Gene loci information

Transcript annotation

  • This transcript has been annotated as Calnexin.

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_1 g10954 g10954.t6 TSS g10954.t6 12994140 12994140
chr_1 g10954 g10954.t6 isoform g10954.t6 12994396 12996438
chr_1 g10954 g10954.t6 exon g10954.t6.exon1 12994396 12994643
chr_1 g10954 g10954.t6 exon g10954.t6.exon2 12994709 12994864
chr_1 g10954 g10954.t6 cds g10954.t6.CDS1 12994757 12994864
chr_1 g10954 g10954.t6 exon g10954.t6.exon3 12994931 12995816
chr_1 g10954 g10954.t6 cds g10954.t6.CDS2 12994931 12995816
chr_1 g10954 g10954.t6 exon g10954.t6.exon4 12995938 12996097
chr_1 g10954 g10954.t6 cds g10954.t6.CDS3 12995938 12995981
chr_1 g10954 g10954.t6 exon g10954.t6.exon5 12996151 12996228
chr_1 g10954 g10954.t6 exon g10954.t6.exon6 12996300 12996438
chr_1 g10954 g10954.t6 TTS g10954.t6 NA NA

Sequences

>g10954.t6 Gene=g10954 Length=1667
GGTAGACATTTTTAATATTAAAGGAAATTATAAAAGAAAATGTGTATTGTAATAAAATTA
GAACATTGTTTCAGTAAAATATTACTTGATATTGAAAGTTAGAACTATTCCTGTTTCATT
ATAATTGAAAAAAACACGTCAGATTTTTCCGTCAAAATTAGGTTATCAGTTTATTTAATT
TAATTAAGCACTTGCAGAGAGAAATAAATGAATAAGCAAAAAGGGTTTTCAATCGCTAGT
AGAATTTTAGTTTAGCGAAATTAACAAAATAATATAGGAAGATTCTAGTGAAAATAATGA
ACCTAAAACTATCGATAATATTACTGTTAAGCCTTAGCTGTTTAACGTTTTTAGTAAATT
GTGAAACTGATGAATTTGATGATGGTGTAGTCGTAGAAGACGAAGAGGAAGTTAGTCAAA
AGAAAGAAGATAAAATAGAATATCAAAGTCCTTATCCAGATCCGAATAAATTCTATTTGT
CAGAACATTTCGACGATCTCAAACGATTCGAAGAGAAATGGGTTAAATCAGAAGCCAAAA
AAGACGATATTGCAGAAGAAATTGCAAAGTATGATGGTGAATGGAGCATTGAAGCACCAC
AGCGTAGTATTCTTGATCGCGATCTTGGATTAGTACTGAAATCAAAAGCAAAACATGCTG
CTATATCGTCTCGTTTAAACAAACCATTTAAATTCGGAAATAAACCATTGGTTGTTCAAT
ATGAAGTAACTTTACAAGATGGACAAGAATGCGGTGGTAGTTATATCAAATTGCTGTCAT
CAGGTGCTGCTACTACTGATTTAAAAAGCTTTCACGATAAAACTCCATATACTATCATGT
TTGGACCAGATAAATGTGGAAATGATATTAAATTACATTTCATTCTTCGTCATGTTAATC
CTAAAAATGGTTCAATTGAAGAGAAACATAGCAAGAAACCAAAAGATCGCATTGAGGAAC
CATTTAAAGACAAACAACCACATCTTTATAAATTAGTTCTTAAACCAGACAATACTTTCC
AAATTTCAGTTGATCATAAAGTTGTGAATGAAGGACATTTGTTAAAAGATATGAATCCAG
CAATTAATCCACCTAAAGAAATCGATGATCCGACTGACTTCAAACCTGAATCATGGGATG
AACGTGAAAAAATTCCTGATCCTACAGCTATAAAGCCTGAAAATTTCGATGTTCCGCCTC
AAATACCAGACCCTAATGCTATTAAACCTGAGAATTGGTTAGATGATGAGGAAAGATTGA
TACCTGATCCTAATGCAGCAAAACCAGAGGACACTTATTATGATATTATGAAGGAAAATG
GGAACCACCACTGATTGAAAATCCATTATGTGAAAATAATGGTTGCGGAAAATGGGAACA
ACCAATGATTGCTAATCCTGAATATAAAGGAAAATGGCGTGCACCTCTCATTGACAATCC
AAATTATCAGGGTAAATGGTCACCAAGAAAAATTCCAAATCCCGATTTCTTTGAGGACAA
TGATCCGTTTACAAGAATAACTACTATTTCGGCTGTGGGAATTGAATTGTGGTCTATGTC
GAATGATATTCTTTTTGATAATATTGTTGTAACTGATGATGAAACTCACGCCTATGAATG
GGCTCAACACACATATGATCTCAAACGCAAACATTTAGATAAGCAAG

>g10954.t6 Gene=g10954 Length=345
MNLKLSIILLLSLSCLTFLVNCETDEFDDGVVVEDEEEVSQKKEDKIEYQSPYPDPNKFY
LSEHFDDLKRFEEKWVKSEAKKDDIAEEIAKYDGEWSIEAPQRSILDRDLGLVLKSKAKH
AAISSRLNKPFKFGNKPLVVQYEVTLQDGQECGGSYIKLLSSGAATTDLKSFHDKTPYTI
MFGPDKCGNDIKLHFILRHVNPKNGSIEEKHSKKPKDRIEEPFKDKQPHLYKLVLKPDNT
FQISVDHKVVNEGHLLKDMNPAINPPKEIDDPTDFKPESWDEREKIPDPTAIKPENFDVP
PQIPDPNAIKPENWLDDEERLIPDPNAAKPEDTYYDIMKENGNHH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10954.t6 Gene3D G3DSA:2.60.120.200 - 49 263 1.6E-84
13 g10954.t6 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 264 342 3.2E-19
21 g10954.t6 MobiDBLite mobidb-lite consensus disorder prediction 275 306 -
22 g10954.t6 MobiDBLite mobidb-lite consensus disorder prediction 275 291 -
23 g10954.t6 MobiDBLite mobidb-lite consensus disorder prediction 321 345 -
2 g10954.t6 PANTHER PTHR11073:SF11 CALNEXIN 39 336 2.8E-113
3 g10954.t6 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 39 336 2.8E-113
7 g10954.t6 PRINTS PR00626 Calreticulin signature 147 165 1.8E-23
6 g10954.t6 PRINTS PR00626 Calreticulin signature 176 192 1.8E-23
4 g10954.t6 PRINTS PR00626 Calreticulin signature 276 289 1.8E-23
5 g10954.t6 PRINTS PR00626 Calreticulin signature 303 325 1.8E-23
1 g10954.t6 Pfam PF00262 Calreticulin family 62 333 8.2E-102
15 g10954.t6 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
16 g10954.t6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 6 -
17 g10954.t6 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 7 18 -
18 g10954.t6 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 19 22 -
14 g10954.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 345 -
20 g10954.t6 ProSitePatterns PS00804 Calreticulin family signature 2. 180 188 -
24 g10954.t6 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 15 5.0
8 g10954.t6 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 54 272 8.55E-60
9 g10954.t6 SUPERFAMILY SSF63887 P-domain of calnexin/calreticulin 263 333 1.83E-19
11 g10954.t6 SignalP_EUK SignalP-noTM SignalP-noTM 1 22 -
19 g10954.t6 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 20 -
10 g10954.t6 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.

Raw TPM values