General information for g16375.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Sodium-coupled monocarboxylate transporter 1.
Parent gene
- The parent gene g16375 is located on chr_4: 9262408..9263568 (+ strand)
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_4 | g16375 | g16375.t1 | TSS | g16375.t1 | 9262287 | 9262287 |
| chr_4 | g16375 | g16375.t1 | isoform | g16375.t1 | 9262408 | 9263568 |
| chr_4 | g16375 | g16375.t1 | exon | g16375.t1.exon1 | 9262408 | 9262723 |
| chr_4 | g16375 | g16375.t1 | cds | g16375.t1.CDS1 | 9262408 | 9262723 |
| chr_4 | g16375 | g16375.t1 | exon | g16375.t1.exon2 | 9262777 | 9262910 |
| chr_4 | g16375 | g16375.t1 | cds | g16375.t1.CDS2 | 9262777 | 9262910 |
| chr_4 | g16375 | g16375.t1 | exon | g16375.t1.exon3 | 9262975 | 9263058 |
| chr_4 | g16375 | g16375.t1 | cds | g16375.t1.CDS3 | 9262975 | 9263058 |
| chr_4 | g16375 | g16375.t1 | exon | g16375.t1.exon4 | 9263407 | 9263568 |
| chr_4 | g16375 | g16375.t1 | cds | g16375.t1.CDS4 | 9263407 | 9263568 |
| chr_4 | g16375 | g16375.t1 | TTS | g16375.t1 | NA | NA |
Sequences
>g16375.t1 Gene=g16375 Length=696
ATGTCGTCAAATACAGAAGAAAATTCAATTCTTTTCTCACAAACTTCTTCACCTTCAACA
ATCGATGTTGACACATTAAGCAAATCAATGAGACACTTTGGAGTTGCTGACTATGCAGTT
TTTATTTTAATGCTTGTTTTTTCATCACTTGTCGGTCTTTATTTTGGCTATCAAGATCAT
AAAATGAAGAAACAAAATAAAAGAAATGGAATTGAAGATGATGCTGCAAATTATTTAGTT
GGTGGAAGAAATATGCAAGTTTTGCCTGTTGCTCTTTCATTAACTGCTTCATTTGTGTCA
GGAATAACTTTATTGGGAACAAGCACAGAAATTTATCTTTATGGCTCGCAGTATTGTTTC
TTTTTAATTGCAATCGTTTTGACTGGTTTTATTATTCATAGCACAATAATTCCAGTGCTT
CATGAACTTGAGATAACGTCAACTTATCAGTATTTAGAAGCAAGATTCAATCGTGAACTT
CGACTTTTTGGATCGATTTCGTTTTGTTTTATGACAATTTTGTGGCTACCAATTGTCATT
TACATGCCAGCATTAGCATTTAATCAAACAACAGGAATTGATATTCACGTCATCACACCG
TTTCAATGTTTTATTTGTATTGTCTACACATCTTTGGGTGGAATTAAAGCTGTTGTCTGG
GACTTATGGAAGAACAATTTTTTCAAAAATTTCTAA
>g16375.t1 Gene=g16375 Length=231
MSSNTEENSILFSQTSSPSTIDVDTLSKSMRHFGVADYAVFILMLVFSSLVGLYFGYQDH
KMKKQNKRNGIEDDAANYLVGGRNMQVLPVALSLTASFVSGITLLGTSTEIYLYGSQYCF
FLIAIVLTGFIIHSTIIPVLHELEITSTYQYLEARFNRELRLFGSISFCFMTILWLPIVI
YMPALAFNQTTGIDIHVITPFQCFICIVYTSLGGIKAVVWDLWKNNFFKNF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g16375.t1 | Gene3D | G3DSA:1.20.1730.10 | - | 66 | 221 | 1.3E-44 |
| 2 | g16375.t1 | PANTHER | PTHR42985 | SODIUM-COUPLED MONOCARBOXYLATE TRANSPORTER | 23 | 220 | 1.4E-85 |
| 3 | g16375.t1 | PANTHER | PTHR42985:SF5 | LP24461P | 23 | 220 | 1.4E-85 |
| 1 | g16375.t1 | Pfam | PF00474 | Sodium:solute symporter family | 78 | 220 | 4.0E-15 |
| 14 | g16375.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 37 | - |
| 21 | g16375.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 38 | 57 | - |
| 11 | g16375.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 58 | 86 | - |
| 20 | g16375.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 108 | - |
| 16 | g16375.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 109 | 119 | - |
| 17 | g16375.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 120 | 141 | - |
| 12 | g16375.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 142 | 161 | - |
| 19 | g16375.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 162 | 185 | - |
| 15 | g16375.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 186 | 196 | - |
| 18 | g16375.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 197 | 219 | - |
| 13 | g16375.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 220 | 231 | - |
| 10 | g16375.t1 | ProSiteProfiles | PS50283 | Sodium:solute symporter family profile. | 34 | 231 | 24.266 |
| 8 | g16375.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 35 | 57 | - |
| 4 | g16375.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 87 | 109 | - |
| 5 | g16375.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 119 | 141 | - |
| 7 | g16375.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 161 | 183 | - |
| 6 | g16375.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 198 | 220 | - |
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