Gene loci information

Transcript annotation

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

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 g12710 g12710.t26 TTS g12710.t26 25414039 25414039
chr_1 g12710 g12710.t26 isoform g12710.t26 25414443 25415531
chr_1 g12710 g12710.t26 exon g12710.t26.exon1 25414443 25415043
chr_1 g12710 g12710.t26 cds g12710.t26.CDS1 25414443 25415043
chr_1 g12710 g12710.t26 exon g12710.t26.exon2 25415101 25415326
chr_1 g12710 g12710.t26 cds g12710.t26.CDS2 25415101 25415326
chr_1 g12710 g12710.t26 exon g12710.t26.exon3 25415471 25415531
chr_1 g12710 g12710.t26 cds g12710.t26.CDS3 25415471 25415531
chr_1 g12710 g12710.t26 TSS g12710.t26 25415638 25415638

Sequences

>g12710.t26 Gene=g12710 Length=888
ATGAAGCATTCATTGCTATTAGTTCTTCTCATTTTACCTGCATTTCTATTTATTTTTGAT
GCTTATATAGGCAGCAAAGTGTTTGTTAGAGCAAATGAAGACGAAATTGATGAGGATTTA
GTTGATGTCGAAAATGAAGGTGATGCAGATGAAGCAAGTGAAAGTGCGCTGACTGGCGAT
GATGTGGAGGCAGATGAGACTGGTGAAAGTACGAAATCTCCTGATGCTGACACTCAATTG
CTCTTTGTTCGACCACTTTATACACCAGGATCACAACTTGAATTACCTGGCGGTGTTCCA
GTAGAGTTCTTAATTGGCTTCTTAAATAAAGGCAAAAATGATTTCATTATTGAGAGTGTT
GAAGCTTCATTCCGTTATCCAATGGATTTCACTTACTACATTCAAAATTTCTCAGCACTT
GCATATAACCGTGAAGTTAAATCAGAGAGTGAAGCAACTGTATCATACTCATTCCTTCCA
TCAGAACAATTTGCTGGTCGTCCTTTTGGTTTGAATATTGCCATTAGTTATCGTGATTCA
ACTGGTGCAGGTTTTATGGAAGCAGTTTTCAATGAAACTGTTCTCATCACAGAATTAGAT
GAAGGTCTTGATGGCGAAACATTCTTTTTATATGTGTTCTTTGCAGCTATTTTTGTTTTA
CTTCTTGTTGTTGGACAACAATTCCTCGGTTCAATTGGCAAGAAGAAACGTTCACAAAAC
ATTCGTAAGCAAGTTGAGACTGGTACATCAAATAACACCGATATTGATTATGAATGGCTT
CCTGCTCAAACAATTAGAAATTTACAAAATTCACCAAATGGCAAAGGAAAAATCTCGCCA
AAACAGAGTCCAAGACAACGTTCAAAACGTGCTGCAAAGGAAGATTAA

>g12710.t26 Gene=g12710 Length=295
MKHSLLLVLLILPAFLFIFDAYIGSKVFVRANEDEIDEDLVDVENEGDADEASESALTGD
DVEADETGESTKSPDADTQLLFVRPLYTPGSQLELPGGVPVEFLIGFLNKGKNDFIIESV
EASFRYPMDFTYYIQNFSALAYNREVKSESEATVSYSFLPSEQFAGRPFGLNIAISYRDS
TGAGFMEAVFNETVLITELDEGLDGETFFLYVFFAAIFVLLLVVGQQFLGSIGKKKRSQN
IRKQVETGTSNNTDIDYEWLPAQTIRNLQNSPNGKGKISPKQSPRQRSKRAAKED

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g12710.t26 MobiDBLite mobidb-lite consensus disorder prediction 44 64 -
9 g12710.t26 MobiDBLite mobidb-lite consensus disorder prediction 44 74 -
7 g12710.t26 MobiDBLite mobidb-lite consensus disorder prediction 266 295 -
8 g12710.t26 MobiDBLite mobidb-lite consensus disorder prediction 266 281 -
2 g12710.t26 PANTHER PTHR12924:SF0 TRANSLOCON-ASSOCIATED PROTEIN SUBUNIT ALPHA 4 288 2.3E-69
3 g12710.t26 PANTHER PTHR12924 TRANSLOCON-ASSOCIATED PROTEIN, ALPHA SUBUNIT 4 288 2.3E-69
1 g12710.t26 Pfam PF03896 Translocon-associated protein (TRAP), alpha subunit 5 294 2.7E-114
13 g12710.t26 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
14 g12710.t26 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
15 g12710.t26 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 16 -
17 g12710.t26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
12 g12710.t26 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 207 -
16 g12710.t26 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 208 229 -
11 g12710.t26 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 230 295 -
10 g12710.t26 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -
4 g12710.t26 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 24 -
5 g12710.t26 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 211 233 -

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:0005789 endoplasmic reticulum 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