Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Transmembrane emp24 domain-containing protein bai.

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_3 g1286 g1286.t17 TSS g1286.t17 9430319 9430319
chr_3 g1286 g1286.t17 isoform g1286.t17 9430438 9431531
chr_3 g1286 g1286.t17 exon g1286.t17.exon1 9430438 9430574
chr_3 g1286 g1286.t17 cds g1286.t17.CDS1 9430438 9430574
chr_3 g1286 g1286.t17 exon g1286.t17.exon2 9430645 9430811
chr_3 g1286 g1286.t17 cds g1286.t17.CDS2 9430645 9430811
chr_3 g1286 g1286.t17 exon g1286.t17.exon3 9430869 9430939
chr_3 g1286 g1286.t17 cds g1286.t17.CDS3 9430869 9430939
chr_3 g1286 g1286.t17 exon g1286.t17.exon4 9431241 9431354
chr_3 g1286 g1286.t17 cds g1286.t17.CDS4 9431241 9431249
chr_3 g1286 g1286.t17 exon g1286.t17.exon5 9431413 9431531
chr_3 g1286 g1286.t17 TTS g1286.t17 9431763 9431763

Sequences

>g1286.t17 Gene=g1286 Length=608
ATGAAAACAAAAGTGGGATTAGTCGTTTTAGGCTTAATTTGCTTATTTGCAAACGTAAGA
GCAATTCGATTTAATTTGCAGCCAAATACACAAAAATGTTTAAGAGATGAAATAAATGCA
AATGTTTTGGTTGTTGGAGAATATGAAGTGTCACAAGCTCCCGGACAAGTAATTGATTAT
GAAGTCCGTGATACAAAGCAACACATTTTGTCTAAAAAGGAAGATATCTCAAGAGGAAAG
TTTAGTTTCACATCAGAAGTTTTTGATGTTTATGAGTTATGTTTTATCTCAAAAGTTCCA
CACAACGTTCGTGGTATTGTTCAAGAAATAAATATCAATATTAAAAAAGGTGTTGAGACA
AAATCATATGAAGGCCCAAATTGAAGCCACTTGAATTAGAGCTTAAGAAGCTCGAAGATC
TTTCAGATGCCATTGTTCAAGATTTTGCGTTAATGAGAAAACGTGAAGAAGAAATGAGAG
ATACAAATGAATCAACAAACAATAGAGTTTTATTCTTCAGTATATTTGGAATGTGCTGTC
TTTTAGGACTCGCTACATGGCAAGTGCTTTATCTTAGAAGATATTTCATTGCTAAGAAGC
TCATTTGA

>g1286.t17 Gene=g1286 Length=127
MKTKVGLVVLGLICLFANVRAIRFNLQPNTQKCLRDEINANVLVVGEYEVSQAPGQVIDY
EVRDTKQHILSKKEDISRGKFSFTSEVFDVYELCFISKVPHNVRGIVQEININIKKGVET
KSYEGPN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g1286.t17 PANTHER PTHR22811 TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 13 124 8.3E-20
3 g1286.t17 PANTHER PTHR22811:SF184 TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 10 13 124 8.3E-20
1 g1286.t17 Pfam PF01105 emp24/gp25L/p24 family/GOLD 21 123 4.3E-15
8 g1286.t17 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
9 g1286.t17 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
10 g1286.t17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 16 -
11 g1286.t17 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
7 g1286.t17 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 127 -
6 g1286.t17 ProSiteProfiles PS50866 GOLD domain profile. 31 116 13.198
5 g1286.t17 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -
4 g1286.t17 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 22 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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