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.t49 TTS g11432.t49 16197707 16197707
chr_1 g11432 g11432.t49 isoform g11432.t49 16197920 16200849
chr_1 g11432 g11432.t49 exon g11432.t49.exon1 16197920 16197935
chr_1 g11432 g11432.t49 cds g11432.t49.CDS1 16197920 16197935
chr_1 g11432 g11432.t49 exon g11432.t49.exon2 16198107 16198353
chr_1 g11432 g11432.t49 cds g11432.t49.CDS2 16198107 16198353
chr_1 g11432 g11432.t49 exon g11432.t49.exon3 16199164 16199299
chr_1 g11432 g11432.t49 cds g11432.t49.CDS3 16199164 16199299
chr_1 g11432 g11432.t49 exon g11432.t49.exon4 16200847 16200849
chr_1 g11432 g11432.t49 cds g11432.t49.CDS4 16200847 16200849
chr_1 g11432 g11432.t49 TSS g11432.t49 16201105 16201105

Sequences

>g11432.t49 Gene=g11432 Length=402
ATGGAAGCATTCTCATTGTTCGACAAAGACGGTGATGGCACAATTACCACAAAAGAATTG
GGCACTGTGATGAGATCACTTGGTCAAAACCCGACAGAAGCTGAACTTCAGGATATGATT
AACGAAGTTGATGCTGACGGCAATGGTACCATAGATTTCCCTGAATTCTTAACTATGATG
GCTCGCAAAATGAAAGATACTGATAGTGAAGAAGAAATTCGGGAAGCATTCCGTGTATTT
GATAAAGATGGCAATGGTTTCATCTCTGCAGCTGAATTGCGCCACGTGATGACAAATTTG
GGAGAAAAATTAACAGATGAAGAAGTCGATGAAATGATTCGTGAGGCAGATATTGATGGT
GACGGACAAGTTAATTACGAAGGTATGATGACATCAAAGTGA

>g11432.t49 Gene=g11432 Length=133
MEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMM
ARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDG
DGQVNYEGMMTSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11432.t49 CDD cd00051 EFh 1 61 8.56807E-21
9 g11432.t49 CDD cd00051 EFh 72 127 8.14468E-20
7 g11432.t49 Gene3D G3DSA:1.10.238.10 - 2 97 1.8E-68
6 g11432.t49 Gene3D G3DSA:1.10.238.10 - 98 131 1.1E-11
3 g11432.t49 PANTHER PTHR23050:SF401 CALMODULIN 2 131 1.0E-82
4 g11432.t49 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 2 131 1.0E-82
2 g11432.t49 Pfam PF13499 EF-hand domain pair 1 60 3.1E-15
1 g11432.t49 Pfam PF13499 EF-hand domain pair 70 129 9.8E-16
10 g11432.t49 ProSitePatterns PS00018 EF-hand calcium-binding domain. 8 20 -
12 g11432.t49 ProSitePatterns PS00018 EF-hand calcium-binding domain. 44 56 -
11 g11432.t49 ProSitePatterns PS00018 EF-hand calcium-binding domain. 81 93 -
17 g11432.t49 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 1 30 15.322
18 g11432.t49 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 31 66 14.792
20 g11432.t49 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 68 103 17.972
19 g11432.t49 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 104 133 8.627
13 g11432.t49 SMART SM00054 efh_1 1 27 2.8E-4
16 g11432.t49 SMART SM00054 efh_1 35 63 7.2E-9
15 g11432.t49 SMART SM00054 efh_1 72 100 5.8E-9
14 g11432.t49 SMART SM00054 efh_1 108 133 0.13
5 g11432.t49 SUPERFAMILY SSF47473 EF-hand 2 130 1.66E-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