Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Sodium-coupled monocarboxylate transporter 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 g12037 g12037.t2 TSS g12037.t2 20582347 20582347
chr_1 g12037 g12037.t2 isoform g12037.t2 20582404 20583856
chr_1 g12037 g12037.t2 exon g12037.t2.exon1 20582404 20582539
chr_1 g12037 g12037.t2 cds g12037.t2.CDS1 20582404 20582539
chr_1 g12037 g12037.t2 exon g12037.t2.exon2 20582608 20582757
chr_1 g12037 g12037.t2 cds g12037.t2.CDS2 20582608 20582757
chr_1 g12037 g12037.t2 exon g12037.t2.exon3 20582827 20582960
chr_1 g12037 g12037.t2 cds g12037.t2.CDS3 20582827 20582960
chr_1 g12037 g12037.t2 exon g12037.t2.exon4 20583062 20583145
chr_1 g12037 g12037.t2 cds g12037.t2.CDS4 20583062 20583145
chr_1 g12037 g12037.t2 exon g12037.t2.exon5 20583204 20583236
chr_1 g12037 g12037.t2 cds g12037.t2.CDS5 20583204 20583236
chr_1 g12037 g12037.t2 exon g12037.t2.exon6 20583304 20583373
chr_1 g12037 g12037.t2 cds g12037.t2.CDS6 20583304 20583373
chr_1 g12037 g12037.t2 exon g12037.t2.exon7 20583509 20583663
chr_1 g12037 g12037.t2 cds g12037.t2.CDS7 20583509 20583531
chr_1 g12037 g12037.t2 exon g12037.t2.exon8 20583721 20583856
chr_1 g12037 g12037.t2 TTS g12037.t2 NA NA

Sequences

>g12037.t2 Gene=g12037 Length=898
ATGACAGAAAACATAACGACGACACCAAAAATATCCATCCAAGACCTAAGTGTCTCAATT
CAAAGATTTGGCGTTGTTGACTATATGATTTTTCTAGGCATGCTAATTTTCTGCACTTTC
ATTGGAATGTATTTTGGTTGGCAAGATCATAAAAGGCGGAAACGATTAATTAGACAAGAT
TCAGCAACACAAGCTGCAGATTATTTGATGGGTGGTCGTGATATGCCAGTCATTCCAATT
GCATTGTCGCTAACTGCATCATTAGTATCAGGAAATATGTTGCTAGGAACTGCCACTGAA
ATGTATCTTTATGGATCGCAGTACATCTTTGCAGTAATTTCACTTGCTCTCTGTGGCCTA
GCCATGCACTATATTATAATTCCAGTATTTCATGGCCTTCAAATAACATCAACATACGAG
TATCTAGAGAGACGTTTTGATAAAAGATTACGAATGTTTGGGTCATTGATGTTTATGATA
GGTGTAAACCTCTTTTTGCCTATCGTCATTTATGTTCCCGCTTTGGCATTTAATCAAACA
ACAGGCATTAATGTTCACATTATTACACCTTTGTGCTTGATAATTTGTGTATTTTACACA
TGTTTAGTACAATATATTATTTTTATTTAGGACTGATGTTGTGCAAGTTATTATTTTGTA
TGTTACACTTTTTGTCATTGCAATTAAGGGAACAATTCAAGTTGGTGGTTTATCAGTGCT
TCTTGAAAGAAATAGAGAAAGTGGAAGATTACAAGGCCCAGATTTACGATTAGATCCTAC
AATTAGACATTCATTTTGGACAATTGTGATTGGTTTTACATTCCTTCAAATCTCAGCTAA
TGGTTTAAATCAGAATATGATTCAAAGATTTATGGCTCTAAGCACTGTAAGAAAAGCA

>g12037.t2 Gene=g12037 Length=209
MTENITTTPKISIQDLSVSIQRFGVVDYMIFLGMLIFCTFIGMYFGWQDHKRRKRLIRQD
SATQAADYLMGGRDMPVIPIALSLTASLVSGNMLLGTATEMYLYGSQYIFAVISLALCGL
AMHYIIIPVFHGLQITSTYEYLERRFDKRLRMFGSLMFMIGVNLFLPIVIYVPALAFNQT
TGINVHIITPLCLIICVFYTCLVQYIIFI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g12037.t2 Gene3D G3DSA:1.20.1730.10 - 57 202 9.0E-40
2 g12037.t2 PANTHER PTHR42985 SODIUM-COUPLED MONOCARBOXYLATE TRANSPORTER 16 202 3.4E-74
3 g12037.t2 PANTHER PTHR42985:SF5 LP24461P 16 202 3.4E-74
1 g12037.t2 Pfam PF00474 Sodium:solute symporter family 68 201 1.4E-11
15 g12037.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 27 -
20 g12037.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 28 47 -
12 g12037.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 48 76 -
18 g12037.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 77 96 -
16 g12037.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 97 107 -
17 g12037.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 108 131 -
13 g12037.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 132 151 -
21 g12037.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 152 175 -
14 g12037.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 176 186 -
19 g12037.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 187 208 -
11 g12037.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 209 209 -
10 g12037.t2 ProSiteProfiles PS50283 Sodium:solute symporter family profile. 24 209 21.173
8 g12037.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 25 47 -
5 g12037.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 77 99 -
7 g12037.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 109 131 -
6 g12037.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 152 171 -
4 g12037.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 186 208 -

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. There were no conditions that were differentially expressed