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.t20 TTS g11432.t20 16197312 16197312
chr_1 g11432 g11432.t20 isoform g11432.t20 16197343 16200849
chr_1 g11432 g11432.t20 exon g11432.t20.exon1 16197343 16197948
chr_1 g11432 g11432.t20 cds g11432.t20.CDS1 16197920 16197948
chr_1 g11432 g11432.t20 exon g11432.t20.exon2 16198111 16198338
chr_1 g11432 g11432.t20 cds g11432.t20.CDS2 16198111 16198338
chr_1 g11432 g11432.t20 exon g11432.t20.exon3 16199164 16199299
chr_1 g11432 g11432.t20 cds g11432.t20.CDS3 16199164 16199299
chr_1 g11432 g11432.t20 exon g11432.t20.exon4 16199438 16199476
chr_1 g11432 g11432.t20 cds g11432.t20.CDS4 16199438 16199476
chr_1 g11432 g11432.t20 exon g11432.t20.exon5 16200847 16200849
chr_1 g11432 g11432.t20 cds g11432.t20.CDS5 16200847 16200849
chr_1 g11432 g11432.t20 TSS g11432.t20 16201105 16201105

Sequences

>g11432.t20 Gene=g11432 Length=1012
ATGGCTGATCAATTAACAGAGGAGCAAATCGCTGAGTTCAAAGAAGCATTCTCATTGTTC
GACAAAGACGGTGATGGCACAATTACCACAAAAGAATTGGGCACTGTGATGAGATCACTT
GGTCAAAACCCGACAGAAGCTGAACTTCAGGATATGATTAACGAAGTTGATGCTGACGAT
TTCCCTGAATTCTTAACTATGATGGCTCGCAAAATGAAAGATACTGATAGTGAAGAAGAA
ATTCGGGAAGCATTCCGTGTATTTGATAAAGATGGCAATGGTTTCATCTCTGCAGCTGAA
TTGCGCCACGTGATGACAAATTTGGGAGAAAAATTAACAGATGAAGAAGTCGATGAAATG
ATTCGTGAGGCAGATATTGATGGTGACGGACAAGTTAATTACGAAGAATTTGTCACCATG
ATGACATCAAAGTGAGCTCCTGTTTTAAGTGTACGTCAGCCTTTGAATACACAACACTAT
TACAATTATAAAAAAACTATAATAAAAAACTGTAATATGATCTTCTATCAATATTTTGTT
TTGTAAAGAAAAGAAGCTACGGAGAATGCTGCATATTTACCATCATGTAGCATTTTCTGC
ATTTTTCTAAATAAGCTTCTAATACAACAAGTGAAAAAAGAGAAAAAATAACATTTTAAA
AAGCGTATATTCGCACCGTAATTTTTTTTATAATTTTTTTAAAAGTTTTTTCAGTTAATT
CAAAAAGATGATGAAGAGAGGAAAAAAGAGATAAAACATTAAAAAACATTGTCCTAAAGA
AATTTGTTGAAAAATTTTCAGAGAATGAATAATAAGAAAAATTTGCAAAAATACTTATTT
AAAATGAATAACAGAAAAAAAAACTATCGCTAAAAGTTTAAATATAAAAGTAATAGTAAA
GTAAGAGAAAAAAATTGAGAGAAAATTTTAAAATCCACTGTACTTTTTGAAAAATTGCAA
TTTAATCAAGCTTATCACACACTTCTCACACAATTCTGTACTATTCAAAATT

>g11432.t20 Gene=g11432 Length=144
MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADD
FPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGFISAAELRHVMTNLGEKLTDEEVDEM
IREADIDGDGQVNYEEFVTMMTSK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g11432.t20 CDD cd00051 EFh 12 69 3.78349E-16
9 g11432.t20 CDD cd00051 EFh 80 142 5.18191E-23
6 g11432.t20 Gene3D G3DSA:1.10.238.10 - 1 50 3.3E-22
8 g11432.t20 Gene3D G3DSA:1.10.238.10 - 51 106 3.3E-22
7 g11432.t20 Gene3D G3DSA:1.10.238.10 - 107 142 2.5E-17
3 g11432.t20 PANTHER PTHR23050:SF401 CALMODULIN 3 144 6.8E-88
4 g11432.t20 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 3 144 6.8E-88
2 g11432.t20 Pfam PF00036 EF hand 12 40 9.9E-10
1 g11432.t20 Pfam PF13499 EF-hand domain pair 78 141 7.2E-19
13 g11432.t20 ProSitePatterns PS00018 EF-hand calcium-binding domain. 21 33 -
12 g11432.t20 ProSitePatterns PS00018 EF-hand calcium-binding domain. 89 101 -
11 g11432.t20 ProSitePatterns PS00018 EF-hand calcium-binding domain. 125 137 -
20 g11432.t20 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 8 43 17.303
21 g11432.t20 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 44 74 5.894
19 g11432.t20 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 76 111 17.972
18 g11432.t20 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 112 144 15.155
15 g11432.t20 SMART SM00054 efh_1 12 40 8.5E-9
17 g11432.t20 SMART SM00054 efh_1 48 71 5.4
16 g11432.t20 SMART SM00054 efh_1 80 108 5.8E-9
14 g11432.t20 SMART SM00054 efh_1 116 144 1.3E-9
5 g11432.t20 SUPERFAMILY SSF47473 EF-hand 5 141 1.94E-52

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