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.t9 TSS g10954.t9 12994140 12994140
chr_1 g10954 g10954.t9 isoform g10954.t9 12994931 12997205
chr_1 g10954 g10954.t9 exon g10954.t9.exon1 12994931 12995816
chr_1 g10954 g10954.t9 cds g10954.t9.CDS1 12995363 12995816
chr_1 g10954 g10954.t9 exon g10954.t9.exon2 12995948 12996097
chr_1 g10954 g10954.t9 cds g10954.t9.CDS2 12995948 12995958
chr_1 g10954 g10954.t9 exon g10954.t9.exon3 12996151 12996228
chr_1 g10954 g10954.t9 exon g10954.t9.exon4 12996300 12996440
chr_1 g10954 g10954.t9 exon g10954.t9.exon5 12996774 12996902
chr_1 g10954 g10954.t9 exon g10954.t9.exon6 12996963 12997205
chr_1 g10954 g10954.t9 TTS g10954.t9 12997495 12997495

Sequences

>g10954.t9 Gene=g10954 Length=1627
GAGGAAGTTAGTCAAAAGAAAGAAGATAAAATAGAATATCAAAGTCCTTATCCAGATCCG
AATAAATTCTATTTGTCAGAACATTTCGACGATCTCAAACGATTCGAAGAGAAATGGGTT
AAATCAGAAGCCAAAAAAGACGATATTGCAGAAGAAATTGCAAAGTATGATGGTGAATGG
AGCATTGAAGCACCACAGCGTAGTATTCTTGATCGCGATCTTGGATTAGTACTGAAATCA
AAAGCAAAACATGCTGCTATATCGTCTCGTTTAAACAAACCATTTAAATTCGGAAATAAA
CCATTGGTTGTTCAATATGAAGTAACTTTACAAGATGGACAAGAATGCGGTGGTAGTTAT
ATCAAATTGCTGTCATCAGGTGCTGCTACTACTGATTTAAAAAGCTTTCACGATAAAACT
CCATATACTATCATGTTTGGACCAGATAAATGTGGAAATGATATTAAATTACATTTCATT
CTTCGTCATGTTAATCCTAAAAATGGTTCAATTGAAGAGAAACATAGCAAGAAACCAAAA
GATCGCATTGAGGAACCATTTAAAGACAAACAACCACATCTTTATAAATTAGTTCTTAAA
CCAGACAATACTTTCCAAATTTCAGTTGATCATAAAGTTGTGAATGAAGGACATTTGTTA
AAAGATATGAATCCAGCAATTAATCCACCTAAAGAAATCGATGATCCGACTGACTTCAAA
CCTGAATCATGGGATGAACGTGAAAAAATTCCTGATCCTACAGCTATAAAGCCTGAAAAT
TTCGATGTTCCGCCTCAAATACCAGACCCTAATGCTATTAAACCTGAGAATTGGTTAGAT
GATGAGGAAAGATTGATACCTGATCCTAATGCAGCAAAACCAGAGGTGATATTATGAAGG
AAAATGGGAACCACCACTGATTGAAAATCCATTATGTGAAAATAATGGTTGCGGAAAATG
GGAACAACCAATGATTGCTAATCCTGAATATAAAGGAAAATGGCGTGCACCTCTCATTGA
CAATCCAAATTATCAGGGTAAATGGTCACCAAGAAAAATTCCAAATCCCGATTTCTTTGA
GGACAATGATCCGTTTACAAGAATAACTACTATTTCGGCTGTGGGAATTGAATTGTGGTC
TATGTCGAATGATATTCTTTTTGATAATATTGTTGTAACTGATGATGAAACTCACGCCTA
TGAATGGGCTCAACACACATATGATCTCAAACGCAAACATTTAGATAAGCAAGCTGAATC
TTTCGTTCAAAAAATGAAAAAGATAGTAAATGAAAATCCTTGGATAGTAGCGCTATTAGT
AGTTGTAATTGGCTTGCCAGTTTCAATTATTTTGTATATGCTATGCTCCTCTTCACCAAA
GAAGGTTGACGATTCCAAAAAGACTGATGCAGTTATTGATGATACTTACGATGAACCGCA
AGTAAAAGATCGAAGAAGTAAATTAGATCTCAATGAGCCTGAAGGTGAAACTGAAGAAGC
GGCAGTAGAAGGGGAGGAAATAAGCAATCAAGAAGCTGAAGAAGAAGAACCTGAGATAAC
ACAAGTTACTGAGGAAATTAAATCTAGTGAACCAATTACAAGAAAGCGAAAAACGCGAAA
AGAATAA

>g10954.t9 Gene=g10954 Length=154
MFGPDKCGNDIKLHFILRHVNPKNGSIEEKHSKKPKDRIEEPFKDKQPHLYKLVLKPDNT
FQISVDHKVVNEGHLLKDMNPAINPPKEIDDPTDFKPESWDEREKIPDPTAIKPENFDVP
PQIPDPNAIKPENWLDDEERLIPDPNAAKPEVIL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g10954.t9 Gene3D G3DSA:2.60.120.200 - 1 83 4.2E-30
12 g10954.t9 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 84 153 5.2E-19
10 g10954.t9 MobiDBLite mobidb-lite consensus disorder prediction 22 43 -
9 g10954.t9 MobiDBLite mobidb-lite consensus disorder prediction 79 126 -
8 g10954.t9 MobiDBLite mobidb-lite consensus disorder prediction 89 111 -
2 g10954.t9 PANTHER PTHR11073:SF11 CALNEXIN 1 151 2.2E-61
3 g10954.t9 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 1 151 2.2E-61
4 g10954.t9 PRINTS PR00626 Calreticulin signature 96 109 6.1E-7
5 g10954.t9 PRINTS PR00626 Calreticulin signature 123 145 6.1E-7
1 g10954.t9 Pfam PF00262 Calreticulin family 1 151 1.9E-54
6 g10954.t9 SUPERFAMILY SSF49899 Concanavalin A-like lectins/glucanases 1 92 2.37E-20
7 g10954.t9 SUPERFAMILY SSF63887 P-domain of calnexin/calreticulin 83 151 1.44E-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.

Raw TPM values