General information for g16754.t17
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t17 | isoform | g16754.t17 | 10833895 | 10834929 |
| chr_4 | g16754 | g16754.t17 | exon | g16754.t17.exon1 | 10833895 | 10833907 |
| chr_4 | g16754 | g16754.t17 | cds | g16754.t17.CDS1 | 10833901 | 10833907 |
| chr_4 | g16754 | g16754.t17 | exon | g16754.t17.exon2 | 10834023 | 10834322 |
| chr_4 | g16754 | g16754.t17 | cds | g16754.t17.CDS2 | 10834023 | 10834322 |
| chr_4 | g16754 | g16754.t17 | exon | g16754.t17.exon3 | 10834387 | 10834929 |
| chr_4 | g16754 | g16754.t17 | cds | g16754.t17.CDS3 | 10834387 | 10834496 |
| chr_4 | g16754 | g16754.t17 | TTS | g16754.t17 | 10834937 | 10834937 |
| chr_4 | g16754 | g16754.t17 | TSS | g16754.t17 | NA | NA |
Sequences
>g16754.t17 Gene=g16754 Length=856
CCACCAATGGTAAAATACAAAGGTGAATGGAAACCAAAACAAATTGATAACCCAGCATAC
AAAGGAATCTGGAAGCATCCAGAAATTGACAATCCAGAATATACAGCTGATGCCAATCTT
TATCTCCGTGAAGAAGTTTGCGCTGTTGGTCTTGATCTCTGGCAAGTCAAATCAGGCACA
ATTTTTGACAATATTTTGTTCACTGATGATGCTGAATATGCTAAAGAAGCAGCTGCTACA
TTCAAGGCTACACAAGATGGTGAAAAGAAAATGAAAGATGAACAAGATGAAGAAGAAAAG
AAGAAGGCTGAAGCTGAAGCAAAAACAGAAGAAAAAGATGAAGACAATGAAGATTTAGAT
GATGAAGAAGACAAAGAAGACAGCAAAGGAGAAGCTGAAGCTGGAGATCATGATGAATTG
TAAAAACCTCACCGACGCTAAAAAATTATCCCAAAAAATTTATTTTCCTTCCCTTATCAT
CACATCCAAAACTTTGTTTTCATTTTTGTACTGAATAATTTCAAAACCGTGTCATTTTGT
GCAAAGAATTTCAATTTTTTATGTTTTTATAATTTTGAGAAATTTTCATCTCAATTTTGT
AGGAATAATTTAAATTATATTAATTTACAAAAGATAAAAAATACACAAACTTGAAAGTAT
AAAACTGTTGATAAGATCCTTCTTTAAAATTTGCTACACACACATAAATAGAAAAATTTC
ATTAATAATTTAGTTTTAATTTAAGTACATAAAAATAACAACTATCAAGTTTGATGTTTT
TATTAAAATCAACTTTTTTGTGTGCATGCAGAAGAAAAAATTACAATAAATTTTCTTTTA
AAAAAAATCAACAAAA
>g16754.t17 Gene=g16754 Length=138
MVKYKGEWKPKQIDNPAYKGIWKHPEIDNPEYTADANLYLREEVCAVGLDLWQVKSGTIF
DNILFTDDAEYAKEAAATFKATQDGEKKMKDEQDEEEKKKAEAEAKTEEKDEDNEDLDDE
EDKEDSKGEAEAGDHDEL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g16754.t17 | Coils | Coil | Coil | 86 | 123 | - |
| 10 | g16754.t17 | Gene3D | G3DSA:2.60.120.200 | - | 12 | 108 | 8.3E-20 |
| 9 | g16754.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 79 | 138 | - |
| 8 | g16754.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 80 | 107 | - |
| 7 | g16754.t17 | MobiDBLite | mobidb-lite | consensus disorder prediction | 108 | 127 | - |
| 2 | g16754.t17 | PANTHER | PTHR11073:SF42 | CALR PROTEIN | 3 | 136 | 9.4E-43 |
| 3 | g16754.t17 | PANTHER | PTHR11073 | CALRETICULIN AND CALNEXIN | 3 | 136 | 9.4E-43 |
| 5 | g16754.t17 | PRINTS | PR00626 | Calreticulin signature | 13 | 32 | 1.3E-16 |
| 4 | g16754.t17 | PRINTS | PR00626 | Calreticulin signature | 46 | 66 | 1.3E-16 |
| 1 | g16754.t17 | Pfam | PF00262 | Calreticulin family | 3 | 64 | 2.7E-18 |
| 6 | g16754.t17 | SUPERFAMILY | SSF63887 | P-domain of calnexin/calreticulin | 3 | 47 | 4.84E-14 |
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.
