Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Translocon-associated protein subunit gamma.

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_2 g6506 g6506.t11 TTS g6506.t11 17322930 17322930
chr_2 g6506 g6506.t11 isoform g6506.t11 17323115 17323836
chr_2 g6506 g6506.t11 exon g6506.t11.exon1 17323115 17323236
chr_2 g6506 g6506.t11 cds g6506.t11.CDS1 17323219 17323236
chr_2 g6506 g6506.t11 exon g6506.t11.exon2 17323382 17323533
chr_2 g6506 g6506.t11 cds g6506.t11.CDS2 17323382 17323533
chr_2 g6506 g6506.t11 exon g6506.t11.exon3 17323701 17323836
chr_2 g6506 g6506.t11 cds g6506.t11.CDS3 17323701 17323836
chr_2 g6506 g6506.t11 TSS g6506.t11 17323893 17323893

Sequences

>g6506.t11 Gene=g6506 Length=410
ATGGTTCAAGAAAAGAAATCAGCTATGTTTACAAAGGAAGAAGAGCTCCTTTTACAGGAT
TTTAATAGAAATGTATCAACTGGCTCAAATATGCTTTTTTACGGCGCGAGCTTCATAACA
TCAGCTTTGCCAATCTGGCTCTATTGGAGAATTCATCAAATTGAATTATTCTCTTCACTC
ATCTTTTTTGTTGCATTAACTGCTTTGAGCACCTACTTGCTATCAATGGCCTACAGAAAC
ACCAAATTCACTCTTAAGCATAAAGTTGCAATCAAACGTGAAGATGCTCAATTACCATCT
TCTTAAGCTTCTACTTGCTTCGTCAAATCTCACCATTATTCAACTATATTATCACAATTG
CTGGAACATCAGGACTTTTAGCATTGCTCTCAACCAGCAAGTCAACATAA

>g6506.t11 Gene=g6506 Length=101
MVQEKKSAMFTKEEELLLQDFNRNVSTGSNMLFYGASFITSALPIWLYWRIHQIELFSSL
IFFVALTALSTYLLSMAYRNTKFTLKHKVAIKREDAQLPSS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g6506.t11 PANTHER PTHR13399 TRANSLOCON-ASSOCIATED PROTEIN TRAP , GAMMA SUBUNIT 6 96 1.8E-32
1 g6506.t11 Pfam PF07074 Translocon-associated protein, gamma subunit (TRAP-gamma) 13 96 2.1E-35
6 g6506.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 30 -
8 g6506.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 31 51 -
7 g6506.t11 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 52 56 -
9 g6506.t11 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 57 78 -
5 g6506.t11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 101 -
3 g6506.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 27 49 -
4 g6506.t11 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 56 78 -

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:0006614 SRP-dependent cotranslational protein targeting to membrane BP
GO:0016021 integral component of membrane CC

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