General information for g1791.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as High-affinity choline transporter 1.
Parent gene
- The parent gene g1791 is located on chr_3: 13033606..13036421 (- 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 | g1791 | g1791.t1 | isoform | g1791.t1 | 13033606 | 13036421 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon1 | 13033606 | 13033830 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS1 | 13033606 | 13033830 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon2 | 13033896 | 13034010 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS2 | 13033896 | 13034010 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon3 | 13034072 | 13034301 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS3 | 13034072 | 13034301 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon4 | 13034593 | 13034635 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS4 | 13034593 | 13034635 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon5 | 13034695 | 13035016 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS5 | 13034695 | 13035016 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon6 | 13035083 | 13035212 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS6 | 13035083 | 13035212 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon7 | 13035268 | 13035566 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS7 | 13035268 | 13035566 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon8 | 13035633 | 13035788 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS8 | 13035633 | 13035788 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon9 | 13036001 | 13036108 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS9 | 13036001 | 13036108 |
| chr_3 | g1791 | g1791.t1 | exon | g1791.t1.exon10 | 13036256 | 13036421 |
| chr_3 | g1791 | g1791.t1 | cds | g1791.t1.CDS10 | 13036256 | 13036421 |
| chr_3 | g1791 | g1791.t1 | TSS | g1791.t1 | NA | NA |
| chr_3 | g1791 | g1791.t1 | TTS | g1791.t1 | NA | NA |
Sequences
>g1791.t1 Gene=g1791 Length=1794
ATGATTAATATAGCTGGAGTTATCAGTATTACAATTTTTTATTTACTCATTTTATTTGTT
GGAATCTGGGCTGGACGTAAGAAAGCAGAAGGAAATGATTCGGAAGAGGAAGTTATGCTT
GCAGGTCGTTCAATTGGCTTATTTGTGGGAATATTCACAATGACAGCAACATGGGTTGGT
GGTGGCTATATCAATGGTACAGCAGAGGCAATTTATACATCTGGTCTTGTATGGTGTCAA
GCACCATTTGGATATGCTCTGAGTTTGGTTTTTGGTGGACTTTTCTTTGCAAATCCAATG
AGAAAACAAGGTTATGTCACGATGTTGGATCCATTACAAGACAGTTTTGGTGAGCGAATG
GGCGGTTTGCTCTTTTTACCAGCATTATGTGGTGAAGTGTTTTGGGCTGCTGGCATTTTG
GCAGCATTGGGCGCAACATTGGCTGTAATTATTGATATGGAGAAGGAGACATCTGTAATT
TTCTCAGCATGCATTGCTGTATTTTACACGCTCTTTGGTGGTCTCTATTCTGTCGCCTAT
ACTGATGTCATACAACTTTTCTGTATCTTCATTGGTCTATGGATGTGCATTCCATTTGCA
TGGAGTAATCCACATGTTAAGCCATTATCGGGGATGGAAGTTGATTGGATTGGCGAGATT
GGTGATAAAAAGTTTTGGTTTTATTGCGATTATGGATTATTGTTGATCTTTGGTGGAATT
CCATGGCAGGTCTATTTTCAACGAGTACTTTCAAGTAAGACAGCAGGCCGTGCTCAAATA
TTGTCATATGTTGCTGCATTTGGTTGTCTTTTAATGGCAATTCCACCAGTTCTTATTGGA
GCAATAGCAAAAGCTACACCATGGAATGAGACAGGATATTCTGGTCCTTGGCCTTTGACA
GCTGAAGAAACAAGTATGATTCTCCCAATGGTACTTCAATATCTCACACCTGATTTCGTA
TCTTTCTTTGGTCTTGGAGCTGTATCTGCAGCTGTCATGTCATCGGCCGATTCATCAGTA
TTATCAGCAGCATCAATGTTTGCTCGCAATGTATACAAACTTATATTTAGACAACGTGCA
TCTGAGATGGAAATCATTTGGGTTATGAGAGTTGGAATTATCGTTGTTGGTATTCTTGCC
ACTGCTATGGCACTCACAATTCCATCAATTTATGGTTTATGGTCGATGTGCTCGGATCTT
GTTTATGTTATCTTATTTCCTCAGCTACTTATGGTCGTTCATTTCAAGCATCATTGTAAT
ACATATGGCAGCTTGTCAGCATATATTGTGGCTTTCTTCGTTCGTCTATCAGGAGGCGAA
CCGATTCTTGGTTTACCAGCAGCAATTCATTTTCCTGGTTATGATGAGGAAACACAAGAG
CAACTTTTTCCATTCCGCACAATGGCTATGTTGCTTAGTCTAATAACATTGGCTGGAGTT
TCTTGGTTAACAAAATTCCTTTTCTTAACTGGAAGACTTGCGCCACAATATGATTACTTT
AGATGTGTTGTGAATATACCAGAAGATGCTGTGCGTGTCGGAGATCCATCAGAAGTTGAC
GGCGAACAGATGAGTGTGATGGCTGGCGCTATGAACAAAATGTATGGCGCAGCAACAATG
GTGGGCAAGGATGAAAGAAATGGAAGAATAAATCCAGCACTTGAGCCAGATGATGATCTA
CCAGCTGTTGAAGCACAAAGGCAAATGCAACAAATGGCACTTAGCAATGCTGCTGCTGCC
ATAAGTAATGTAGCCCAAACCGTCCCTGGTGGACAAGGCACTACGGCATTTTAA
>g1791.t1 Gene=g1791 Length=597
MINIAGVISITIFYLLILFVGIWAGRKKAEGNDSEEEVMLAGRSIGLFVGIFTMTATWVG
GGYINGTAEAIYTSGLVWCQAPFGYALSLVFGGLFFANPMRKQGYVTMLDPLQDSFGERM
GGLLFLPALCGEVFWAAGILAALGATLAVIIDMEKETSVIFSACIAVFYTLFGGLYSVAY
TDVIQLFCIFIGLWMCIPFAWSNPHVKPLSGMEVDWIGEIGDKKFWFYCDYGLLLIFGGI
PWQVYFQRVLSSKTAGRAQILSYVAAFGCLLMAIPPVLIGAIAKATPWNETGYSGPWPLT
