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.t7 TSS g16754.t7 10830399 10830399
chr_4 g16754 g16754.t7 isoform g16754.t7 10830521 10833571
chr_4 g16754 g16754.t7 exon g16754.t7.exon1 10830521 10830608
chr_4 g16754 g16754.t7 exon g16754.t7.exon2 10830714 10830818
chr_4 g16754 g16754.t7 exon g16754.t7.exon3 10833086 10833571
chr_4 g16754 g16754.t7 cds g16754.t7.CDS1 10833156 10833569
chr_4 g16754 g16754.t7 TTS g16754.t7 10834292 10834292

Sequences

>g16754.t7 Gene=g16754 Length=679
ATGAAGACAGTGTCGAGAATTTTCCTTCTACTAAGCGCACTAGCGTTAGTAAGCTGTGAA
GTCTTCTTTGAAGAGAAATTCAGCGATGACTCATGGGAAAAGAAATGGGTTTATTCACAA
CATCCAGGCAAAGAATTTGGTCAGTTTAAGAGAACTGCTGGCAAATTTTTCAATGATGAG
GAAGCTGATAAAGGTTGTTTCATTCATGTTTAGTTTTTTATTGCTTAATGTCAAGTTAAA
TTATTAGCTAAATTTTACTCATTATGATTTTTTTAAATTTCCAGTGTGGTGGTGGATACC
TCAAAATCTTTGACTGCAACCTTGATCAGAAGGACATGCATGGTGAATCACCATATTTGA
TCATGTTTGGACCAGATATTTGCGGACCAGGCACAAAGAAAGTTCATGTTATCTTCAGCT
ACAAAGGCAAAAATCATTTGATCAAGAAAGAAATTCGCTGCAAAGATGATGTCTTCACTC
ACTTTTATACCTTGATTGTTCAACCAGATAACACTTATGAAGTTTTGATTGATAATGAGA
AAGTTGAATCAGGATCATTGGAAGATGATTGGGATTTCTTGCCACCAAAGACAATCAAAG
ATCCAGAAGCAAAGAAACCAGAAGATTGGGATGAACGTGCAACCATTCCAGACCCAGATG
ATAAAAAACCAGAAGATTG

>g16754.t7 Gene=g16754 Length=138
MIFLNFQCGGGYLKIFDCNLDQKDMHGESPYLIMFGPDICGPGTKKVHVIFSYKGKNHLI
KKEIRCKDDVFTHFYTLIVQPDNTYEVLIDNEKVESGSLEDDWDFLPPKTIKDPEAKKPE
DWDERATIPDPDDKKPED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g16754.t7 Gene3D G3DSA:2.60.120.200 - 3 108 6.7E-41
12 g16754.t7 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 109 138 1.5E-6
10 g16754.t7 MobiDBLite mobidb-lite consensus disorder prediction 105 138 -
2 g16754.t7 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 5 138 1.8E-73
3 g16754.t7 PANTHER PTHR11073:SF41 CALRETICULIN 5 138 1.8E-73
5 g16754.t7 PRINTS PR00626 Calreticulin signature 3 21 8.9E-18
4 g16754.t7 PRINTS PR00626 Calreticulin signature 29 45 8.9E-18
6 g16754.t7 PRINTS PR00626 Calreticulin signature 118 131 8.9E-18
1 g16754.t7 Pfam PF00262 Calreticulin family 6 138 3.2E-37
9 g16754.t7 ProSitePatterns PS00804 Calreticulin family signature 2. 33 41 -
8 g16754.t7 ProSitePatterns PS00805 Calreticulin family repeated motif signature. 111 123 -
7 g16754.t7 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 6 120 7.12E-40

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.

Raw TPM values