General information for g16754.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Calreticulin.
Parent gene
- The parent gene g16754 is located on chr_4: 10834325..10835586 (+ strand)
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.t6 | TSS | g16754.t6 | 10830399 | 10830399 |
| chr_4 | g16754 | g16754.t6 | isoform | g16754.t6 | 10830521 | 10833571 |
| chr_4 | g16754 | g16754.t6 | exon | g16754.t6.exon1 | 10830521 | 10830608 |
| chr_4 | g16754 | g16754.t6 | exon | g16754.t6.exon2 | 10830714 | 10830902 |
| chr_4 | g16754 | g16754.t6 | exon | g16754.t6.exon3 | 10833177 | 10833571 |
| chr_4 | g16754 | g16754.t6 | cds | g16754.t6.CDS1 | 10833228 | 10833569 |
| chr_4 | g16754 | g16754.t6 | TTS | g16754.t6 | 10834292 | 10834292 |
Sequences
>g16754.t6 Gene=g16754 Length=672
ATGAAGACAGTGTCGAGAATTTTCCTTCTACTAAGCGCACTAGCGTTAGTAAGCTGTGAA
GTCTTCTTTGAAGAGAAATTCAGCGATGACTCATGGGAAAAGAAATGGGTTTATTCACAA
CATCCAGGCAAAGAATTTGGTCAGTTTAAGAGAACTGCTGGCAAATTTTTCAATGATGAG
GAAGCTGATAAAGGTAAGTTATTGAAAAATTATTAAAAAATCTCTTACGTGTCGAAAGAA
TGAAGAAAAAGAAGAATAAAAACTATCGGCAAACGGATGTGGTGGTGGATACCTCAAAAT
CTTTGACTGCAACCTTGATCAGAAGGACATGCATGGTGAATCACCATATTTGATCATGTT
TGGACCAGATATTTGCGGACCAGGCACAAAGAAAGTTCATGTTATCTTCAGCTACAAAGG
CAAAAATCATTTGATCAAGAAAGAAATTCGCTGCAAAGATGATGTCTTCACTCACTTTTA
TACCTTGATTGTTCAACCAGATAACACTTATGAAGTTTTGATTGATAATGAGAAAGTTGA
ATCAGGATCATTGGAAGATGATTGGGATTTCTTGCCACCAAAGACAATCAAAGATCCAGA
AGCAAAGAAACCAGAAGATTGGGATGAACGTGCAACCATTCCAGACCCAGATGATAAAAA
ACCAGAAGATTG
>g16754.t6 Gene=g16754 Length=114
MHGESPYLIMFGPDICGPGTKKVHVIFSYKGKNHLIKKEIRCKDDVFTHFYTLIVQPDNT
YEVLIDNEKVESGSLEDDWDFLPPKTIKDPEAKKPEDWDERATIPDPDDKKPED
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g16754.t6 | Gene3D | G3DSA:2.60.120.200 | - | 1 | 74 | 5.4E-51 |
| 11 | g16754.t6 | Gene3D | G3DSA:2.10.250.10 | Calnexin lumenal domain | 75 | 113 | 5.4E-51 |
| 9 | g16754.t6 | MobiDBLite | mobidb-lite | consensus disorder prediction | 81 | 114 | - |
| 2 | g16754.t6 | PANTHER | PTHR11073 | CALRETICULIN AND CALNEXIN | 1 | 114 | 1.3E-63 |
| 3 | g16754.t6 | PANTHER | PTHR11073:SF41 | CALRETICULIN | 1 | 114 | 1.3E-63 |
| 5 | g16754.t6 | PRINTS | PR00626 | Calreticulin signature | 5 | 21 | 5.5E-12 |
| 4 | g16754.t6 | PRINTS | PR00626 | Calreticulin signature | 94 | 107 | 5.5E-12 |
| 1 | g16754.t6 | Pfam | PF00262 | Calreticulin family | 3 | 114 | 1.9E-31 |
| 8 | g16754.t6 | ProSitePatterns | PS00804 | Calreticulin family signature 2. | 9 | 17 | - |
| 7 | g16754.t6 | ProSitePatterns | PS00805 | Calreticulin family repeated motif signature. | 87 | 99 | - |
| 6 | g16754.t6 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 1 | 96 | 2.37E-32 |
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.
