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.t18 TSS g1286.t18 9430319 9430319
chr_3 g1286 g1286.t18 isoform g1286.t18 9430438 9431531
chr_3 g1286 g1286.t18 exon g1286.t18.exon1 9430438 9430574
chr_3 g1286 g1286.t18 cds g1286.t18.CDS1 9430438 9430574
chr_3 g1286 g1286.t18 exon g1286.t18.exon2 9430645 9430801
chr_3 g1286 g1286.t18 cds g1286.t18.CDS2 9430645 9430801
chr_3 g1286 g1286.t18 exon g1286.t18.exon3 9430869 9430939
chr_3 g1286 g1286.t18 cds g1286.t18.CDS3 9430869 9430895
chr_3 g1286 g1286.t18 exon g1286.t18.exon4 9431228 9431327
chr_3 g1286 g1286.t18 exon g1286.t18.exon5 9431429 9431531
chr_3 g1286 g1286.t18 TTS g1286.t18 9431763 9431763

Sequences

>g1286.t18 Gene=g1286 Length=568
ATGAAAACAAAAGTGGGATTAGTCGTTTTAGGCTTAATTTGCTTATTTGCAAACGTAAGA
GCAATTCGATTTAATTTGCAGCCAAATACACAAAAATGTTTAAGAGATGAAATAAATGCA
AATGTTTTGGTTGTTGGAGAATATGAAGTGTCACAAGCTCCCGGACAAGTAATTGATTAT
GAAGTCCGTGATACAAAGCAACACATTTTGTCTAAAAAGGAAGATATCTCAAGAGGAAAG
TTTAGTTTCACATCAGAAGTTTTTGATGTTTATGAGTTATGTTTTATCTCAAAAACGTTC
GTGGTATTGTTCAAGAAATAAATATCAATATTAAAAAAGGTGTTGAGACAAAATCATATG
AAGGCATCGCTGAAGCAGCCAAATTGAAGCCACTTGAATTAGAGCTTAAGAAGCTCGAAG
ATCTTTCAGATGCCATTGTTCAAGATTTTGCGTTAATGAGAAAACAGTTTTATTCTTCAG
TATATTTGGAATGTGCTGTCTTTTAGGACTCGCTACATGGCAAGTGCTTTATCTTAGAAG
ATATTTCATTGCTAAGAAGCTCATTTGA

>g1286.t18 Gene=g1286 Length=106
MKTKVGLVVLGLICLFANVRAIRFNLQPNTQKCLRDEINANVLVVGEYEVSQAPGQVIDY
EVRDTKQHILSKKEDISRGKFSFTSEVFDVYELCFISKTFVVLFKK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g1286.t18 PANTHER PTHR22811:SF183 TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 10 16 99 3.2E-15
3 g1286.t18 PANTHER PTHR22811 TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 16 99 3.2E-15
1 g1286.t18 Pfam PF01105 emp24/gp25L/p24 family/GOLD 21 98 1.9E-13
8 g1286.t18 Phobius SIGNAL_PEPTIDE Signal peptide region 1 21 -
9 g1286.t18 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 4 -
10 g1286.t18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 5 16 -
11 g1286.t18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 17 21 -
7 g1286.t18 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 22 106 -
6 g1286.t18 ProSiteProfiles PS50866 GOLD domain profile. 31 106 12.875
5 g1286.t18 SignalP_EUK SignalP-noTM SignalP-noTM 1 21 -
4 g1286.t18 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