Gene loci information

Transcript annotation

  • This transcript has been annotated as 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_3 g3434 g3434.t5 TTS g3434.t5 25415495 25415495
chr_3 g3434 g3434.t5 isoform g3434.t5 25415651 25417833
chr_3 g3434 g3434.t5 exon g3434.t5.exon1 25415651 25416112
chr_3 g3434 g3434.t5 cds g3434.t5.CDS1 25415651 25416112
chr_3 g3434 g3434.t5 exon g3434.t5.exon2 25416168 25416657
chr_3 g3434 g3434.t5 cds g3434.t5.CDS2 25416168 25416657
chr_3 g3434 g3434.t5 exon g3434.t5.exon3 25416767 25416864
chr_3 g3434 g3434.t5 cds g3434.t5.CDS3 25416767 25416864
chr_3 g3434 g3434.t5 exon g3434.t5.exon4 25416926 25416968
chr_3 g3434 g3434.t5 cds g3434.t5.CDS4 25416926 25416968
chr_3 g3434 g3434.t5 exon g3434.t5.exon5 25417087 25417240
chr_3 g3434 g3434.t5 cds g3434.t5.CDS5 25417087 25417235
chr_3 g3434 g3434.t5 exon g3434.t5.exon6 25417302 25417370
chr_3 g3434 g3434.t5 exon g3434.t5.exon7 25417431 25417482
chr_3 g3434 g3434.t5 exon g3434.t5.exon8 25417534 25417570
chr_3 g3434 g3434.t5 exon g3434.t5.exon9 25417757 25417833
chr_3 g3434 g3434.t5 TSS g3434.t5 NA NA

Sequences

>g3434.t5 Gene=g3434 Length=1482
AAGTCGCTTTATTTTATTGATCAATAAGAAGTTTCTAGAGATAAATTCAAAACTAGAGTG
TCTTTGCATTGAATTCATCAATCGAGTCACTTACTATATCGTAGATGATAATATATTGTG
TGGTTGCCCATCGTTATATTTGTTCCTGCATTAGCGCTTAATCATGTGTCTGGCATTGAT
GTACATTTGATAACACCATTAACGTGTGTCTGCTGCATTTTCTATACATGTGTTGGTGGA
ATGAAAGCGGTGATTTACACAGATGTCTTTCAATCGCTAATGATGTTTGGAGCAATGTTG
TTAGTCATTATTAAAGGCACTTACGATATAGGCGGATTGGATGTTGTGATTACGCGCAAT
GTCGCGAGTAAACGTATCGAAGCACCAGACACATCATTTGACTTAACTGAACGCCATACA
ATATGGTCGTTGTGCATAGGAGGTTTTGTATATTGGCTTAAAGCGAACGCAATCAGTCAA
AATATGATTCAACGTTATTTATCATTGCCAAGTTTAGCGGCAGCCAAAAGAGCACTATGG
ATCTTTATCTCTGGCGTTTTTATTTTACTGGCCATTTGCTCCTATTGTGGATTATTGATT
TATGCAACCTACTTTGAATGTGACCCGCTTACAACAAAACTAGTCAAAGCAAAAGATCAA
TTGCTACCGCTGCTTGTTATGGACATTTTGGGTGAATATCCAGGATTAGTTGGCATGTTT
GTCGCTGGAGTATTTTCTGCTGCACTCTCGTCACTCTCAACGGGACTTAACAGTATGTCA
GCAGTAATTTTAGAAGACTTCTTTAAACCATTCTCGAGAAAGCCACTGACCGATCGTCAG
ACCAAATACATCATGAGAAGTGTTGTAGTGATTTTTGGTGGCATTTGTGTGGCATTAGTT
TATGTAGTTGAACATTTGGGCTCCGTGCTAATGCTCTCAATGTCGCTTGGCAGCATAGCA
CAAGGTCCACTGCTTGGTGTATTTACATGTGGTGTATTATTTCCATGGGTGACGGGAACT
GGCGCATTGGTGGGCAGTGCAACAGCTCTATCATTTATGACGTGGCTTTGCATCAGTGCT
CAACGGGCGATCTCAACAGGCGAATTGAAATTCAGTACTAAGGAAATTTCTACAAGTGGC
TGCACTTACCATTTTATTGACGCAGATCCAATGAACATGTTAGCCATCAATACGACGGCA
GTATCGATTCCAAACTACACGACATCGGAGCCAACTGGTTTTCAAATTCATCACATTTCC
TACATATGGTATACACTCGTTGGCAGCGCAATTTGTATCATTGTTTCGCTAATCACGTCA
TATTTCACGGGACCTAATAATCCTACCGACTTGAATCCGAATTTACTTGCACCATTTGTG
CGAAAATTAATCACAGCAAGAAACACTACGACGACAATAACAGCGGCAGCATCAAAAAAG
AAATCCATTTATCGTGGCCGCGATGATGAAAGTCAATTATGA

>g3434.t5 Gene=g3434 Length=413
MKAVIYTDVFQSLMMFGAMLLVIIKGTYDIGGLDVVITRNVASKRIEAPDTSFDLTERHT
IWSLCIGGFVYWLKANAISQNMIQRYLSLPSLAAAKRALWIFISGVFILLAICSYCGLLI
YATYFECDPLTTKLVKAKDQLLPLLVMDILGEYPGLVGMFVAGVFSAALSSLSTGLNSMS
AVILEDFFKPFSRKPLTDRQTKYIMRSVVVIFGGICVALVYVVEHLGSVLMLSMSLGSIA
QGPLLGVFTCGVLFPWVTGTGALVGSATALSFMTWLCISAQRAISTGELKFSTKEISTSG
CTYHFIDADPMNMLAINTTAVSIPNYTTSEPTGFQIHHISYIWYTLVGSAICIIVSLITS
YFTGPNNPTDLNPNLLAPFVRKLITARNTTTTITAAASKKKSIYRGRDDESQL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g3434.t5 Gene3D G3DSA:1.20.1730.10 - 1 375 5.4E-64
2 g3434.t5 PANTHER PTHR42985:SF33 FI02094P 1 399 6.8E-178
3 g3434.t5 PANTHER PTHR42985 SODIUM-COUPLED MONOCARBOXYLATE TRANSPORTER 1 399 6.8E-178
1 g3434.t5 Pfam PF00474 Sodium:solute symporter family 1 266 3.0E-20
13 g3434.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
27 g3434.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 28 -
18 g3434.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 29 58 -
23 g3434.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 77 -
14 g3434.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 78 97 -
21 g3434.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 98 124 -
19 g3434.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 125 155 -
26 g3434.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 156 183 -
16 g3434.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 184 202 -
25 g3434.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 203 223 -
20 g3434.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 224 242 -
24 g3434.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 243 276 -
15 g3434.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 277 340 -
22 g3434.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 341 362 -
17 g3434.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 363 413 -
12 g3434.t5 ProSiteProfiles PS50283 Sodium:solute symporter family profile. 1 283 27.58
10 g3434.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 9 31 -
9 g3434.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 78 -
8 g3434.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 99 121 -
6 g3434.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 150 172 -
7 g3434.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 207 229 -
5 g3434.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 244 266 -
4 g3434.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 341 363 -

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