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.t32 TTS g11432.t32 16197707 16197707
chr_1 g11432 g11432.t32 isoform g11432.t32 16197920 16199476
chr_1 g11432 g11432.t32 exon g11432.t32.exon1 16197920 16197948
chr_1 g11432 g11432.t32 cds g11432.t32.CDS1 16197921 16197948
chr_1 g11432 g11432.t32 exon g11432.t32.exon2 16198107 16198353
chr_1 g11432 g11432.t32 cds g11432.t32.CDS2 16198107 16198353
chr_1 g11432 g11432.t32 exon g11432.t32.exon3 16199164 16199299
chr_1 g11432 g11432.t32 cds g11432.t32.CDS3 16199164 16199233
chr_1 g11432 g11432.t32 exon g11432.t32.exon4 16199438 16199476
chr_1 g11432 g11432.t32 TSS g11432.t32 NA NA

Sequences

>g11432.t32 Gene=g11432 Length=451
GCTGATCAATTAACAGAGGAGCAAATCGCTGAGTTCAAAGAAGCATTCTCATTGTTCGAC
AAAGACGGTGATGGCACAATTACCACAAAAGAATTGGGCACTGTGATGAGATCACTTGGT
CAAAACCCGACAGAAGCTGAACTTCAGGATATGATTAACGAAGTTGATGCTGACGGCAAT
GGTACCATAGATTTCCCTGAATTCTTAACTATGATGGCTCGCAAAATGAAAGATACTGAT
AGTGAAGAAGAAATTCGGGAAGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTCATC
TCTGCAGCTGAATTGCGCCACGTGATGACAAATTTGGGAGAAAAATTAACAGATGAAGAA
GTCGATGAAATGATTCGTGAGGCAGATATTGATGGTGACGGACAAGTTAATTACGAAGGT
ATAATTTGTCACCATGATGACATCAAAGTGA

>g11432.t32 Gene=g11432 Length=115
MRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKD
GNGFISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEGIICHHDDIKV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11432.t32 CDD cd00051 EFh 12 75 4.09082E-12
9 g11432.t32 CDD cd00051 EFh 49 104 2.54655E-20
7 g11432.t32 Gene3D G3DSA:1.10.238.10 - 1 35 3.5E-20
6 g11432.t32 Gene3D G3DSA:1.10.238.10 - 36 112 1.4E-31
3 g11432.t32 PANTHER PTHR23050:SF401 CALMODULIN 1 107 1.2E-67
4 g11432.t32 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 1 107 1.2E-67
2 g11432.t32 Pfam PF00036 EF hand 12 39 6.4E-9
1 g11432.t32 Pfam PF13499 EF-hand domain pair 47 104 1.3E-15
11 g11432.t32 ProSitePatterns PS00018 EF-hand calcium-binding domain. 21 33 -
10 g11432.t32 ProSitePatterns PS00018 EF-hand calcium-binding domain. 58 70 -
15 g11432.t32 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 8 43 14.792
17 g11432.t32 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 45 80 17.972
16 g11432.t32 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 81 104 7.651
14 g11432.t32 SMART SM00054 efh_1 12 40 7.2E-9
13 g11432.t32 SMART SM00054 efh_1 49 77 5.8E-9
12 g11432.t32 SMART SM00054 efh_1 85 113 1.4
5 g11432.t32 SUPERFAMILY SSF47473 EF-hand 1 111 9.32E-41

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