Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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 g9403 g9403.t1 TSS g9403.t1 2646783 2646783
chr_1 g9403 g9403.t1 isoform g9403.t1 2646886 2648105
chr_1 g9403 g9403.t1 exon g9403.t1.exon1 2646886 2646927
chr_1 g9403 g9403.t1 cds g9403.t1.CDS1 2646886 2646927
chr_1 g9403 g9403.t1 exon g9403.t1.exon2 2647634 2647991
chr_1 g9403 g9403.t1 cds g9403.t1.CDS2 2647634 2647991
chr_1 g9403 g9403.t1 exon g9403.t1.exon3 2648050 2648105
chr_1 g9403 g9403.t1 cds g9403.t1.CDS3 2648050 2648105
chr_1 g9403 g9403.t1 TTS g9403.t1 2648132 2648132

Sequences

>g9403.t1 Gene=g9403 Length=456
ATGGCTAAAAAAATTCCAGCAGAGAAACTTAAAGAATATCAAGAAGTTTTCAATGTCTAC
GACATCAATAGAGATGGACAAATAAACACATCAGAACTAGATACAGTAATGAAAGTCCTT
GGTGAAGAATTAACAGAAGCACGACTTCAAAAACTCATAAATGAAGTTGATCTCGATGGA
AGTGGTACAATAAATTTTGATGAATTTATCAAACTGATGCAAAAAGTTGAAGAGACAGAT
TTTGAAAAAGCAGAATCACTTCGTGCTGCTTTTAAAGTTTTTGACAAGGACAACAATGGT
TTTGTATCATTTGATGAATTGAAATATATTTTGACAAGTTTTGGTGAGAAATTGACTGAT
GAAGAAGTTCAAGATATTTTACATGAAGCTGATAAAGATCGTAATGGAAAACTTGATTAT
GAAGAATTCATTGCAATGTATTTGGAAAAAGAATAA

>g9403.t1 Gene=g9403 Length=151
MAKKIPAEKLKEYQEVFNVYDINRDGQINTSELDTVMKVLGEELTEARLQKLINEVDLDG
SGTINFDEFIKLMQKVEETDFEKAESLRAAFKVFDKDNNGFVSFDELKYILTSFGEKLTD
EEVQDILHEADKDRNGKLDYEEFIAMYLEKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g9403.t1 Gene3D G3DSA:1.10.238.10 - 1 77 6.0E-25
15 g9403.t1 Gene3D G3DSA:1.10.238.10 - 78 151 3.9E-25
3 g9403.t1 PANTHER PTHR23050:SF413 CALMODULIN-LIKE PROTEIN 10 1 147 7.7E-44
4 g9403.t1 PANTHER PTHR23050 CALCIUM BINDING PROTEIN 1 147 7.7E-44
1 g9403.t1 Pfam PF13499 EF-hand domain pair 13 74 4.8E-14
2 g9403.t1 Pfam PF13499 EF-hand domain pair 85 147 1.9E-15
13 g9403.t1 ProSitePatterns PS00018 EF-hand calcium-binding domain. 21 33 -
11 g9403.t1 ProSitePatterns PS00018 EF-hand calcium-binding domain. 57 69 -
12 g9403.t1 ProSitePatterns PS00018 EF-hand calcium-binding domain. 95 107 -
10 g9403.t1 ProSitePatterns PS00018 EF-hand calcium-binding domain. 131 143 -
16 g9403.t1 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 8 43 14.039
17 g9403.t1 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 44 79 14.179
18 g9403.t1 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 82 117 16.606
19 g9403.t1 ProSiteProfiles PS50222 EF-hand calcium-binding domain profile. 118 151 13.23
7 g9403.t1 SMART SM00054 efh_1 12 40 1.3E-4
6 g9403.t1 SMART SM00054 efh_1 48 76 3.0E-7
9 g9403.t1 SMART SM00054 efh_1 86 114 2.7E-7
8 g9403.t1 SMART SM00054 efh_1 122 150 1.8E-4
5 g9403.t1 SUPERFAMILY SSF47473 EF-hand 2 148 1.64E-45

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

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. There were no conditions that were differentially expressed