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.t19 TSS g1286.t19 9430319 9430319
chr_3 g1286 g1286.t19 isoform g1286.t19 9430438 9431531
chr_3 g1286 g1286.t19 exon g1286.t19.exon1 9430438 9430574
chr_3 g1286 g1286.t19 exon g1286.t19.exon2 9430645 9430801
chr_3 g1286 g1286.t19 cds g1286.t19.CDS1 9430786 9430801
chr_3 g1286 g1286.t19 exon g1286.t19.exon3 9430869 9430939
chr_3 g1286 g1286.t19 cds g1286.t19.CDS2 9430869 9430939
chr_3 g1286 g1286.t19 exon g1286.t19.exon4 9431228 9431354
chr_3 g1286 g1286.t19 cds g1286.t19.CDS3 9431228 9431354
chr_3 g1286 g1286.t19 exon g1286.t19.exon5 9431413 9431531
chr_3 g1286 g1286.t19 cds g1286.t19.CDS4 9431413 9431531
chr_3 g1286 g1286.t19 TTS g1286.t19 9431763 9431763

Sequences

>g1286.t19 Gene=g1286 Length=611
ATGAAAACAAAAGTGGGATTAGTCGTTTTAGGCTTAATTTGCTTATTTGCAAACGTAAGA
GCAATTCGATTTAATTTGCAGCCAAATACACAAAAATGTTTAAGAGATGAAATAAATGCA
AATGTTTTGGTTGTTGGAGAATATGAAGTGTCACAAGCTCCCGGACAAGTAATTGATTAT
GAAGTCCGTGATACAAAGCAACACATTTTGTCTAAAAAGGAAGATATCTCAAGAGGAAAG
TTTAGTTTCACATCAGAAGTTTTTGATGTTTATGAGTTATGTTTTATCTCAAAAACGTTC
GTGGTATTGTTCAAGAAATAAATATCAATATTAAAAAAGGTGTTGAGACAAAATCATATG
AAGGCATCGCTGAAGCAGCCAAATTGAAGCCACTTGAATTAGAGCTTAAGAAGCTCGAAG
ATCTTTCAGATGCCATTGTTCAAGATTTTGCGTTAATGAGAAAACGTGAAGAAGAAATGA
GAGATACAAATGAATCAACAAACAATAGAGTTTTATTCTTCAGTATATTTGGAATGTGCT
GTCTTTTAGGACTCGCTACATGGCAAGTGCTTTATCTTAGAAGATATTTCATTGCTAAGA
AGCTCATTTGA

>g1286.t19 Gene=g1286 Length=110
MFYLKNVRGIVQEININIKKGVETKSYEGIAEAAKLKPLELELKKLEDLSDAIVQDFALM
RKREEEMRDTNESTNNRVLFFSIFGMCCLLGLATWQVLYLRRYFIAKKLI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g1286.t19 PANTHER PTHR22811:SF183 TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 10 12 109 1.7E-42
3 g1286.t19 PANTHER PTHR22811 TRANSMEMBRANE EMP24 DOMAIN-CONTAINING PROTEIN 12 109 1.7E-42
1 g1286.t19 Pfam PF01105 emp24/gp25L/p24 family/GOLD 12 104 3.2E-26
7 g1286.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 77 -
8 g1286.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 78 100 -
6 g1286.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 101 110 -
5 g1286.t19 SMART SM01190 EMP24_GP25L_2 1 105 1.8E-8
4 g1286.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 78 100 -

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