Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Peptide transporter family 1.

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 g13638 g13638.t3 isoform g13638.t3 31380680 31381190
chr_1 g13638 g13638.t3 exon g13638.t3.exon1 31380680 31381190
chr_1 g13638 g13638.t3 cds g13638.t3.CDS1 31380758 31381093
chr_1 g13638 g13638.t3 TTS g13638.t3 31381167 31381167
chr_1 g13638 g13638.t3 TSS g13638.t3 NA NA

Sequences

>g13638.t3 Gene=g13638 Length=511
TTATAGGTTACTGATGTTCTTATTGTCACCGAACCAAATTCAGTTAGTATGTTATGGTTG
ATACCACAATATGTCATTATGACACTCGGTGAAGTCATGTATTCAGTCACAGGTCTTCAA
TTTTCATATACACAAGCTCCTGAAAGTATGAAGTCAGTCTTACAAGGCTGTTGGCAGCTG
ACTGTTGGCGTTGGAAATTTAATCGTTACAATTATTGTTGGTGCGAAATTCTTCAATTCG
CAAACATATGAATTTTTACTGTTTGCATTGTTGATGTTTGTTGATATGGGAATATTCATG
TGGCTTGGTATTCGATATAAGCCAATTCCTCTTGACCAATTGAAAAATGTTGAAGAAGAT
GACAATGAGACCAAAAAAGCTGATCCTTTAGATTTCAAACCTCACGACAATTAAAATCAT
GATGACTTTTAGTTTTTTATTGCAAATATAAGTTTTCTTCTTTTATACATCAATAAAAAT
ATTTTTTGAAAAAAAAAATTAAAAATTTTAT

>g13638.t3 Gene=g13638 Length=111
MTLGEVMYSVTGLQFSYTQAPESMKSVLQGCWQLTVGVGNLIVTIIVGAKFFNSQTYEFL
LFALLMFVDMGIFMWLGIRYKPIPLDQLKNVEEDDNETKKADPLDFKPHDN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g13638.t3 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 1 97 1.4E-21
7 g13638.t3 MobiDBLite mobidb-lite consensus disorder prediction 91 111 -
2 g13638.t3 PANTHER PTHR11654 OLIGOPEPTIDE TRANSPORTER-RELATED 1 91 1.7E-34
3 g13638.t3 PANTHER PTHR11654:SF465 - 1 91 1.7E-34
1 g13638.t3 Pfam PF00854 POT family 1 47 4.8E-6
11 g13638.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 31 -
12 g13638.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 32 52 -
9 g13638.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 53 58 -
13 g13638.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 78 -
10 g13638.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 79 111 -
6 g13638.t3 SUPERFAMILY SSF103473 MFS general substrate transporter 3 92 2.88E-5
5 g13638.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 30 52 -
4 g13638.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 78 -

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:0016020 membrane CC
GO:0055085 transmembrane transport BP
GO:0022857 transmembrane transporter activity MF

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