Gene loci information

Transcript annotation

  • This transcript has been annotated as ER lumen protein-retaining receptor.

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 g14088 g14088.t8 TSS g14088.t8 34572860 34572860
chr_1 g14088 g14088.t8 isoform g14088.t8 34573527 34574243
chr_1 g14088 g14088.t8 exon g14088.t8.exon1 34573527 34573768
chr_1 g14088 g14088.t8 cds g14088.t8.CDS1 34573604 34573768
chr_1 g14088 g14088.t8 exon g14088.t8.exon2 34573830 34573976
chr_1 g14088 g14088.t8 cds g14088.t8.CDS2 34573830 34573976
chr_1 g14088 g14088.t8 exon g14088.t8.exon3 34574042 34574147
chr_1 g14088 g14088.t8 cds g14088.t8.CDS3 34574042 34574147
chr_1 g14088 g14088.t8 exon g14088.t8.exon4 34574209 34574243
chr_1 g14088 g14088.t8 cds g14088.t8.CDS4 34574209 34574243
chr_1 g14088 g14088.t8 TTS g14088.t8 34574484 34574484

Sequences

>g14088.t8 Gene=g14088 Length=530
AAATATTATTCGCAATAGTTTATTTTAGTCGTTATTTGGATCTTTTTACGACATTCATCA
GTCTTTACAACACCTTTATGAAAGTGGTGTTTATTGGTTCTTCACTTGGAACGTTGTACT
TGATGTACGGCAAATTTCGTGCTACATATGATCACAATCACGATTCATTCCGAATTGAAT
TCTTGCTCGTTCCTTGTGTTCTTCTCGGATTGCTCATCAATCATGATTTTACAGTTCTTG
AAGTATTATGGACATTCTCAATTTATTTGGAATCGGTAGCAATTTTACCTCAACTCTTCC
TTGTTAGTAAGACAGGAGAAGCGGAAAGTATTACAAGCCATTATCTTTTTGCACTTGGAT
CATATCGTGCATTGTATATTCTTAATTGGATTTACCGATACATTGTCGAAAGTCATTATG
ATTTGATTGCGATTGTAGCTGGTATTGTTCAGACAATTTTGTATTGCGATTTCTTCTATT
TGTATATAACGAAAGTGTTGAAAGGAAAAAAACTTCAATTACCAGCCTAG

>g14088.t8 Gene=g14088 Length=150
MKVVFIGSSLGTLYLMYGKFRATYDHNHDSFRIEFLLVPCVLLGLLINHDFTVLEVLWTF
SIYLESVAILPQLFLVSKTGEAESITSHYLFALGSYRALYILNWIYRYIVESHYDLIAIV
AGIVQTILYCDFFYLYITKVLKGKKLQLPA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g14088.t8 PANTHER PTHR10585 ER LUMEN PROTEIN RETAINING RECEPTOR 1 150 3.9E-76
3 g14088.t8 PANTHER PTHR10585:SF83 ER LUMEN PROTEIN-RETAINING RECEPTOR 2 1 150 3.9E-76
4 g14088.t8 PRINTS PR00660 ER lumen protein retaining receptor signature 58 78 2.2E-37
5 g14088.t8 PRINTS PR00660 ER lumen protein retaining receptor signature 80 94 2.2E-37
7 g14088.t8 PRINTS PR00660 ER lumen protein retaining receptor signature 94 112 2.2E-37
6 g14088.t8 PRINTS PR00660 ER lumen protein retaining receptor signature 122 137 2.2E-37
1 g14088.t8 Pfam PF00810 ER lumen protein retaining receptor 1 107 1.2E-43
13 g14088.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 30 -
19 g14088.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 31 51 -
16 g14088.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 52 56 -
21 g14088.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 57 77 -
15 g14088.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 78 88 -
20 g14088.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 110 -
17 g14088.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 111 115 -
18 g14088.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 137 -
14 g14088.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 138 150 -
12 g14088.t8 ProSitePatterns PS00952 ER lumen protein retaining receptor signature 2. 64 73 -
10 g14088.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 30 47 -
8 g14088.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 57 76 -
9 g14088.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 106 -
11 g14088.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 116 138 -

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:0046923 ER retention sequence binding MF
GO:0016021 integral component of membrane CC
GO:0006621 protein retention in ER lumen BP

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