Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t8 TSS g10954.t8 12994140 12994140
chr_1 g10954 g10954.t8 isoform g10954.t8 12994931 12995816
chr_1 g10954 g10954.t8 exon g10954.t8.exon1 12994931 12995816
chr_1 g10954 g10954.t8 cds g10954.t8.CDS1 12995363 12995815
chr_1 g10954 g10954.t8 TTS g10954.t8 NA NA

Sequences

>g10954.t8 Gene=g10954 Length=886
GAGGAAGTTAGTCAAAAGAAAGAAGATAAAATAGAATATCAAAGTCCTTATCCAGATCCG
AATAAATTCTATTTGTCAGAACATTTCGACGATCTCAAACGATTCGAAGAGAAATGGGTT
AAATCAGAAGCCAAAAAAGACGATATTGCAGAAGAAATTGCAAAGTATGATGGTGAATGG
AGCATTGAAGCACCACAGCGTAGTATTCTTGATCGCGATCTTGGATTAGTACTGAAATCA
AAAGCAAAACATGCTGCTATATCGTCTCGTTTAAACAAACCATTTAAATTCGGAAATAAA
CCATTGGTTGTTCAATATGAAGTAACTTTACAAGATGGACAAGAATGCGGTGGTAGTTAT
ATCAAATTGCTGTCATCAGGTGCTGCTACTACTGATTTAAAAAGCTTTCACGATAAAACT
CCATATACTATCATGTTTGGACCAGATAAATGTGGAAATGATATTAAATTACATTTCATT
CTTCGTCATGTTAATCCTAAAAATGGTTCAATTGAAGAGAAACATAGCAAGAAACCAAAA
GATCGCATTGAGGAACCATTTAAAGACAAACAACCACATCTTTATAAATTAGTTCTTAAA
CCAGACAATACTTTCCAAATTTCAGTTGATCATAAAGTTGTGAATGAAGGACATTTGTTA
AAAGATATGAATCCAGCAATTAATCCACCTAAAGAAATCGATGATCCGACTGACTTCAAA
CCTGAATCATGGGATGAACGTGAAAAAATTCCTGATCCTACAGCTATAAAGCCTGAAAAT
TTCGATGTTCCGCCTCAAATACCAGACCCTAATGCTATTAAACCTGAGAATTGGTTAGAT
GATGAGGAAAGATTGATACCTGATCCTAATGCAGCAAAACCAGAGG

>g10954.t8 Gene=g10954 Length=151
MFGPDKCGNDIKLHFILRHVNPKNGSIEEKHSKKPKDRIEEPFKDKQPHLYKLVLKPDNT
FQISVDHKVVNEGHLLKDMNPAINPPKEIDDPTDFKPESWDEREKIPDPTAIKPENFDVP
PQIPDPNAIKPENWLDDEERLIPDPNAAKPE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g10954.t8 Gene3D G3DSA:2.60.120.200 - 1 83 4.0E-30
13 g10954.t8 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 84 151 1.5E-18
9 g10954.t8 MobiDBLite mobidb-lite consensus disorder prediction 23 44 -
10 g10954.t8 MobiDBLite mobidb-lite consensus disorder prediction 79 151 -
8 g10954.t8 MobiDBLite mobidb-lite consensus disorder prediction 89 111 -
11 g10954.t8 MobiDBLite mobidb-lite consensus disorder prediction 131 151 -
2 g10954.t8 PANTHER PTHR11073:SF11 CALNEXIN 1 151 4.3E-61
3 g10954.t8 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 1 151 4.3E-61
4 g10954.t8 PRINTS PR00626 Calreticulin signature 96 109 6.0E-7
5 g10954.t8 PRINTS PR00626 Calreticulin signature 123 145 6.0E-7
1 g10954.t8 Pfam PF00262 Calreticulin family 1 151 4.0E-54
6 g10954.t8 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 1 92 2.22E-20
7 g10954.t8 SUPERFAMILY SSF63887 P-domain of calnexin/calreticulin 83 151 3.66E-19

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. There were no conditions that were differentially expressed