Gene loci information

Transcript annotation

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

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 g7546 g7546.t1 TTS g7546.t1 24457655 24457655
chr_2 g7546 g7546.t1 isoform g7546.t1 24457824 24459128
chr_2 g7546 g7546.t1 exon g7546.t1.exon1 24457824 24458024
chr_2 g7546 g7546.t1 cds g7546.t1.CDS1 24457824 24458024
chr_2 g7546 g7546.t1 exon g7546.t1.exon2 24458083 24458460
chr_2 g7546 g7546.t1 cds g7546.t1.CDS2 24458083 24458460
chr_2 g7546 g7546.t1 exon g7546.t1.exon3 24458603 24458664
chr_2 g7546 g7546.t1 cds g7546.t1.CDS3 24458603 24458664
chr_2 g7546 g7546.t1 TSS g7546.t1 24458694 24458694
chr_2 g7546 g7546.t1 exon g7546.t1.exon4 24459122 24459128
chr_2 g7546 g7546.t1 cds g7546.t1.CDS4 24459122 24459128

Sequences

>g7546.t1 Gene=g7546 Length=648
ATGACAAAAAGTAATTTTCATAATAATTTAATTAATTCGCAAAGTACACTCTATTATAAA
ATAATTAAGATGAACAAGCTAGTGAAATGTCTTGCATTATTCTTCTTTGCATCAATGGTG
ATGGCTACTGATTCAGGAGATTCTCGAGCACGATTATTAGTTTCAAAACAAATCCTCAAT
AAATATCTTGTTGAACAACGCGATGTCATGGTAAAATATACTTTATTCAATATTGGAAAT
GGTGCCGCCACACACGTCAGCTTAGAAGATCAAGGTTTTCCAGCTGAAGCTTTTGATTTA
GTCAGCGGAAAGTTGGAAGTTCAAATTGATAGAATTGCACCAGCTACAAATGTCACTCAT
GTAGTTGTTGTTCGACCAAGAGCGCACGGATACTTTAACTTCACTGCAGCTGCTATTAGC
TACCGTCCAGTTGAATCATCACCAGCTCTTCAATACGCAATTAGTTCAGAGCCAGGCGAA
GGTGGAATTATTAATTTGGCTCAATTCAACAAACAATTCTCATCACATCTCTTTGATTGG
ATTGCTTTCGTCATCATGTGTCTCCCAACAGTAGCCATTCCATACAGTTTATTCTACAAA
TCAAAGACAAAGTACGAGCTCTTGGCACAAAAGAAAAAGGCCAACTAA

>g7546.t1 Gene=g7546 Length=215
MTKSNFHNNLINSQSTLYYKIIKMNKLVKCLALFFFASMVMATDSGDSRARLLVSKQILN
KYLVEQRDVMVKYTLFNIGNGAATHVSLEDQGFPAEAFDLVSGKLEVQIDRIAPATNVTH
VVVVRPRAHGYFNFTAAAISYRPVESSPALQYAISSEPGEGGIINLAQFNKQFSSHLFDW
IAFVIMCLPTVAIPYSLFYKSKTKYELLAQKKKAN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g7546.t1 PANTHER PTHR12861:SF3 TRANSLOCON-ASSOCIATED PROTEIN SUBUNIT BETA 24 212 7.3E-50
4 g7546.t1 PANTHER PTHR12861 TRANSLOCON-ASSOCIATED PROTEIN, BETA SUBUNIT PRECURSOR TRAP-BETA SIGNAL SEQUENCE RECEPTOR BETA SUBUNIT 24 212 7.3E-50
14 g7546.t1 PIRSF PIRSF016400 TRAP-beta 24 214 7.2E-68
2 g7546.t1 Pfam PF05753 Translocon-associated protein beta (TRAPB) 33 207 4.9E-63
9 g7546.t1 Phobius SIGNAL_PEPTIDE Signal peptide region 1 42 -
10 g7546.t1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 26 -
11 g7546.t1 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 27 37 -
13 g7546.t1 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 38 42 -
8 g7546.t1 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 43 176 -
12 g7546.t1 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 177 198 -
7 g7546.t1 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 199 215 -
1 g7546.t1 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM 1 42 -
6 g7546.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 21 43 -
5 g7546.t1 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 177 199 -

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:0005783 endoplasmic reticulum CC
GO:0016021 integral component of membrane CC

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

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