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_3 g3434 g3434.t6 isoform g3434.t6 25417101 25418936
chr_3 g3434 g3434.t6 exon g3434.t6.exon1 25417101 25417240
chr_3 g3434 g3434.t6 exon g3434.t6.exon2 25417302 25417370
chr_3 g3434 g3434.t6 cds g3434.t6.CDS1 25417358 25417370
chr_3 g3434 g3434.t6 exon g3434.t6.exon3 25417427 25417482
chr_3 g3434 g3434.t6 cds g3434.t6.CDS2 25417427 25417482
chr_3 g3434 g3434.t6 exon g3434.t6.exon4 25418366 25418431
chr_3 g3434 g3434.t6 cds g3434.t6.CDS3 25418366 25418431
chr_3 g3434 g3434.t6 exon g3434.t6.exon5 25418495 25418654
chr_3 g3434 g3434.t6 cds g3434.t6.CDS4 25418495 25418654
chr_3 g3434 g3434.t6 exon g3434.t6.exon6 25418716 25418936
chr_3 g3434 g3434.t6 cds g3434.t6.CDS5 25418716 25418936
chr_3 g3434 g3434.t6 TSS g3434.t6 25418987 25418987
chr_3 g3434 g3434.t6 TTS g3434.t6 NA NA

Sequences

>g3434.t6 Gene=g3434 Length=712
ATGGAGGGCATTAACGTTGACGACATTCGAATTTCGTTACAAAAGTTTGGTTGGCCAGAT
TATTTAATTTTTCTCTGCATGCTGCTTATTAGTGCTCTAATCGGCGTGTATTTCGGCTTT
ATTGAGAAAAAATCAAAAGGTGCTGGCGATGACGAGGTAAACTATTTAGTTGGAGGTCGA
AAGATGAAAATATTTCCCGTTGCGATGTCTCTGATTGCAAGCTTTATATCAGGCATTAGC
TTACTAGGTACTCCAACTGAGATCTACATTTATGGAATTTCATACTTTTATATAATGGGT
GGAATTATTATCACAGCATTTGTAATGATGACTGTGTATCTTCCAGTTTTTCATGATCTT
CAATTAACTAGCACATATGAGTACCTACAGACACGTTTCGATAGAAAAATGCGCTTATTT
GGCTGCATTCTTTTTATATTCTCGCAGATTGTGTGGTTGCCCATCGTTATATTTGTTCCT
GCATTAGCGCTTAATCATGGTTTTGTCTGGCATTGATGTACATTTGATAACACCATTAAC
GTGTGTCTGCTGCATTTTCTATACATGTGTTGGTGGAATGAAAGCGGTGATTTACACAGA
TGTCTTTCAATCGCTAATGATGTTTGGAGCAATGTTGTTAGTCATTATTAAAGGCACTTA
CGATATAGGCGGATTGGATGTTGTGATTACGCGCAATGTCGCGAGTAAACGT

>g3434.t6 Gene=g3434 Length=171
MEGINVDDIRISLQKFGWPDYLIFLCMLLISALIGVYFGFIEKKSKGAGDDEVNYLVGGR
KMKIFPVAMSLIASFISGISLLGTPTEIYIYGISYFYIMGGIIITAFVMMTVYLPVFHDL
QLTSTYEYLQTRFDRKMRLFGCILFIFSQIVWLPIVIFVPALALNHGFVWH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g3434.t6 Gene3D G3DSA:1.20.1730.10 - 43 171 3.4E-32
2 g3434.t6 PANTHER PTHR42985 SODIUM-COUPLED MONOCARBOXYLATE TRANSPORTER 12 166 1.3E-63
3 g3434.t6 PANTHER PTHR42985:SF5 LP24461P 12 166 1.3E-63
1 g3434.t6 Pfam PF00474 Sodium:solute symporter family 55 140 9.1E-12
13 g3434.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 20 -
17 g3434.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 21 41 -
11 g3434.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 42 61 -
16 g3434.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 62 82 -
12 g3434.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 83 87 -
18 g3434.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 88 116 -
10 g3434.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 117 136 -
15 g3434.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 137 163 -
14 g3434.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 164 171 -
9 g3434.t6 ProSiteProfiles PS50283 Sodium:solute symporter family profile. 17 171 18.784
5 g3434.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 41 -
6 g3434.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 64 86 -
4 g3434.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 96 118 -
7 g3434.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 139 161 -

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