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.t36 TTS g11432.t36 16197707 16197707
chr_1 g11432 g11432.t36 isoform g11432.t36 16197920 16200849
chr_1 g11432 g11432.t36 exon g11432.t36.exon1 16197920 16197948
chr_1 g11432 g11432.t36 cds g11432.t36.CDS1 16197920 16197948
chr_1 g11432 g11432.t36 exon g11432.t36.exon2 16198111 16198353
chr_1 g11432 g11432.t36 cds g11432.t36.CDS2 16198111 16198353
chr_1 g11432 g11432.t36 exon g11432.t36.exon3 16199164 16199299
chr_1 g11432 g11432.t36 cds g11432.t36.CDS3 16199164 16199299
chr_1 g11432 g11432.t36 exon g11432.t36.exon4 16200826 16200849
chr_1 g11432 g11432.t36 cds g11432.t36.CDS4 16200826 16200849
chr_1 g11432 g11432.t36 TSS g11432.t36 16201105 16201105

Sequences

>g11432.t36 Gene=g11432 Length=432
ATGGTAATTATCTCACATTATTTTGAAGCATTCTCATTGTTCGACAAAGACGGTGATGGC
ACAATTACCACAAAAGAATTGGGCACTGTGATGAGATCACTTGGTCAAAACCCGACAGAA
GCTGAACTTCAGGATATGATTAACGAAGTTGATGCTGACGGCAATGGTACCATAGATTTC
CCTGAATTCTTAACTATGATGGCTCGCAAAATGAAAGATACTGATAGTGAAGAAGAAATT
CGGGAAGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTCATCTCTGCAGCTGAATTG
CGCCACGTGATGACAAATTTGGGAGAAAAATTAACAGATGAAGAAGTCGATGAAATGATT
CGTGAGGCAGATATTGATGGTGACGGACAAGTTAATTACGAAGAATTTGTCACCATGATG
ACATCAAAGTGA

>g11432.t36 Gene=g11432 Length=143
MVIISHYFEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDF
PEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEMI
READIDGDGQVNYEEFVTMMTSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11432.t36 CDD cd00051 EFh 9 68 6.00096E-21
11 g11432.t36 CDD cd00051 EFh 79 141 6.14148E-24
8 g11432.t36 Gene3D G3DSA:1.10.238.10 - 5 32 5.1E-8
7 g11432.t36 Gene3D G3DSA:1.10.238.10 - 33 67 2.9E-20
6 g11432.t36 Gene3D G3DSA:1.10.238.10 - 68 117 9.4E-28
9 g11432.t36 Gene3D G3DSA:1.10.238.10 - 118 143 3.1E-7
3 g11432.t36 PANTHER PTHR23050:SF401 CALMODULIN 4 143 5.5E-89
4 g11432.t36 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 4 143 5.5E-89
2 g11432.t36 Pfam PF13499 EF-hand domain pair 7 67 2.1E-15
1 g11432.t36 Pfam PF13499 EF-hand domain pair 77 140 7.1E-19
14 g11432.t36 ProSitePatterns PS00018 EF-hand calcium-binding domain. 15 27 -
12 g11432.t36 ProSitePatterns PS00018 EF-hand calcium-binding domain. 51 63 -
13 g11432.t36 ProSitePatterns PS00018 EF-hand calcium-binding domain. 88 100 -
15 g11432.t36 ProSitePatterns PS00018 EF-hand calcium-binding domain. 124 136 -
23 g11432.t36 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 2 37 14.848
20 g11432.t36 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 38 73 14.792
21 g11432.t36 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 75 110 17.972
22 g11432.t36 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 111 143 15.155
18 g11432.t36 SMART SM00054 efh_1 6 34 4.6E-6
16 g11432.t36 SMART SM00054 efh_1 42 70 7.2E-9
19 g11432.t36 SMART SM00054 efh_1 79 107 5.8E-9
17 g11432.t36 SMART SM00054 efh_1 115 143 1.3E-9
5 g11432.t36 SUPERFAMILY SSF47473 EF-hand 5 142 7.0E-55

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. There were no conditions that were differentially expressed