General information for g10954.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Calnexin.
Parent gene
- The parent gene g10954 is located on chr_1: 12996310..12997205 (+ 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_1 | g10954 | g10954.t4 | TSS | g10954.t4 | 12994140 | 12994140 |
| chr_1 | g10954 | g10954.t4 | isoform | g10954.t4 | 12994229 | 12997205 |
| chr_1 | g10954 | g10954.t4 | exon | g10954.t4.exon1 | 12994229 | 12994233 |
| chr_1 | g10954 | g10954.t4 | exon | g10954.t4.exon2 | 12994709 | 12994864 |
| chr_1 | g10954 | g10954.t4 | cds | g10954.t4.CDS1 | 12994757 | 12994864 |
| chr_1 | g10954 | g10954.t4 | exon | g10954.t4.exon3 | 12994931 | 12995816 |
| chr_1 | g10954 | g10954.t4 | cds | g10954.t4.CDS2 | 12994931 | 12995816 |
| chr_1 | g10954 | g10954.t4 | exon | g10954.t4.exon4 | 12995938 | 12996097 |
| chr_1 | g10954 | g10954.t4 | cds | g10954.t4.CDS3 | 12995938 | 12995981 |
| chr_1 | g10954 | g10954.t4 | exon | g10954.t4.exon5 | 12996151 | 12996228 |
| chr_1 | g10954 | g10954.t4 | exon | g10954.t4.exon6 | 12996300 | 12996440 |
| chr_1 | g10954 | g10954.t4 | exon | g10954.t4.exon7 | 12996774 | 12996902 |
| chr_1 | g10954 | g10954.t4 | exon | g10954.t4.exon8 | 12996963 | 12997205 |
| chr_1 | g10954 | g10954.t4 | TTS | g10954.t4 | 12997495 | 12997495 |
Sequences
>g10954.t4 Gene=g10954 Length=1798
ACTAGAGTTTAGCGAAATTAACAAAATAATATAGGAAGATTCTAGTGAAAATAATGAACC
TAAAACTATCGATAATATTACTGTTAAGCCTTAGCTGTTTAACGTTTTTAGTAAATTGTG
AAACTGATGAATTTGATGATGGTGTAGTCGTAGAAGACGAAGAGGAAGTTAGTCAAAAGA
AAGAAGATAAAATAGAATATCAAAGTCCTTATCCAGATCCGAATAAATTCTATTTGTCAG
AACATTTCGACGATCTCAAACGATTCGAAGAGAAATGGGTTAAATCAGAAGCCAAAAAAG
ACGATATTGCAGAAGAAATTGCAAAGTATGATGGTGAATGGAGCATTGAAGCACCACAGC
GTAGTATTCTTGATCGCGATCTTGGATTAGTACTGAAATCAAAAGCAAAACATGCTGCTA
TATCGTCTCGTTTAAACAAACCATTTAAATTCGGAAATAAACCATTGGTTGTTCAATATG
AAGTAACTTTACAAGATGGACAAGAATGCGGTGGTAGTTATATCAAATTGCTGTCATCAG
GTGCTGCTACTACTGATTTAAAAAGCTTTCACGATAAAACTCCATATACTATCATGTTTG
GACCAGATAAATGTGGAAATGATATTAAATTACATTTCATTCTTCGTCATGTTAATCCTA
AAAATGGTTCAATTGAAGAGAAACATAGCAAGAAACCAAAAGATCGCATTGAGGAACCAT
TTAAAGACAAACAACCACATCTTTATAAATTAGTTCTTAAACCAGACAATACTTTCCAAA
TTTCAGTTGATCATAAAGTTGTGAATGAAGGACATTTGTTAAAAGATATGAATCCAGCAA
TTAATCCACCTAAAGAAATCGATGATCCGACTGACTTCAAACCTGAATCATGGGATGAAC
GTGAAAAAATTCCTGATCCTACAGCTATAAAGCCTGAAAATTTCGATGTTCCGCCTCAAA
TACCAGACCCTAATGCTATTAAACCTGAGAATTGGTTAGATGATGAGGAAAGATTGATAC
CTGATCCTAATGCAGCAAAACCAGAGGACACTTATTATGATATTATGAAGGAAAATGGGA
ACCACCACTGATTGAAAATCCATTATGTGAAAATAATGGTTGCGGAAAATGGGAACAACC
AATGATTGCTAATCCTGAATATAAAGGAAAATGGCGTGCACCTCTCATTGACAATCCAAA
TTATCAGGGTAAATGGTCACCAAGAAAAATTCCAAATCCCGATTTCTTTGAGGACAATGA
TCCGTTTACAAGAATAACTACTATTTCGGCTGTGGGAATTGAATTGTGGTCTATGTCGAA
TGATATTCTTTTTGATAATATTGTTGTAACTGATGATGAAACTCACGCCTATGAATGGGC
TCAACACACATATGATCTCAAACGCAAACATTTAGATAAGCAAGCTGAATCTTTCGTTCA
AAAAATGAAAAAGATAGTAAATGAAAATCCTTGGATAGTAGCGCTATTAGTAGTTGTAAT
