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.t4 TSS g14088.t4 34572860 34572860
chr_1 g14088 g14088.t4 isoform g14088.t4 34572934 34574243
chr_1 g14088 g14088.t4 exon g14088.t4.exon1 34572934 34573024
chr_1 g14088 g14088.t4 cds g14088.t4.CDS1 34572934 34573024
chr_1 g14088 g14088.t4 exon g14088.t4.exon2 34573509 34573768
chr_1 g14088 g14088.t4 cds g14088.t4.CDS2 34573509 34573768
chr_1 g14088 g14088.t4 exon g14088.t4.exon3 34573830 34574243
chr_1 g14088 g14088.t4 cds g14088.t4.CDS3 34573830 34573982
chr_1 g14088 g14088.t4 TTS g14088.t4 34574484 34574484

Sequences

>g14088.t4 Gene=g14088 Length=765
ATGAATATATTTAGATTAGCCGGTGATTTGTCGCACTTATTAGCCATAATTATATTGCTC
CTTAAAATATGGAAAACGAGGTCTTGTGCAGGAATTTCCGGCAAATCACAAATATTATTC
GCAATAGTTTATTTTAGTCGTTATTTGGATCTTTTTACGACATTCATCAGTCTTTACAAC
ACCTTTATGAAAGTGGTGTTTATTGGTTCTTCACTTGGAACGTTGTACTTGATGTACGGC
AAATTTCGTGCTACATATGATCACAATCACGATTCATTCCGAATTGAATTCTTGCTCGTT
CCTTGTGTTCTTCTCGGATTGCTCATCAATCATGATTTTACAGTTCTTGAAGTATTATGG
ACATTCTCAATTTATTTGGAATCGGTAGCAATTTTACCTCAACTCTTCCTTGTTAGTAAG
ACAGGAGAAGCGGAAAGTATTACAAGCCATTATCTTTTTGCACTTGGATCATATCGTGCA
TTGTATATTCTTAATTGGGTATGAATGTTATTAAAACTTATCTATTAAATTATTGAAATT
TTTATATAATCTATTCTTAATAGATTTACCGATACATTGTCGAAAGTCATTATGATTTGA
TTGCGATTGTAGCTGGTATTGTTCAGACAATTTTGTATTGCGATTTCTTCTATTTGTATA
TAACGAAAGGTATGCAAAAATTATTATAGATATTTAATTTTTTTCCTAATTTGAATTCTT
CTTTTTGCAGTGTTGAAAGGAAAAAAACTTCAATTACCAGCCTAG

>g14088.t4 Gene=g14088 Length=167
MNIFRLAGDLSHLLAIIILLLKIWKTRSCAGISGKSQILFAIVYFSRYLDLFTTFISLYN
TFMKVVFIGSSLGTLYLMYGKFRATYDHNHDSFRIEFLLVPCVLLGLLINHDFTVLEVLW
TFSIYLESVAILPQLFLVSKTGEAESITSHYLFALGSYRALYILNWV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g14088.t4 PANTHER PTHR10585 ER LUMEN PROTEIN RETAINING RECEPTOR 1 167 4.3E-88
3 g14088.t4 PANTHER PTHR10585:SF83 ER LUMEN PROTEIN-RETAINING RECEPTOR 2 1 167 4.3E-88
7 g14088.t4 PRINTS PR00660 ER lumen protein retaining receptor signature 4 23 1.2E-59
6 g14088.t4 PRINTS PR00660 ER lumen protein retaining receptor signature 31 51 1.2E-59
5 g14088.t4 PRINTS PR00660 ER lumen protein retaining receptor signature 52 68 1.2E-59
9 g14088.t4 PRINTS PR00660 ER lumen protein retaining receptor signature 120 140 1.2E-59
4 g14088.t4 PRINTS PR00660 ER lumen protein retaining receptor signature 142 156 1.2E-59
8 g14088.t4 PRINTS PR00660 ER lumen protein retaining receptor signature 156 167 1.2E-59
1 g14088.t4 Pfam PF00810 ER lumen protein retaining receptor 28 167 4.0E-56
19 g14088.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
25 g14088.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 24 -
17 g14088.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 25 35 -
22 g14088.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 36 56 -
20 g14088.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 57 61 -
24 g14088.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 62 80 -
16 g14088.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 81 91 -
23 g14088.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 92 109 -
18 g14088.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 110 114 -
21 g14088.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 115 138 -
15 g14088.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 139 167 -
14 g14088.t4 ProSitePatterns PS00951 ER lumen protein retaining receptor signature 1. 31 48 -
13 g14088.t4 ProSitePatterns PS00952 ER lumen protein retaining receptor signature 2. 126 135 -
10 g14088.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
12 g14088.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 92 109 -
11 g14088.t4 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. There were no conditions that were differentially expressed