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.t30 TTS g11432.t30 16197707 16197707
chr_1 g11432 g11432.t30 isoform g11432.t30 16197844 16200849
chr_1 g11432 g11432.t30 exon g11432.t30.exon1 16197844 16197905
chr_1 g11432 g11432.t30 cds g11432.t30.CDS1 16197889 16197905
chr_1 g11432 g11432.t30 exon g11432.t30.exon2 16198135 16198353
chr_1 g11432 g11432.t30 cds g11432.t30.CDS2 16198135 16198353
chr_1 g11432 g11432.t30 exon g11432.t30.exon3 16199164 16199299
chr_1 g11432 g11432.t30 cds g11432.t30.CDS3 16199164 16199299
chr_1 g11432 g11432.t30 exon g11432.t30.exon4 16199438 16199476
chr_1 g11432 g11432.t30 cds g11432.t30.CDS4 16199438 16199476
chr_1 g11432 g11432.t30 exon g11432.t30.exon5 16200847 16200849
chr_1 g11432 g11432.t30 cds g11432.t30.CDS5 16200847 16200849
chr_1 g11432 g11432.t30 TSS g11432.t30 16201105 16201105

Sequences

>g11432.t30 Gene=g11432 Length=459
ATGGCTGATCAATTAACAGAGGAGCAAATCGCTGAGTTCAAAGAAGCATTCTCATTGTTC
GACAAAGACGGTGATGGCACAATTACCACAAAAGAATTGGGCACTGTGATGAGATCACTT
GGTCAAAACCCGACAGAAGCTGAACTTCAGGATATGATTAACGAAGTTGATGCTGACGGC
AATGGTACCATAGATTTCCCTGAATTCTTAACTATGATGGCTCGCAAAATGAAAGATACT
GATAGTGAAGAAGAAATTCGGGAAGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTC
ATCTCTGCAGCTGAATTGCGCCACGTGATGACAAATTTGGGAGAAAAATTAACAGATGAA
GAAGTCGATGAAATGATTCGTGAGGCAGATATTGATGTGTACGTCAGCCTTTGAATACAC
AACACTATTACAATTATAAAAAAACTATAATAAAAAACT

>g11432.t30 Gene=g11432 Length=137
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDE
EVDEMIREADIDVYVSL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11432.t30 CDD cd00051 EFh 12 74 2.30726E-22
13 g11432.t30 CDD cd00051 EFh 85 132 2.05166E-15
11 g11432.t30 Gene3D G3DSA:1.10.238.10 - 1 38 7.2E-11
9 g11432.t30 Gene3D G3DSA:1.10.238.10 - 39 73 2.7E-20
10 g11432.t30 Gene3D G3DSA:1.10.238.10 - 74 126 8.5E-28
3 g11432.t30 PANTHER PTHR23050:SF401 CALMODULIN 3 132 9.2E-84
4 g11432.t30 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 3 132 9.2E-84
6 g11432.t30 PRINTS PR00450 Recoverin family signature 5 24 9.4E-5
5 g11432.t30 PRINTS PR00450 Recoverin family signature 52 73 9.4E-5
7 g11432.t30 PRINTS PR00450 Recoverin family signature 99 117 9.4E-5
2 g11432.t30 Pfam PF13499 EF-hand domain pair 12 73 1.0E-15
1 g11432.t30 Pfam PF13499 EF-hand domain pair 83 132 5.7E-11
16 g11432.t30 ProSitePatterns PS00018 EF-hand calcium-binding domain. 21 33 -
14 g11432.t30 ProSitePatterns PS00018 EF-hand calcium-binding domain. 57 69 -
15 g11432.t30 ProSitePatterns PS00018 EF-hand calcium-binding domain. 94 106 -
20 g11432.t30 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 8 43 17.303
21 g11432.t30 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 44 79 14.792
22 g11432.t30 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 81 116 17.972
19 g11432.t30 SMART SM00054 efh_1 12 40 8.5E-9
18 g11432.t30 SMART SM00054 efh_1 48 76 7.2E-9
17 g11432.t30 SMART SM00054 efh_1 85 113 5.8E-9
8 g11432.t30 SUPERFAMILY SSF47473 EF-hand 2 132 4.61E-50

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. There were no conditions that were differentially expressed