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.t61 TTS g11432.t61 16197707 16197707
chr_1 g11432 g11432.t61 isoform g11432.t61 16198111 16200849
chr_1 g11432 g11432.t61 exon g11432.t61.exon1 16198111 16198353
chr_1 g11432 g11432.t61 cds g11432.t61.CDS1 16198112 16198353
chr_1 g11432 g11432.t61 exon g11432.t61.exon2 16199164 16199299
chr_1 g11432 g11432.t61 cds g11432.t61.CDS2 16199164 16199299
chr_1 g11432 g11432.t61 exon g11432.t61.exon3 16199438 16199476
chr_1 g11432 g11432.t61 cds g11432.t61.CDS3 16199438 16199476
chr_1 g11432 g11432.t61 exon g11432.t61.exon4 16200847 16200849
chr_1 g11432 g11432.t61 cds g11432.t61.CDS4 16200847 16200849
chr_1 g11432 g11432.t61 TSS g11432.t61 16201105 16201105

Sequences

>g11432.t61 Gene=g11432 Length=421
ATGGCTGATCAATTAACAGAGGAGCAAATCGCTGAGTTCAAAGAAGCATTCTCATTGTTC
GACAAAGACGGTGATGGCACAATTACCACAAAAGAATTGGGCACTGTGATGAGATCACTT
GGTCAAAACCCGACAGAAGCTGAACTTCAGGATATGATTAACGAAGTTGATGCTGACGGC
AATGGTACCATAGATTTCCCTGAATTCTTAACTATGATGGCTCGCAAAATGAAAGATACT
GATAGTGAAGAAGAAATTCGGGAAGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTC
ATCTCTGCAGCTGAATTGCGCCACGTGATGACAAATTTGGGAGAAAAATTAACAGATGAA
GAAGTCGATGAAATGATTCGTGAGGCAGATATTGATGGTGACGGACAAGTTAATTACGAA
G

>g11432.t61 Gene=g11432 Length=140
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG
NGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDE
EVDEMIREADIDGDGQVNYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g11432.t61 CDD cd00051 EFh 12 74 3.88647E-22
13 g11432.t61 CDD cd00051 EFh 85 140 1.13167E-19
10 g11432.t61 Gene3D G3DSA:1.10.238.10 - 1 50 3.1E-22
11 g11432.t61 Gene3D G3DSA:1.10.238.10 - 51 111 4.8E-30
9 g11432.t61 Gene3D G3DSA:1.10.238.10 - 112 140 1.0E-11
3 g11432.t61 PANTHER PTHR23050:SF401 CALMODULIN 3 140 1.0E-89
4 g11432.t61 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 3 140 1.0E-89
6 g11432.t61 PRINTS PR00450 Recoverin family signature 5 24 9.8E-5
5 g11432.t61 PRINTS PR00450 Recoverin family signature 52 73 9.8E-5
7 g11432.t61 PRINTS PR00450 Recoverin family signature 99 117 9.8E-5
2 g11432.t61 Pfam PF13499 EF-hand domain pair 12 73 1.1E-15
1 g11432.t61 Pfam PF13499 EF-hand domain pair 83 140 3.9E-15
16 g11432.t61 ProSitePatterns PS00018 EF-hand calcium-binding domain. 21 33 -
14 g11432.t61 ProSitePatterns PS00018 EF-hand calcium-binding domain. 57 69 -
15 g11432.t61 ProSitePatterns PS00018 EF-hand calcium-binding domain. 94 106 -
21 g11432.t61 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 8 43 17.303
23 g11432.t61 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 44 79 14.792
24 g11432.t61 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 81 116 17.972
22 g11432.t61 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 117 140 11.835
19 g11432.t61 SMART SM00054 efh_1 12 40 8.5E-9
18 g11432.t61 SMART SM00054 efh_1 48 76 7.2E-9
17 g11432.t61 SMART SM00054 efh_1 85 113 5.8E-9
20 g11432.t61 SMART SM00054 efh_1 121 140 20.0
8 g11432.t61 SUPERFAMILY SSF47473 EF-hand 2 140 2.36E-54

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.

Raw TPM values