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.t7 TSS g1286.t7 9430319 9430319
chr_3 g1286 g1286.t7 isoform g1286.t7 9430438 9431354
chr_3 g1286 g1286.t7 exon g1286.t7.exon1 9430438 9430574
chr_3 g1286 g1286.t7 cds g1286.t7.CDS1 9430438 9430574
chr_3 g1286 g1286.t7 exon g1286.t7.exon2 9430645 9430811
chr_3 g1286 g1286.t7 cds g1286.t7.CDS2 9430645 9430811
chr_3 g1286 g1286.t7 exon g1286.t7.exon3 9430869 9430943
chr_3 g1286 g1286.t7 cds g1286.t7.CDS3 9430869 9430943
chr_3 g1286 g1286.t7 exon g1286.t7.exon4 9431228 9431354
chr_3 g1286 g1286.t7 cds g1286.t7.CDS4 9431228 9431235
chr_3 g1286 g1286.t7 TTS g1286.t7 9431763 9431763

Sequences

>g1286.t7 Gene=g1286 Length=506
ATGAAAACAAAAGTGGGATTAGTCGTTTTAGGCTTAATTTGCTTATTTGCAAACGTAAGA
GCAATTCGATTTAATTTGCAGCCAAATACACAAAAATGTTTAAGAGATGAAATAAATGCA
AATGTTTTGGTTGTTGGAGAATATGAAGTGTCACAAGCTCCCGGACAAGTAATTGATTAT
GAAGTCCGTGATACAAAGCAACACATTTTGTCTAAAAAGGAAGATATCTCAAGAGGAAAG
TTTAGTTTCACATCAGAAGTTTTTGATGTTTATGAGTTATGTTTTATCTCAAAAGTTCCA
CACAACGTTCGTGGTATTGTTCAAGAAATAAATATCAATATTAAAAAAGGTGTTGAGACA
AAATCATATGAAGGCGTAAATCGCTGAAGCAGCCAAATTGAAGCCACTTGAATTAGAGCT
TAAGAAGCTCGAAGATCTTTCAGATGCCATTGTTCAAGATTTTGCGTTAATGAGAAAACG
TGAAGAAGAAATGAGAGATACAAATG

>g1286.t7 Gene=g1286 Length=128
MKTKVGLVVLGLICLFANVRAIRFNLQPNTQKCLRDEINANVLVVGEYEVSQAPGQVIDY
EVRDTKQHILSKKEDISRGKFSFTSEVFDVYELCFISKVPHNVRGIVQEININIKKGVET
KSYEGVNR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g1286.t7 PANTHER PTHR22811 TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 13 125 4.3E-20
3 g1286.t7 PANTHER PTHR22811:SF184 TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 10 13 125 4.3E-20
1 g1286.t7 Pfam PF01105 emp24/gp25L/p24 family/GOLD 21 124 3.2E-15
8 g1286.t7 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
9 g1286.t7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
10 g1286.t7 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 16 -
11 g1286.t7 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
7 g1286.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 128 -
6 g1286.t7 ProSiteProfiles PS50866 GOLD domain profile. 31 116 13.198
5 g1286.t7 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -
4 g1286.t7 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.

Raw TPM values