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.t7 TSS g10954.t7 12994140 12994140
chr_1 g10954 g10954.t7 isoform g10954.t7 12994757 12997205
chr_1 g10954 g10954.t7 exon g10954.t7.exon1 12994757 12995309
chr_1 g10954 g10954.t7 exon g10954.t7.exon2 12995556 12995816
chr_1 g10954 g10954.t7 exon g10954.t7.exon3 12995938 12996097
chr_1 g10954 g10954.t7 cds g10954.t7.CDS1 12996032 12996097
chr_1 g10954 g10954.t7 exon g10954.t7.exon4 12996151 12996228
chr_1 g10954 g10954.t7 cds g10954.t7.CDS2 12996151 12996228
chr_1 g10954 g10954.t7 exon g10954.t7.exon5 12996300 12996440
chr_1 g10954 g10954.t7 cds g10954.t7.CDS3 12996300 12996440
chr_1 g10954 g10954.t7 exon g10954.t7.exon6 12996774 12996902
chr_1 g10954 g10954.t7 cds g10954.t7.CDS4 12996774 12996902
chr_1 g10954 g10954.t7 exon g10954.t7.exon7 12996963 12997205
chr_1 g10954 g10954.t7 cds g10954.t7.CDS5 12996963 12997205
chr_1 g10954 g10954.t7 TTS g10954.t7 12997495 12997495

Sequences

>g10954.t7 Gene=g10954 Length=1565
ATGAACCTAAAACTATCGATAATATTACTGTTAAGCCTTAGCTGTTTAACGTTTTTAGTA
AATTGTGAAACTGATGAATTTGATGATGGTGTAGTCGTAGAAGACGAAGTAAGTATAATA
AAAATGATCATTGCACTCACATGATCAAGAAAAATTATTTCTTTTATTCATTAGGAGGAA
GTTAGTCAAAAGAAAGAAGATAAAATAGAATATCAAAGTCCTTATCCAGATCCGAATAAA
TTCTATTTGTCAGAACATTTCGACGATCTCAAACGATTCGAAGAGAAATGGGTTAAATCA
GAAGCCAAAAAAGACGATATTGCAGAAGAAATTGCAAAGTATGATGGTGAATGGAGCATT
GAAGCACCACAGCGTAGTATTCTTGATCGCGATCTTGGATTAGTACTGAAATCAAAAGCA
AAACATGCTGCTATATCGTCTCGTTTAAACAAACCATTTAAATTCGGAAATAAACCATTG
GTTGTTCAATATGAAGTAACTTTACAAGATGGACAAGAATGCGGTGGTAGTTATATCAAA
TTGCTGTCATCAGTTGATCATAAAGTTGTGAATGAAGGACATTTGTTAAAAGATATGAAT
CCAGCAATTAATCCACCTAAAGAAATCGATGATCCGACTGACTTCAAACCTGAATCATGG
GATGAACGTGAAAAAATTCCTGATCCTACAGCTATAAAGCCTGAAAATTTCGATGTTCCG
CCTCAAATACCAGACCCTAATGCTATTAAACCTGAGAATTGGTTAGATGATGAGGAAAGA
TTGATACCTGATCCTAATGCAGCAAAACCAGAGGACACTTATTATGATATTATGAAGGAA
AATGGGAACCACCACTGATTGAAAATCCATTATGTGAAAATAATGGTTGCGGAAAATGGG
AACAACCAATGATTGCTAATCCTGAATATAAAGGAAAATGGCGTGCACCTCTCATTGACA
ATCCAAATTATCAGGGTAAATGGTCACCAAGAAAAATTCCAAATCCCGATTTCTTTGAGG
ACAATGATCCGTTTACAAGAATAACTACTATTTCGGCTGTGGGAATTGAATTGTGGTCTA
TGTCGAATGATATTCTTTTTGATAATATTGTTGTAACTGATGATGAAACTCACGCCTATG
AATGGGCTCAACACACATATGATCTCAAACGCAAACATTTAGATAAGCAAGCTGAATCTT
TCGTTCAAAAAATGAAAAAGATAGTAAATGAAAATCCTTGGATAGTAGCGCTATTAGTAG
TTGTAATTGGCTTGCCAGTTTCAATTATTTTGTATATGCTATGCTCCTCTTCACCAAAGA
AGGTTGACGATTCCAAAAAGACTGATGCAGTTATTGATGATACTTACGATGAACCGCAAG
TAAAAGATCGAAGAAGTAAATTAGATCTCAATGAGCCTGAAGGTGAAACTGAAGAAGCGG
CAGTAGAAGGGGAGGAAATAAGCAATCAAGAAGCTGAAGAAGAAGAACCTGAGATAACAC
AAGTTACTGAGGAAATTAAATCTAGTGAACCAATTACAAGAAAGCGAAAAACGCGAAAAG
AATAA

>g10954.t7 Gene=g10954 Length=218
MIANPEYKGKWRAPLIDNPNYQGKWSPRKIPNPDFFEDNDPFTRITTISAVGIELWSMSN
DILFDNIVVTDDETHAYEWAQHTYDLKRKHLDKQAESFVQKMKKIVNENPWIVALLVVVI
GLPVSIILYMLCSSSPKKVDDSKKTDAVIDDTYDEPQVKDRRSKLDLNEPEGETEEAAVE
GEEISNQEAEEEEPEITQVTEEIKSSEPITRKRKTRKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g10954.t7 Gene3D G3DSA:2.10.250.10 Calnexin lumenal domain 1 42 4.3E-34
7 g10954.t7 Gene3D G3DSA:2.60.120.200 - 44 79 4.3E-34
14 g10954.t7 MobiDBLite mobidb-lite consensus disorder prediction 152 171 -
15 g10954.t7 MobiDBLite mobidb-lite consensus disorder prediction 152 218 -
13 g10954.t7 MobiDBLite mobidb-lite consensus disorder prediction 172 197 -
2 g10954.t7 PANTHER PTHR11073 CALRETICULIN AND CALNEXIN 1 192 7.0E-47
3 g10954.t7 PANTHER PTHR11073:SF7 CALMEGIN 1 192 7.0E-47
4 g10954.t7 PRINTS PR00626 Calreticulin signature 2 21 5.9E-14
5 g10954.t7 PRINTS PR00626 Calreticulin signature 50 70 5.9E-14
1 g10954.t7 Pfam PF00262 Calreticulin family 1 69 1.6E-31
9 g10954.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 110 -
11 g10954.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 111 131 -
10 g10954.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 132 218 -
6 g10954.t7 SUPERFAMILY SSF63887 P-domain of calnexin/calreticulin 1 42 1.57E-13
12 g10954.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 111 133 -

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