Gene loci information

Transcript annotation

  • This transcript has been annotated as 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 g10696 g10696.t5 TSS g10696.t5 11404019 11404019
chr_1 g10696 g10696.t5 isoform g10696.t5 11404995 11406491
chr_1 g10696 g10696.t5 exon g10696.t5.exon1 11404995 11405074
chr_1 g10696 g10696.t5 cds g10696.t5.CDS1 11405047 11405074
chr_1 g10696 g10696.t5 exon g10696.t5.exon2 11405137 11405168
chr_1 g10696 g10696.t5 cds g10696.t5.CDS2 11405137 11405168
chr_1 g10696 g10696.t5 exon g10696.t5.exon3 11405235 11405377
chr_1 g10696 g10696.t5 cds g10696.t5.CDS3 11405235 11405377
chr_1 g10696 g10696.t5 exon g10696.t5.exon4 11405435 11406491
chr_1 g10696 g10696.t5 cds g10696.t5.CDS4 11405435 11406491
chr_1 g10696 g10696.t5 TTS g10696.t5 11406509 11406509

Sequences

>g10696.t5 Gene=g10696 Length=1312
TATTTATGTACCAGCTTTAGCATTCAGTCAAACAACTGGTATTGATGTACACATGATTAC
ACCTATCGTGATGGGCATCTGCATATTTTATACATGCTTAGGTGGCATAAAGGCTGTTGT
ATGGACTGATGTTATTCAGATTATGCTCATGTATGGAACATTAGTTGTGATTATTGTTAG
AGGCACTTCACTCGTTGGAGGATTTTCTGTAGTCATAGAGAAAAATATTGAGAGTGGAAG
ACTGGCACCACCTGATTTTAATTTTGATCCTACTTTGAGAACTTCATTTTGGATAATGGT
CATTGGTGGTTCATTTTTTCGTTTATATGCTGGAATAAATCAATCAATGATACAGCGATA
TATGGCATTGAAGAACGTCCATGTAGCACGAAAATGTCAATATGTCTATTTAGGTGGAAT
AATTATTTTGAATCTCATGTGTTATTACAATGGTCTACTACTTTATGCTTATTTTTATGA
TTGTGATCCATTGACAACAAAATTGGCAAAGGCAAAAGATCAATTAATGCCACTCTTGGT
GATGGAAATATTGCGAGATATTCCTGGAATGCCTGGATTATTTATAGCTGGTGTGTTTTC
TGCTGCACTTTCATCACTTTCAACAGCTTTAAACTCATTTTCTGCGGTTGTTCTCGAGGA
CTTTTGCAAACCATTTGCAAAGGATGGTGTGTCAGAACGAACAAGTGCAATAATAATGCG
TATGACAGTGTTAGTGGTTGGAGTGATGAGCGTAGCTCTTGTATATGTTGTGCAGCATAT
GGGATCCGTGCTTCAACTAGCATACACTATACCATCAGTTGCATTCGGGCCGATGTTGGG
CATTTATATAATTGGACTTTGTATTCCGCACATTGGAAAACGTGCGACATTCTATGGAGC
TTTGACCGGATGTAGTGTAATGATTGCTTTCATTTCGAAAGTACAAATTGAAGTTGCTTT
GGGCAAAATTAGTCACCCAATAAAACCAGTCTCAATTGATGGTTGTACATACGATTTTGT
AGCTACTAATATGACAACAAACATCAATGAGCCTTCAGTTACGGAAAGAAATATCTTTCA
CATTTCATTTATATATTACACTCTACTGGGGTCGGTTATCGTTATCGTAACATCAATACT
ATACAGTTTTATTGTGGGCTTCAATGATCTTAGTGATGTCGATATTAATTTGCTTGCTCC
TTTCCTGAGAAAATACTTTAAGAATGCAGAAAGAGATGATGAAGACAAAAAGTACCAAAT
AATTCTTGACAGAGACTCTATTATAGATAAGAAAAAAAATTGTGACGAATAA

>g10696.t5 Gene=g10696 Length=419
MITPIVMGICIFYTCLGGIKAVVWTDVIQIMLMYGTLVVIIVRGTSLVGGFSVVIEKNIE
SGRLAPPDFNFDPTLRTSFWIMVIGGSFFRLYAGINQSMIQRYMALKNVHVARKCQYVYL
GGIIILNLMCYYNGLLLYAYFYDCDPLTTKLAKAKDQLMPLLVMEILRDIPGMPGLFIAG
VFSAALSSLSTALNSFSAVVLEDFCKPFAKDGVSERTSAIIMRMTVLVVGVMSVALVYVV
QHMGSVLQLAYTIPSVAFGPMLGIYIIGLCIPHIGKRATFYGALTGCSVMIAFISKVQIE
VALGKISHPIKPVSIDGCTYDFVATNMTTNINEPSVTERNIFHISFIYYTLLGSVIVIVT
SILYSFIVGFNDLSDVDINLLAPFLRKYFKNAERDDEDKKYQIILDRDSIIDKKKNCDE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g10696.t5 Gene3D G3DSA:1.20.1730.10 - 1 377 6.2E-69
2 g10696.t5 PANTHER PTHR42985 SODIUM-COUPLED MONOCARBOXYLATE TRANSPORTER 1 393 1.4E-145
3 g10696.t5 PANTHER PTHR42985:SF5 LP24461P 1 393 1.4E-145
1 g10696.t5 Pfam PF00474 Sodium:solute symporter family 5 286 7.8E-28
23 g10696.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 5 -
33 g10696.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 6 24 -
17 g10696.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 25 30 -
34 g10696.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 31 55 -
24 g10696.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 56 74 -
30 g10696.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 75 95 -
16 g10696.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 96 115 -
31 g10696.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 116 141 -
25 g10696.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 142 175 -
32 g10696.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 176 200 -
19 g10696.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 201 219 -
29 g10696.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 220 240 -
21 g10696.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 241 245 -
28 g10696.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 246 271 -
18 g10696.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 272 277 -
27 g10696.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 278 299 -
22 g10696.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 300 345 -
26 g10696.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 346 370 -
20 g10696.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 371 419 -
15 g10696.t5 ProSiteProfiles PS50283 Sodium:solute symporter family profile. 1 300 31.419
14 g10696.t5 TIGRFAM TIGR00813 sss: transporter, solute:sodium symporter (SSS) family 6 286 1.1E-56
5 g10696.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 5 24 -
8 g10696.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 31 53 -
9 g10696.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 77 96 -
4 g10696.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 117 139 -
11 g10696.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 176 198 -
7 g10696.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 219 241 -
10 g10696.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 251 273 -
12 g10696.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 280 302 -
6 g10696.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 346 368 -

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