General information for g16754.t1
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.t1 | TSS | g16754.t1 | 10830399 | 10830399 |
| chr_4 | g16754 | g16754.t1 | isoform | g16754.t1 | 10830521 | 10834496 |
| chr_4 | g16754 | g16754.t1 | exon | g16754.t1.exon1 | 10830521 | 10830608 |
| chr_4 | g16754 | g16754.t1 | cds | g16754.t1.CDS1 | 10830521 | 10830608 |
| chr_4 | g16754 | g16754.t1 | exon | g16754.t1.exon2 | 10830714 | 10830818 |
| chr_4 | g16754 | g16754.t1 | cds | g16754.t1.CDS2 | 10830714 | 10830818 |
| chr_4 | g16754 | g16754.t1 | exon | g16754.t1.exon3 | 10832163 | 10832281 |
| chr_4 | g16754 | g16754.t1 | cds | g16754.t1.CDS3 | 10832163 | 10832281 |
| chr_4 | g16754 | g16754.t1 | exon | g16754.t1.exon4 | 10833177 | 10833571 |
| chr_4 | g16754 | g16754.t1 | cds | g16754.t1.CDS4 | 10833177 | 10833571 |
| chr_4 | g16754 | g16754.t1 | exon | g16754.t1.exon5 | 10833816 | 10833903 |
| chr_4 | g16754 | g16754.t1 | cds | g16754.t1.CDS5 | 10833816 | 10833903 |
| chr_4 | g16754 | g16754.t1 | exon | g16754.t1.exon6 | 10834010 | 10834322 |
| chr_4 | g16754 | g16754.t1 | cds | g16754.t1.CDS6 | 10834010 | 10834322 |
| chr_4 | g16754 | g16754.t1 | exon | g16754.t1.exon7 | 10834387 | 10834496 |
| chr_4 | g16754 | g16754.t1 | cds | g16754.t1.CDS7 | 10834387 | 10834496 |
| chr_4 | g16754 | g16754.t1 | TTS | g16754.t1 | 10834937 | 10834937 |
Sequences
>g16754.t1 Gene=g16754 Length=1218
ATGAAGACAGTGTCGAGAATTTTCCTTCTACTAAGCGCACTAGCGTTAGTAAGCTGTGAA
GTCTTCTTTGAAGAGAAATTCAGCGATGACTCATGGGAAAAGAAATGGGTTTATTCACAA
CATCCAGGCAAAGAATTTGGTCAGTTTAAGAGAACTGCTGGCAAATTTTTCAATGATGAG
GAAGCTGATAAAGGTCTTCAAACTTCACAAGATGCTCGTTTCTATGCTTTGTCAACTAAA
TTTACACCTTTTAGCAATAAAGATAAACCACTTGTGATACAATTCTCTGTAAAGCATGAG
CAGAACATTGATTGTGGTGGTGGATACCTCAAAATCTTTGACTGCAACCTTGATCAGAAG
GACATGCATGGTGAATCACCATATTTGATCATGTTTGGACCAGATATTTGCGGACCAGGC
ACAAAGAAAGTTCATGTTATCTTCAGCTACAAAGGCAAAAATCATTTGATCAAGAAAGAA
ATTCGCTGCAAAGATGATGTCTTCACTCACTTTTATACCTTGATTGTTCAACCAGATAAC
ACTTATGAAGTTTTGATTGATAATGAGAAAGTTGAATCAGGATCATTGGAAGATGATTGG
GATTTCTTGCCACCAAAGACAATCAAAGATCCAGAAGCAAAGAAACCAGAAGATTGGGAT
GAACGTGCAACCATTCCAGACCCAGATGATAAAAAACCAGAAGATTGGGATCAACCAGAA
CACATTCCAGACCCAGATGCCACAAAACCAGAAGATTGGGATGATGAAATTGATGGAGAT
TTTGAACCACCAATGATTGACAATCCAGAATACAAAGGTGAATGGAAACCAAAACAAATT
GATAACCCAGCATACAAAGGAATCTGGAAGCATCCAGAAATTGACAATCCAGAATATACA
GCTGATGCCAATCTTTATCTCCGTGAAGAAGTTTGCGCTGTTGGTCTTGATCTCTGGCAA
GTCAAATCAGGCACAATTTTTGACAATATTTTGTTCACTGATGATGCTGAATATGCTAAA
GAAGCAGCTGCTACATTCAAGGCTACACAAGATGGTGAAAAGAAAATGAAAGATGAACAA
GATGAAGAAGAAAAGAAGAAGGCTGAAGCTGAAGCAAAAACAGAAGAAAAAGATGAAGAC
AATGAAGATTTAGATGATGAAGAAGACAAAGAAGACAGCAAAGGAGAAGCTGAAGCTGGA
GATCATGATGAATTGTAA
>g16754.t1 Gene=g16754 Length=405
MKTVSRIFLLLSALALVSCEVFFEEKFSDDSWEKKWVYSQHPGKEFGQFKRTAGKFFNDE
EADKGLQTSQDARFYALSTKFTPFSNKDKPLVIQFSVKHEQNIDCGGGYLKIFDCNLDQK
DMHGESPYLIMFGPDICGPGTKKVHVIFSYKGKNHLIKKEIRCKDDVFTHFYTLIVQPDN
TYEVLIDNEKVESGSLEDDWDFLPPKTIKDPEAKKPEDWDERATIPDPDDKKPEDWDQPE
HIPDPDATKPEDWDDEIDGDFEPPMIDNPEYKGEWKPKQIDNPAYKGIWKHPEIDNPEYT
ADANLYLREEVCAVGLDLWQVKSGTIFDNILFTDDAEYAKEAAATFKATQDGEKKMKDEQ
