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.t39 TTS g11432.t39 16197707 16197707
chr_1 g11432 g11432.t39 isoform g11432.t39 16197920 16200849
chr_1 g11432 g11432.t39 exon g11432.t39.exon1 16197920 16197948
chr_1 g11432 g11432.t39 cds g11432.t39.CDS1 16197920 16197948
chr_1 g11432 g11432.t39 exon g11432.t39.exon2 16198111 16198353
chr_1 g11432 g11432.t39 cds g11432.t39.CDS2 16198111 16198353
chr_1 g11432 g11432.t39 exon g11432.t39.exon3 16199164 16199337
chr_1 g11432 g11432.t39 cds g11432.t39.CDS3 16199164 16199233
chr_1 g11432 g11432.t39 exon g11432.t39.exon4 16200847 16200849
chr_1 g11432 g11432.t39 TSS g11432.t39 16201105 16201105

Sequences

>g11432.t39 Gene=g11432 Length=449
ATGTTCGTGTGTGTGTGTGTGTCTCGTGTATATTTTTATAGGAAGCATTCTCATTGTTCG
ACAAAGACGGTGATGGCACAATTACCACAAAAGAATTGGGCACTGTGATGAGATCACTTG
GTCAAAACCCGACAGAAGCTGAACTTCAGGATATGATTAACGAAGTTGATGCTGACGGCA
ATGGTACCATAGATTTCCCTGAATTCTTAACTATGATGGCTCGCAAAATGAAAGATACTG
ATAGTGAAGAAGAAATTCGGGAAGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTCA
TCTCTGCAGCTGAATTGCGCCACGTGATGACAAATTTGGGAGAAAAATTAACAGATGAAG
AAGTCGATGAAATGATTCGTGAGGCAGATATTGATGGTGACGGACAAGTTAATTACGAAG
AATTTGTCACCATGATGACATCAAAGTGA

>g11432.t39 Gene=g11432 Length=113
MRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKD
GNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVTMMTSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g11432.t39 CDD cd00051 EFh 12 75 7.14125E-12
10 g11432.t39 CDD cd00051 EFh 49 111 7.33387E-24
6 g11432.t39 Gene3D G3DSA:1.10.238.10 - 1 37 3.4E-20
8 g11432.t39 Gene3D G3DSA:1.10.238.10 - 38 87 5.4E-28
7 g11432.t39 Gene3D G3DSA:1.10.238.10 - 88 113 2.1E-7
3 g11432.t39 PANTHER PTHR23050:SF401 CALMODULIN 1 113 7.9E-73
4 g11432.t39 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 1 113 7.9E-73
2 g11432.t39 Pfam PF00036 EF hand 12 39 6.2E-9
1 g11432.t39 Pfam PF13499 EF-hand domain pair 47 110 3.9E-19
13 g11432.t39 ProSitePatterns PS00018 EF-hand calcium-binding domain. 21 33 -
11 g11432.t39 ProSitePatterns PS00018 EF-hand calcium-binding domain. 58 70 -
12 g11432.t39 ProSitePatterns PS00018 EF-hand calcium-binding domain. 94 106 -
17 g11432.t39 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 8 43 14.792
19 g11432.t39 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 45 80 17.972
18 g11432.t39 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 81 113 15.155
16 g11432.t39 SMART SM00054 efh_1 12 40 7.2E-9
15 g11432.t39 SMART SM00054 efh_1 49 77 5.8E-9
14 g11432.t39 SMART SM00054 efh_1 85 113 1.3E-9
5 g11432.t39 SUPERFAMILY SSF47473 EF-hand 1 112 5.71E-44

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