General information for g22.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Sodium-dependent nutrient amino acid transporter 1.
Parent gene
- The parent gene g22 is located on chr_3: 325993..328112 (+ 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_3 | g22 | g22.t1 | TSS | g22.t1 | 325579 | 325579 |
| chr_3 | g22 | g22.t1 | isoform | g22.t1 | 325993 | 328112 |
| chr_3 | g22 | g22.t1 | exon | g22.t1.exon1 | 325993 | 326179 |
| chr_3 | g22 | g22.t1 | cds | g22.t1.CDS1 | 325993 | 326179 |
| chr_3 | g22 | g22.t1 | exon | g22.t1.exon2 | 326256 | 326271 |
| chr_3 | g22 | g22.t1 | cds | g22.t1.CDS2 | 326256 | 326271 |
| chr_3 | g22 | g22.t1 | exon | g22.t1.exon3 | 326378 | 326412 |
| chr_3 | g22 | g22.t1 | cds | g22.t1.CDS3 | 326378 | 326412 |
| chr_3 | g22 | g22.t1 | exon | g22.t1.exon4 | 327084 | 327215 |
| chr_3 | g22 | g22.t1 | cds | g22.t1.CDS4 | 327084 | 327215 |
| chr_3 | g22 | g22.t1 | exon | g22.t1.exon5 | 327278 | 327296 |
| chr_3 | g22 | g22.t1 | cds | g22.t1.CDS5 | 327278 | 327296 |
| chr_3 | g22 | g22.t1 | exon | g22.t1.exon6 | 327376 | 327719 |
| chr_3 | g22 | g22.t1 | cds | g22.t1.CDS6 | 327376 | 327719 |
| chr_3 | g22 | g22.t1 | exon | g22.t1.exon7 | 327889 | 328112 |
| chr_3 | g22 | g22.t1 | cds | g22.t1.CDS7 | 327889 | 328112 |
| chr_3 | g22 | g22.t1 | TTS | g22.t1 | NA | NA |
Sequences
>g22.t1 Gene=g22 Length=957
ATGACTCAAGCATACGATAACCCAACATTTGCAAACGATAAATCAGTTGTTGCCAATAGC
ACTTTGGCATTCACAATTGATCACAAAAGTGACGAAAACAATGCACAGACAAAAAAGCAT
GGAACAACTCGCGATACATGGGGAAAAGATGTAGAATTTCTTTTGTCATGCATTGCTATG
GCAGTAGGATTAGGCAACGTATGGCGATTCCCTTTCACTGCTTTAAGGAATGGAGGAGCA
TCGTTTTTGATTCCATACATTATTGTTCTTGTATTGGTTGGCAAGCCTGGATATTTCTTA
GAGATGATCATGGGACAGTTTTCGTCACGTGGAACAGTAAAAGTATATGACAGTGTTCCT
GCTATGAGAGGAATTGGCATCGGTCAAACTTTCACTCTACCTTGGAGTGAATGTAATCCT
AATTGGAATGTCTCATGTTATTCTTCAAATGGAAATAATGGGTCAAATGTTGTTATGAAT
GGTACAACCAAATCGTCAGCTGAACTTTATTTTTTCAAAGAAGTTCTTCATGAAAGAAAA
TTAGAAGATGGAATAGGAATGCCAAACTGGAATCTTGTTTTATTTCGTGTTCTTTCATGG
GCAATTGTTTTCTTCATTCTCTTCAAAGGAGTCAAAATGTCTGGCAAAGCTTCATACATA
ACTGGAATTGCTCCATTCATCTTTCTTGCAATTTTCCTCGTCCGTGCGCTTACACTTGAA
GGAGCTTGGGATGTCACAACATTAGACACTTTGACATCTATAGTTGTTGGTTCAATCACT
TTTGGTATTATTGGTCATTTATCACATGAACTTAATACTCCAATTGAGACAGTAATCAAA
TCTGGTCCTGGTTTAGTTTCGGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNAAGATATAAAAATTTTAAAGAGACTTTGAAGAATCAAACAAAATATTGTCATTAA
>g22.t1 Gene=g22 Length=318
MTQAYDNPTFANDKSVVANSTLAFTIDHKSDENNAQTKKHGTTRDTWGKDVEFLLSCIAM
AVGLGNVWRFPFTALRNGGASFLIPYIIVLVLVGKPGYFLEMIMGQFSSRGTVKVYDSVP
AMRGIGIGQTFTLPWSECNPNWNVSCYSSNGNNGSNVVMNGTTKSSAELYFFKEVLHERK
LEDGIGMPNWNLVLFRVLSWAIVFFILFKGVKMSGKASYITGIAPFIFLAIFLVRALTLE
GAWDVTTLDTLTSIVVGSITFGIIGHLSHELNTPIETVIKSGPGLVSGXXXXXXXXXXXX
XRYKNFKETLKNQTKYCH
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g22.t1 | Coils | Coil | Coil | 302 | 309 | - |
| 3 | g22.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 20 | 132 | 4.4E-93 |
| 6 | g22.t1 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 20 | 132 | 4.4E-93 |
| 5 | g22.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 132 | 244 | 4.4E-93 |
| 8 | g22.t1 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 132 | 244 | 4.4E-93 |
| 4 | g22.t1 | PANTHER | PTHR11616 | SODIUM/CHLORIDE DEPENDENT TRANSPORTER | 245 | 285 | 4.4E-93 |
| 7 | g22.t1 | PANTHER | PTHR11616:SF269 | TRANSPORTER | 245 | 285 | 4.4E-93 |
| 9 | g22.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 52 | 73 | 2.0E-14 |
| 10 | g22.t1 | PRINTS | PR00176 | Sodium/chloride neurotransmitter symporter signature | 81 | 100 | 2.0E-14 |
| 2 | g22.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 44 | 129 | 1.5E-29 |
| 1 | g22.t1 | Pfam | PF00209 | Sodium:neurotransmitter symporter family | 130 | 244 | 9.6E-23 |
| 17 | g22.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 52 | - |
| 22 | g22.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 70 | - |
| 14 | g22.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 71 | 81 | - |
| 21 | g22.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 100 | - |
| 16 | g22.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 101 | 189 | - |
| 23 | g22.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 190 | 208 | - |
| 13 | g22.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 209 | 219 | - |
| 20 | g22.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 220 | 238 | - |
| 18 | g22.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 239 | 249 | - |
| 19 | g22.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 250 | 267 | - |
| 15 | g22.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 268 | 318 | - |
| 28 | g22.t1 | ProSitePatterns | PS00610 | Sodium:neurotransmitter symporter family signature 1. | 68 | 82 | - |
| 29 | g22.t1 | ProSiteProfiles | PS50267 | Sodium:neurotransmitter symporter family profile. | 43 | 244 | 29.816 |
| 11 | g22.t1 | SUPERFAMILY | SSF161070 | SNF-like | 44 | 286 | 2.75E-62 |
| 26 | g22.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 53 | 72 | - |
| 24 | g22.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 82 | 104 | - |
| 27 | g22.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 190 | 207 | - |
| 25 | g22.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 217 | 239 | - |
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:0016021 | integral component of membrane | CC |
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.
