAAG
AAAAGAAGCTACGGAGAATGCTGCATATTTACCATCATGTAGCATTTTCTGCATTTTTCT
AAATAAGCTTCTAATACAACAAGTGAAAAAAGAGAAAAAATAACATTTTAAAAAGCGTAT
ATTCGCACCGTAATTTTTTTTATAATTTTTTTAAAAGTTTTTTCAGTTAATTCAAAAAGA
TGATGAAGAGAGGAAAAAAGAGATAAAACATTAAAAAACATTGTCCTAAAGAAATTTGTT
GAAAAATTTTCAGAGAATGAATAATAAGAAAAATTTGCAAAAATACTTATTTAAAATGAA
TAACAGAAAAAAAAACTATCGCTAAAAGTTTAAATATAAAAGTAATAGTAAAGTAAGAGA
AAAAAATTGAGAGAAAATTTTAAAATCCACTGTACTTTTTGAAAAATTGCAATTTAATCA
AGCTTATCACACACTTCTCACACAATTCTGTACTATTCAAAATTCAAAAAATAAATATAT
GATTTCATTTAAAATA

>g11432.t15 Gene=g11432 Length=98
MINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMT
NLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11432.t15 CDD cd00051 EFh 1 60 3.2907E-10
9 g11432.t15 CDD cd00051 EFh 34 96 3.10885E-23
8 g11432.t15 Gene3D G3DSA:1.10.238.10 - 1 22 5.5E-10
6 g11432.t15 Gene3D G3DSA:1.10.238.10 - 23 72 3.7E-28
7 g11432.t15 Gene3D G3DSA:1.10.238.10 - 73 98 1.6E-7
3 g11432.t15 PANTHER PTHR23050:SF401 CALMODULIN 1 98 2.2E-61
4 g11432.t15 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 1 98 2.2E-61
2 g11432.t15 Pfam PF00036 EF hand 1 24 2.9E-7
1 g11432.t15 Pfam PF13499 EF-hand domain pair 32 95 2.6E-19
11 g11432.t15 ProSitePatterns PS00018 EF-hand calcium-binding domain. 6 18 -
13 g11432.t15 ProSitePatterns PS00018 EF-hand calcium-binding domain. 43 55 -
12 g11432.t15 ProSitePatterns PS00018 EF-hand calcium-binding domain. 79 91 -
19 g11432.t15 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 1 28 12.868
18 g11432.t15 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 30 65 17.972
17 g11432.t15 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 66 98 15.155
16 g11432.t15 SMART SM00054 efh_1 1 25 0.0028
14 g11432.t15 SMART SM00054 efh_1 34 62 5.8E-9
15 g11432.t15 SMART SM00054 efh_1 70 98 1.3E-9
5 g11432.t15 SUPERFAMILY SSF47473 EF-hand 1 97 3.63E-39

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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