DEEEKKKAEAEAKTEEKDEDNEDLDDEEDKEDSKGEAEAGDHDEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g16754.t1 | Coils | Coil | Coil | 353 | 390 | - |
| 16 | g16754.t1 | Gene3D | G3DSA:2.60.120.200 | - | 12 | 224 | 1.3E-80 |
| 17 | g16754.t1 | Gene3D | G3DSA:2.10.250.10 | Calnexin lumenal domain | 225 | 286 | 2.6E-23 |
| 15 | g16754.t1 | Gene3D | G3DSA:2.60.120.200 | - | 293 | 374 | 1.2E-16 |
| 30 | g16754.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 196 | 248 | - |
| 33 | g16754.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 196 | 253 | - |
| 32 | g16754.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 346 | 405 | - |
| 31 | g16754.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 347 | 374 | - |
| 29 | g16754.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 375 | 394 | - |
| 3 | g16754.t1 | PANTHER | PTHR11073 | CALRETICULIN AND CALNEXIN | 1 | 402 | 4.4E-186 |
| 4 | g16754.t1 | PANTHER | PTHR11073:SF41 | CALRETICULIN | 1 | 402 | 4.4E-186 |
| 24 | g16754.t1 | PIRSF | PIRSF002356 | Calreticulin | 1 | 405 | 9.8E-197 |
| 7 | g16754.t1 | PRINTS | PR00626 | Calreticulin signature | 100 | 118 | 2.1E-53 |
| 6 | g16754.t1 | PRINTS | PR00626 | Calreticulin signature | 126 | 142 | 2.1E-53 |
| 8 | g16754.t1 | PRINTS | PR00626 | Calreticulin signature | 215 | 228 | 2.1E-53 |
| 10 | g16754.t1 | PRINTS | PR00626 | Calreticulin signature | 242 | 264 | 2.1E-53 |
| 5 | g16754.t1 | PRINTS | PR00626 | Calreticulin signature | 280 | 299 | 2.1E-53 |
| 9 | g16754.t1 | PRINTS | PR00626 | Calreticulin signature | 313 | 333 | 2.1E-53 |
| 1 | g16754.t1 | Pfam | PF00262 | Calreticulin family | 23 | 257 | 2.6E-59 |
| 2 | g16754.t1 | Pfam | PF00262 | Calreticulin family | 259 | 331 | 7.5E-23 |
| 20 | g16754.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 19 | - |
| 21 | g16754.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 22 | g16754.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 14 | - |
| 23 | g16754.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 15 | 19 | - |
| 19 | g16754.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 20 | 405 | - |
| 26 | g16754.t1 | ProSitePatterns | PS00803 | Calreticulin family signature 1. | 98 | 113 | - |
| 28 | g16754.t1 | ProSitePatterns | PS00804 | Calreticulin family signature 2. | 130 | 138 | - |
| 27 | g16754.t1 | ProSitePatterns | PS00805 | Calreticulin family repeated motif signature. | 242 | 254 | - |
| 34 | g16754.t1 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 19 | 6.0 |
| 11 | g16754.t1 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 16 | 218 | 2.69E-61 |
| 12 | g16754.t1 | SUPERFAMILY | SSF63887 | P-domain of calnexin/calreticulin | 201 | 314 | 6.41E-45 |
| 14 | g16754.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 19 | - |
| 25 | g16754.t1 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 13 | g16754.t1 | 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 transcript has been annotated with K08057 (calreticulin)
Pathway
- This transcript belongs to the following pathways
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.
