Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Calreticulin.

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_4 g16754 g16754.t2 TSS g16754.t2 10830399 10830399
chr_4 g16754 g16754.t2 isoform g16754.t2 10830521 10832276
chr_4 g16754 g16754.t2 exon g16754.t2.exon1 10830521 10830608
chr_4 g16754 g16754.t2 cds g16754.t2.CDS1 10830521 10830608
chr_4 g16754 g16754.t2 exon g16754.t2.exon2 10830714 10830818
chr_4 g16754 g16754.t2 cds g16754.t2.CDS2 10830714 10830818
chr_4 g16754 g16754.t2 exon g16754.t2.exon3 10832163 10832276
chr_4 g16754 g16754.t2 cds g16754.t2.CDS3 10832163 10832275
chr_4 g16754 g16754.t2 TTS g16754.t2 NA NA

Sequences

>g16754.t2 Gene=g16754 Length=307
ATGAAGACAGTGTCGAGAATTTTCCTTCTACTAAGCGCACTAGCGTTAGTAAGCTGTGAA
GTCTTCTTTGAAGAGAAATTCAGCGATGACTCATGGGAAAAGAAATGGGTTTATTCACAA
CATCCAGGCAAAGAATTTGGTCAGTTTAAGAGAACTGCTGGCAAATTTTTCAATGATGAG
GAAGCTGATAAAGGTCTTCAAACTTCACAAGATGCTCGTTTCTATGCTTTGTCAACTAAA
TTTACACCTTTTAGCAATAAAGATAAACCACTTGTGATACAATTCTCTGTAAAGCATGAG
CAGAACA

>g16754.t2 Gene=g16754 Length=102
MKTVSRIFLLLSALALVSCEVFFEEKFSDDSWEKKWVYSQHPGKEFGQFKRTAGKFFNDE
EADKGLQTSQDARFYALSTKFTPFSNKDKPLVIQFSVKHEQN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g16754.t2 Gene3D G3DSA:2.60.120.200 - 12 102 4.1E-27
2 g16754.t2 PANTHER PTHR11073:SF2 CALRETICULIN 10 102 1.4E-29
3 g16754.t2 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 10 102 1.4E-29
1 g16754.t2 Pfam PF00262 Calreticulin family 23 101 1.7E-7
9 g16754.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
10 g16754.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
11 g16754.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 14 -
12 g16754.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
8 g16754.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 102 -
14 g16754.t2 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 19 6.0
4 g16754.t2 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 16 102 2.37E-14
6 g16754.t2 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
13 g16754.t2 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 23 -
5 g16754.t2 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM 1 23 -

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:0006457 protein folding BP
GO:0005783 endoplasmic reticulum CC
GO:0051082 unfolded protein binding MF
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