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.t11 TTS g11432.t11 16196923 16196923
chr_1 g11432 g11432.t11 isoform g11432.t11 16196935 16200849
chr_1 g11432 g11432.t11 exon g11432.t11.exon1 16196935 16197948
chr_1 g11432 g11432.t11 cds g11432.t11.CDS1 16197920 16197948
chr_1 g11432 g11432.t11 exon g11432.t11.exon2 16198111 16198353
chr_1 g11432 g11432.t11 cds g11432.t11.CDS2 16198111 16198353
chr_1 g11432 g11432.t11 exon g11432.t11.exon3 16199164 16199299
chr_1 g11432 g11432.t11 cds g11432.t11.CDS3 16199164 16199299
chr_1 g11432 g11432.t11 exon g11432.t11.exon4 16200811 16200849
chr_1 g11432 g11432.t11 cds g11432.t11.CDS4 16200811 16200849
chr_1 g11432 g11432.t11 TSS g11432.t11 16201105 16201105

Sequences

>g11432.t11 Gene=g11432 Length=1432
ATGGTAATTATCTCACATTATTTTTATATTGATCGCAAAGAAGCATTCTCATTGTTCGAC
AAAGACGGTGATGGCACAATTACCACAAAAGAATTGGGCACTGTGATGAGATCACTTGGT
CAAAACCCGACAGAAGCTGAACTTCAGGATATGATTAACGAAGTTGATGCTGACGGCAAT
GGTACCATAGATTTCCCTGAATTCTTAACTATGATGGCTCGCAAAATGAAAGATACTGAT
AGTGAAGAAGAAATTCGGGAAGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTCATC
TCTGCAGCTGAATTGCGCCACGTGATGACAAATTTGGGAGAAAAATTAACAGATGAAGAA
GTCGATGAAATGATTCGTGAGGCAGATATTGATGGTGACGGACAAGTTAATTACGAAGAA
TTTGTCACCATGATGACATCAAAGTGAGCTCCTGTTTTAAGTGTACGTCAGCCTTTGAAT
ACACAACACTATTACAATTATAAAAAAACTATAATAAAAAACTGTAATATGATCTTCTAT
CAATATTTTGTTTTGTAAAGAAAAGAAGCTACGGAGAATGCTGCATATTTACCATCATGT
AGCATTTTCTGCATTTTTCTAAATAAGCTTCTAATACAACAAGTGAAAAAAGAGAAAAAA
TAACATTTTAAAAAGCGTATATTCGCACCGTAATTTTTTTTATAATTTTTTTAAAAGTTT
TTTCAGTTAATTCAAAAAGATGATGAAGAGAGGAAAAAAGAGATAAAACATTAAAAAACA
TTGTCCTAAAGAAATTTGTTGAAAAATTTTCAGAGAATGAATAATAAGAAAAATTTGCAA
AAATACTTATTTAAAATGAATAACAGAAAAAAAAACTATCGCTAAAAGTTTAAATATAAA
AGTAATAGTAAAGTAAGAGAAAAAAATTGAGAGAAAATTTTAAAATCCACTGTACTTTTT
GAAAAATTGCAATTTAATCAAGCTTATCACACACTTCTCACACAATTCTGTACTATTCAA
AATTCAAAAAATAAATATATGATTTCATTTAAAATAGCTTTTAATTTTCTTATTATTAAT
TCGTAAATAAATATATCTTTAAAAATCATAATTAATGGAAGAAACAAGCAAACAAAAAAC
ACAGTCGAGATAATAGTAACAGAGAGGAAATTTATCTCATTCAACATTCTGTAAGAAAAT
CAAAATTTACGTTTTTAACAAGAAGATGAAAAAAGAAGTAAACATATAGTTATTTAATAT
TCTTGTATTAAATATATTTATGTAACAGTTCGATGATTATTATTATAATTAAAAGAAGAG
AGAAACCAAGAAAAAAATTTCAAGTGGAATTATTTAAAAATGTACCATTATAAAAGCTAA
AAAAATCACCAAGTTTCATTTTAAAAATAAATTTAATAAAATCCTATATTAT

>g11432.t11 Gene=g11432 Length=148
MVIISHYFYIDRKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGN
GTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEE
VDEMIREADIDGDGQVNYEEFVTMMTSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g11432.t11 CDD cd00051 EFh 13 73 2.49792E-21
10 g11432.t11 CDD cd00051 EFh 84 146 7.21534E-24
8 g11432.t11 Gene3D G3DSA:1.10.238.10 - 9 37 1.7E-8
6 g11432.t11 Gene3D G3DSA:1.10.238.10 - 38 72 3.0E-20
7 g11432.t11 Gene3D G3DSA:1.10.238.10 - 73 122 1.0E-27
9 g11432.t11 Gene3D G3DSA:1.10.238.10 - 123 148 3.3E-7
3 g11432.t11 PANTHER PTHR23050:SF401 CALMODULIN 11 148 4.0E-89
4 g11432.t11 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 11 148 4.0E-89
2 g11432.t11 Pfam PF13499 EF-hand domain pair 13 72 3.4E-15
1 g11432.t11 Pfam PF13499 EF-hand domain pair 82 145 7.7E-19
14 g11432.t11 ProSitePatterns PS00018 EF-hand calcium-binding domain. 20 32 -
15 g11432.t11 ProSitePatterns PS00018 EF-hand calcium-binding domain. 56 68 -
13 g11432.t11 ProSitePatterns PS00018 EF-hand calcium-binding domain. 93 105 -
12 g11432.t11 ProSitePatterns PS00018 EF-hand calcium-binding domain. 129 141 -
21 g11432.t11 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 13 42 14.346
20 g11432.t11 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 43 78 14.792
22 g11432.t11 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 80 115 17.972
23 g11432.t11 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 116 148 15.155
16 g11432.t11 SMART SM00054 efh_1 11 39 6.3E-6
18 g11432.t11 SMART SM00054 efh_1 47 75 7.2E-9
19 g11432.t11 SMART SM00054 efh_1 84 112 5.8E-9
17 g11432.t11 SMART SM00054 efh_1 120 148 1.3E-9
5 g11432.t11 SUPERFAMILY SSF47473 EF-hand 13 147 2.12E-54

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

## Warning: Removed 1 row(s) containing missing values (geom_path).

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.

Raw TPM values