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.t9 TTS g6506.t9 17322930 17322930
chr_2 g6506 g6506.t9 isoform g6506.t9 17323115 17323836
chr_2 g6506 g6506.t9 exon g6506.t9.exon1 17323115 17323533
chr_2 g6506 g6506.t9 cds g6506.t9.CDS1 17323115 17323444
chr_2 g6506 g6506.t9 exon g6506.t9.exon2 17323711 17323836
chr_2 g6506 g6506.t9 TSS g6506.t9 17323893 17323893

Sequences

>g6506.t9 Gene=g6506 Length=545
ATGGTTCAAGAAAAGAAATCAGCTATGTTTACAAAGGAAGAAGAGCTCCTTTTACAGGAT
TTTAATAGAAATGTATCAACTGGCTCAAATATGCTTTTTTACGGCGCGAGCTTCATAACA
TCAGCTGGCTCTATTGGAGAATTCATCAAATTGAATTATTCTCTTCACTCATCTTTTTTG
TTGCATTAACTGCTTTGAGCACCTACTTGCTATCAATGGCCTACAGAAACACCAAATTCA
CTCTTAAGCATAAAGTTGCAATCAAACGTGAAGATGCTGTAACTCGTGAAATGACACAAT
TATTGGCTGATGATAAAATGTCACGAAAAGAAAAGGATGAAAGAATTTTGTGGAAGAAAA
ATGAAGTTGCTGATTTTGAAGCTACTGTTTTCTCAATCTTCTATAACAATGCACTTTTCT
TAGCAATTACCATCTTCTTAAGCTTCTACTTGCTTCGTCAAATCTCACCATTATTCAACT
ATATTATCACAATTGCTGGAACATCAGGACTTTTAGCATTGCTCTCAACCAGCAAGTCAA
CATAA

>g6506.t9 Gene=g6506 Length=109
MAYRNTKFTLKHKVAIKREDAVTREMTQLLADDKMSRKEKDERILWKKNEVADFEATVFS
IFYNNALFLAITIFLSFYLLRQISPLFNYIITIAGTSGLLALLSTSKST

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g6506.t9 PANTHER PTHR13399 TRANSLOCON-ASSOCIATED PROTEIN TRAP , GAMMA SUBUNIT 1 107 3.1E-47
1 g6506.t9 Pfam PF07074 Translocon-associated protein, gamma subunit (TRAP-gamma) 1 106 3.6E-50
5 g6506.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 55 -
9 g6506.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 56 80 -
7 g6506.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 81 85 -
8 g6506.t9 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 86 103 -
6 g6506.t9 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 104 109 -
4 g6506.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 58 80 -
3 g6506.t9 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 85 104 -

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