AEETSMILPMVLQYLTPDFVSFFGLGAVSAAVMSSADSSVLSAASMFARNVYKLIFRQRA
SEMEIIWVMRVGIIVVGILATAMALTIPSIYGLWSMCSDLVYVILFPQLLMVVHFKHHCN
TYGSLSAYIVAFFVRLSGGEPILGLPAAIHFPGYDEETQEQLFPFRTMAMLLSLITLAGV
SWLTKFLFLTGRLAPQYDYFRCVVNIPEDAVRVGDPSEVDGEQMSVMAGAMNKMYGAATM
VGKDERNGRINPALEPDDDLPAVEAQRQMQQMALSNAAAAISNVAQTVPGGQGTTAF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 45 | g1791.t1 | CDD | cd11474 | SLC5sbd_CHT | 7 | 481 | 0.0 |
| 16 | g1791.t1 | Gene3D | G3DSA:1.20.1730.10 | - | 27 | 487 | 1.2E-63 |
| 2 | g1791.t1 | PANTHER | PTHR45897 | HIGH-AFFINITY CHOLINE TRANSPORTER 1 | 1 | 515 | 5.7E-230 |
| 1 | g1791.t1 | Pfam | PF00474 | Sodium:solute symporter family | 40 | 430 | 3.5E-31 |
| 28 | g1791.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 5 | - |
| 44 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 6 | 24 | - |
| 19 | g1791.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 25 | 44 | - |
| 38 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 45 | 64 | - |
| 29 | g1791.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 65 | 69 | - |
| 36 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 70 | 97 | - |
| 22 | g1791.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 98 | 122 | - |
| 40 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 123 | 151 | - |
| 26 | g1791.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 152 | 156 | - |
| 42 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 157 | 176 | - |
| 20 | g1791.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 177 | 182 | - |
| 39 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 183 | 201 | - |
| 31 | g1791.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 202 | 224 | - |
| 43 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 225 | 246 | - |
| 21 | g1791.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 247 | 257 | - |
| 34 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 258 | 283 | - |
| 25 | g1791.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 284 | 318 | - |
| 41 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 319 | 344 | - |
| 18 | g1791.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 345 | 364 | - |
| 32 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 365 | 387 | - |
| 30 | g1791.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 388 | 392 | - |
| 35 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 393 | 413 | - |
| 23 | g1791.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 414 | 424 | - |
| 33 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 425 | 449 | - |
| 27 | g1791.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 450 | 468 | - |
| 37 | g1791.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 469 | 488 | - |
| 24 | g1791.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 489 | 597 | - |
| 17 | g1791.t1 | ProSiteProfiles | PS50283 | Sodium:solute symporter family profile. | 3 | 445 | 40.601 |
| 8 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 4 | 26 | - |
| 9 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 39 | 61 | - |
| 7 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 76 | 98 | - |
| 6 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 122 | 144 | - |
| 5 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 159 | 178 | - |
| 15 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 183 | 202 | - |
| 10 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 225 | 247 | - |
| 12 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 260 | 282 | - |
| 13 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 322 | 344 | - |
| 4 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 365 | 387 | - |
| 11 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 391 | 413 | - |
| 3 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 425 | 447 | - |
| 14 | g1791.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 467 | 489 | - |
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 transcript has been annotated with K14387 (solute carrier family 5 (high affinity choline transporter), member 7)
Pathway
- This transcript belongs to the following pathways
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