Gene loci information

Transcript annotation

  • This transcript has been annotated as 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.t9 TSS g16754.t9 10830399 10830399
chr_4 g16754 g16754.t9 isoform g16754.t9 10830521 10834016
chr_4 g16754 g16754.t9 exon g16754.t9.exon1 10830521 10830608
chr_4 g16754 g16754.t9 cds g16754.t9.CDS1 10830521 10830608
chr_4 g16754 g16754.t9 exon g16754.t9.exon2 10830714 10830818
chr_4 g16754 g16754.t9 cds g16754.t9.CDS2 10830714 10830818
chr_4 g16754 g16754.t9 exon g16754.t9.exon3 10832163 10832281
chr_4 g16754 g16754.t9 cds g16754.t9.CDS3 10832163 10832281
chr_4 g16754 g16754.t9 exon g16754.t9.exon4 10833177 10833571
chr_4 g16754 g16754.t9 cds g16754.t9.CDS4 10833177 10833571
chr_4 g16754 g16754.t9 exon g16754.t9.exon5 10833816 10833903
chr_4 g16754 g16754.t9 cds g16754.t9.CDS5 10833816 10833903
chr_4 g16754 g16754.t9 exon g16754.t9.exon6 10834010 10834016
chr_4 g16754 g16754.t9 cds g16754.t9.CDS6 10834010 10834015
chr_4 g16754 g16754.t9 TTS g16754.t9 10834937 10834937

Sequences

>g16754.t9 Gene=g16754 Length=802
ATGAAGACAGTGTCGAGAATTTTCCTTCTACTAAGCGCACTAGCGTTAGTAAGCTGTGAA
GTCTTCTTTGAAGAGAAATTCAGCGATGACTCATGGGAAAAGAAATGGGTTTATTCACAA
CATCCAGGCAAAGAATTTGGTCAGTTTAAGAGAACTGCTGGCAAATTTTTCAATGATGAG
GAAGCTGATAAAGGTCTTCAAACTTCACAAGATGCTCGTTTCTATGCTTTGTCAACTAAA
TTTACACCTTTTAGCAATAAAGATAAACCACTTGTGATACAATTCTCTGTAAAGCATGAG
CAGAACATTGATTGTGGTGGTGGATACCTCAAAATCTTTGACTGCAACCTTGATCAGAAG
GACATGCATGGTGAATCACCATATTTGATCATGTTTGGACCAGATATTTGCGGACCAGGC
ACAAAGAAAGTTCATGTTATCTTCAGCTACAAAGGCAAAAATCATTTGATCAAGAAAGAA
ATTCGCTGCAAAGATGATGTCTTCACTCACTTTTATACCTTGATTGTTCAACCAGATAAC
ACTTATGAAGTTTTGATTGATAATGAGAAAGTTGAATCAGGATCATTGGAAGATGATTGG
GATTTCTTGCCACCAAAGACAATCAAAGATCCAGAAGCAAAGAAACCAGAAGATTGGGAT
GAACGTGCAACCATTCCAGACCCAGATGATAAAAAACCAGAAGATTGGGATCAACCAGAA
CACATTCCAGACCCAGATGCCACAAAACCAGAAGATTGGGATGATGAAATTGATGGAGAT
TTTGAACCACCAATGATTGACA

>g16754.t9 Gene=g16754 Length=267
MKTVSRIFLLLSALALVSCEVFFEEKFSDDSWEKKWVYSQHPGKEFGQFKRTAGKFFNDE
EADKGLQTSQDARFYALSTKFTPFSNKDKPLVIQFSVKHEQNIDCGGGYLKIFDCNLDQK
DMHGESPYLIMFGPDICGPGTKKVHVIFSYKGKNHLIKKEIRCKDDVFTHFYTLIVQPDN
TYEVLIDNEKVESGSLEDDWDFLPPKTIKDPEAKKPEDWDERATIPDPDDKKPEDWDQPE
HIPDPDATKPEDWDDEIDGDFEPPMID

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g16754.t9 Gene3D G3DSA:2.60.120.200 - 21 195 9.1E-99
13 g16754.t9 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 196 248 9.1E-99
23 g16754.t9 MobiDBLite mobidb-lite consensus disorder prediction 196 267 -
24 g16754.t9 MobiDBLite mobidb-lite consensus disorder prediction 196 248 -
25 g16754.t9 MobiDBLite mobidb-lite consensus disorder prediction 249 267 -
2 g16754.t9 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 1 266 2.7E-135
3 g16754.t9 PANTHER PTHR11073:SF41 CALRETICULIN 1 266 2.7E-135
5 g16754.t9 PRINTS PR00626 Calreticulin signature 100 118 2.6E-32
4 g16754.t9 PRINTS PR00626 Calreticulin signature 126 142 2.6E-32
6 g16754.t9 PRINTS PR00626 Calreticulin signature 215 228 2.6E-32
7 g16754.t9 PRINTS PR00626 Calreticulin signature 242 264 2.6E-32
1 g16754.t9 Pfam PF00262 Calreticulin family 23 257 4.0E-58
15 g16754.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 19 -
16 g16754.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
17 g16754.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 14 -
18 g16754.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 15 19 -
14 g16754.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 20 267 -
20 g16754.t9 ProSitePatterns PS00803 Calreticulin family signature 1. 98 113 -
22 g16754.t9 ProSitePatterns PS00804 Calreticulin family signature 2. 130 138 -
21 g16754.t9 ProSitePatterns PS00805 Calreticulin family repeated motif signature. 242 254 -
26 g16754.t9 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 19 6.0
8 g16754.t9 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 16 218 7.75E-62
9 g16754.t9 SUPERFAMILY SSF63887 P-domain of calnexin/calreticulin 201 267 1.01E-22
11 g16754.t9 SignalP_EUK SignalP-noTM SignalP-noTM 1 19 -
19 g16754.t9 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 23 -
10 g16754.t9 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:0005515 protein binding MF
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