Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Sodium-coupled monocarboxylate transporter 2.

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.t3 isoform g12037.t3 20583721 20584878
chr_1 g12037 g12037.t3 exon g12037.t3.exon1 20583721 20584322
chr_1 g12037 g12037.t3 cds g12037.t3.CDS1 20583815 20584322
chr_1 g12037 g12037.t3 exon g12037.t3.exon2 20584382 20584605
chr_1 g12037 g12037.t3 cds g12037.t3.CDS2 20584382 20584605
chr_1 g12037 g12037.t3 exon g12037.t3.exon3 20584793 20584878
chr_1 g12037 g12037.t3 cds g12037.t3.CDS3 20584793 20584840
chr_1 g12037 g12037.t3 TTS g12037.t3 20584990 20584990
chr_1 g12037 g12037.t3 TSS g12037.t3 NA NA

Sequences

>g12037.t3 Gene=g12037 Length=912
TTTACGATTAGATCCTACAATTAGACATTCATTTTGGACAATTGTGATTGGTTTTACATT
CCTTCAAATCTCAGCTAATGGTTTAAATCAGAATATGATTCAAAGATTTATGGCTCTAAG
CACTGTAAGAAAAGCAAGAATAGGGAATGTAATCAACATCATAGGCATCATCATCATGAT
TTCAGTGTCATGTTATAATGGTCTCTTAACATATGCAATTTATTACAATTGTGATCCTCT
AACAACAGGACTTGCTAAAGCTAAAGATCAATTACTACCACTCATGGTTATGGAAAACTT
TACTGATATTCCTGGTTTAGCTGGTTTCTTTGTGGCTGGTGTTTTTGCTGCCGCTCTTAG
CACATTGTCAACTGCTTACAATTCAATGGCTGCTGTCGTTTTTGAAGATTTCTTCAAAAG
AAATTCAAAGAAAGGAGTTTCTGATGCTATGACATTTATAATTATGCGTGGCACTGTTTT
GGCATTTGGAACTGTTAGTGTTTTGCTTGTATATATTGTGCAACATATGGGTCAATTGCT
ACAGCTCACATTCTCAATTCCTGCTACTTCACTTGGTCCAATGCTTGGTGTGTTTATAAT
TGGATTGATGATTCCATGGATAGGAAAAAGAGCAACATTTTATAGTGTGATTATCGTTTA
CTTTTCAATGCTCGCTTTTGTATTGAAAGCACAATTTCAAGTTGCTCAAGGAACGATAAA
ATTTGATGAACGTCCAACATCGACTGAAGGATGTCTCTATAATTTTACTAGTGATTTTAC
TACAACGACAATTTCTTCAATTTCTTCAACAACATTAATTCCTGAATGTGTGAAAAAGAT
GAAAATGATAATGAAGATCGTGGGCTTGAAATGAATTTTTGGAAAAATTCAAAGTCTGAT
GTAAAAATGTAA

>g12037.t3 Gene=g12037 Length=259
MIQRFMALSTVRKARIGNVINIIGIIIMISVSCYNGLLTYAIYYNCDPLTTGLAKAKDQL
LPLMVMENFTDIPGLAGFFVAGVFAAALSTLSTAYNSMAAVVFEDFFKRNSKKGVSDAMT
FIIMRGTVLAFGTVSVLLVYIVQHMGQLLQLTFSIPATSLGPMLGVFIIGLMIPWIGKRA
TFYSVIIVYFSMLAFVLKAQFQVAQGTIKFDERPTSTEGCLYNFTSDFTTTTISSISSTT
LIPECVKKMKMIMKIVGLK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g12037.t3 Gene3D G3DSA:1.20.1730.10 - 1 255 4.8E-39
2 g12037.t3 PANTHER PTHR42985 SODIUM-COUPLED MONOCARBOXYLATE TRANSPORTER 1 255 7.2E-78
3 g12037.t3 PANTHER PTHR42985:SF5 LP24461P 1 255 7.2E-78
1 g12037.t3 Pfam PF00474 Sodium:solute symporter family 2 187 5.6E-12
13 g12037.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 19 -
20 g12037.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 43 -
15 g12037.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 44 71 -
19 g12037.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 72 97 -
14 g12037.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 98 117 -
22 g12037.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 118 142 -
16 g12037.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 143 147 -
21 g12037.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 148 173 -
12 g12037.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 174 179 -
18 g12037.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 180 197 -
17 g12037.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 198 259 -
10 g12037.t3 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile. 1 33 5.0
11 g12037.t3 ProSiteProfiles PS50283 Sodium:solute symporter family profile. 1 202 22.195
4 g12037.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
7 g12037.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 78 100 -
6 g12037.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 121 143 -
8 g12037.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 153 175 -
5 g12037.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 182 204 -

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