TGGCTTGCCAGTTTCAATTATTTTGTATATGCTATGCTCCTCTTCACCAAAGAAGGTTGA
CGATTCCAAAAAGACTGATGCAGTTATTGATGATACTTACGATGAACCGCAAGTAAAAGA
TCGAAGAAGTAAATTAGATCTCAATGAGCCTGAAGGTGAAACTGAAGAAGCGGCAGTAGA
AGGGGAGGAAATAAGCAATCAAGAAGCTGAAGAAGAAGAACCTGAGATAACACAAGTTAC
TGAGGAAATTAAATCTAGTGAACCAATTACAAGAAAGCGAAAAACGCGAAAAGAATAA
>g10954.t4 Gene=g10954 Length=345
MNLKLSIILLLSLSCLTFLVNCETDEFDDGVVVEDEEEVSQKKEDKIEYQSPYPDPNKFY
LSEHFDDLKRFEEKWVKSEAKKDDIAEEIAKYDGEWSIEAPQRSILDRDLGLVLKSKAKH
AAISSRLNKPFKFGNKPLVVQYEVTLQDGQECGGSYIKLLSSGAATTDLKSFHDKTPYTI
MFGPDKCGNDIKLHFILRHVNPKNGSIEEKHSKKPKDRIEEPFKDKQPHLYKLVLKPDNT
FQISVDHKVVNEGHLLKDMNPAINPPKEIDDPTDFKPESWDEREKIPDPTAIKPENFDVP
PQIPDPNAIKPENWLDDEERLIPDPNAAKPEDTYYDIMKENGNHH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g10954.t4 | Gene3D | G3DSA:2.60.120.200 | - | 49 | 263 | 1.6E-84 |
| 13 | g10954.t4 | Gene3D | G3DSA:2.10.250.10 | Calnexin lumenal domain | 264 | 342 | 3.2E-19 |
| 21 | g10954.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 275 | 306 | - |
| 22 | g10954.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 275 | 291 | - |
| 23 | g10954.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 321 | 345 | - |
| 2 | g10954.t4 | PANTHER | PTHR11073:SF11 | CALNEXIN | 39 | 336 | 2.8E-113 |
| 3 | g10954.t4 | PANTHER | PTHR11073 | CALRETICULIN AND CALNEXIN | 39 | 336 | 2.8E-113 |
| 7 | g10954.t4 | PRINTS | PR00626 | Calreticulin signature | 147 | 165 | 1.8E-23 |
| 6 | g10954.t4 | PRINTS | PR00626 | Calreticulin signature | 176 | 192 | 1.8E-23 |
| 4 | g10954.t4 | PRINTS | PR00626 | Calreticulin signature | 276 | 289 | 1.8E-23 |
| 5 | g10954.t4 | PRINTS | PR00626 | Calreticulin signature | 303 | 325 | 1.8E-23 |
| 1 | g10954.t4 | Pfam | PF00262 | Calreticulin family | 62 | 333 | 8.2E-102 |
| 15 | g10954.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 22 | - |
| 16 | g10954.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 6 | - |
| 17 | g10954.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 7 | 18 | - |
| 18 | g10954.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 19 | 22 | - |
| 14 | g10954.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 23 | 345 | - |
| 20 | g10954.t4 | ProSitePatterns | PS00804 | Calreticulin family signature 2. | 180 | 188 | - |
| 24 | g10954.t4 | ProSiteProfiles | PS51257 | Prokaryotic membrane lipoprotein lipid attachment site profile. | 1 | 15 | 5.0 |
| 8 | g10954.t4 | SUPERFAMILY | SSF49899 | Concanavalin A-like lectins/glucanases | 54 | 272 | 8.55E-60 |
| 9 | g10954.t4 | SUPERFAMILY | SSF63887 | P-domain of calnexin/calreticulin | 263 | 333 | 1.83E-19 |
| 11 | g10954.t4 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 22 | - |
| 19 | g10954.t4 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 20 | - |
| 10 | g10954.t4 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 24 | - |
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.
