General information for g12840.t10
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Proton-coupled amino acid transporter-like protein pathetic.
Parent gene
- The parent gene g12840 is located on chr_1: 26500392..26501973 (- 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_1 | g12840 | g12840.t10 | TTS | g12840.t10 | 26499912 | 26499912 |
| chr_1 | g12840 | g12840.t10 | isoform | g12840.t10 | 26500392 | 26501973 |
| chr_1 | g12840 | g12840.t10 | exon | g12840.t10.exon1 | 26500392 | 26500525 |
| chr_1 | g12840 | g12840.t10 | cds | g12840.t10.CDS1 | 26500393 | 26500525 |
| chr_1 | g12840 | g12840.t10 | exon | g12840.t10.exon2 | 26500583 | 26500839 |
| chr_1 | g12840 | g12840.t10 | cds | g12840.t10.CDS2 | 26500583 | 26500839 |
| chr_1 | g12840 | g12840.t10 | exon | g12840.t10.exon3 | 26501142 | 26501427 |
| chr_1 | g12840 | g12840.t10 | cds | g12840.t10.CDS3 | 26501142 | 26501159 |
| chr_1 | g12840 | g12840.t10 | exon | g12840.t10.exon4 | 26501814 | 26501973 |
| chr_1 | g12840 | g12840.t10 | TSS | g12840.t10 | 26501969 | 26501969 |
Sequences
>g12840.t10 Gene=g12840 Length=837
TGGTATGTATCAAATTGTAAATATGGAAAAGATAGAAAAATAAATTATTATAAAAATTAA
ACAAAAATAAGTAAGGCTTATTAATAAAATGGTGATTATTAAAAGATTAATAGGGCTTCG
CTATATTAGCAATTATACAAATTCATCAATAAATCGTCAGTTAAAGTGTTCATTTTCTTG
CTGTTTTTTGTTATGAAAGTTTTGAGAGGATGCTTGCTGCTTGGATGGGATTTGAGCGTG
AGGATTTACATTCTTATCATACTCATTCCAATTCTTTTTATCGGACAAATCAGAAGTTTA
AAGTTCCTTGTGCCATTCTCAGGAAGTGCAAATGTTTTCATTGTTGTTGTGTTTGCAATT
GTACTTTACTATATCTTCAAGGAACCACTAGATATAAGTGATAAGCCAAGTATTGTTAGT
TGGACTAAATGGCCTGTTTTCTTCAGGGTATCGGTGCAGTCATGCCTGTTGAAAATTCTA
TGGAAAAACCACAACAATTTCTTGGTTATCCGTCCGTACTTCTAATTGCTATGATTATCG
TCACTGTTATGTATGCTGTCATCGGTTTCCTCGGCTTTGTACGATTTGGTGATGAAATAA
GAGGATCAATTACACTCAATTTACCAACAGATGAATGGCCAGCAGTCACTGGACAATCAC
TCATTGGTATTGCTATTTTACTCACATTTGGTCTTCAATTTTACATTCCAATGGACATTC
TATTGAGAAAACTTGAAAATAGAATTGCAAAGAAAAGAAATATTTCAGAAATTGCAATTA
GAACCGGTATTATGCTTGCGATGGGAGCAGTAGCAATAGCAGTTCCTGATCTTGAAC
>g12840.t10 Gene=g12840 Length=136
MACFLQGIGAVMPVENSMEKPQQFLGYPSVLLIAMIIVTVMYAVIGFLGFVRFGDEIRGS
ITLNLPTDEWPAVTGQSLIGIAILLTFGLQFYIPMDILLRKLENRIAKKRNISEIAIRTG
IMLAMGAVAIAVPDLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g12840.t10 | PANTHER | PTHR22950:SF494 | GH04538P | 5 | 136 | 3.6E-42 |
| 3 | g12840.t10 | PANTHER | PTHR22950 | AMINO ACID TRANSPORTER | 5 | 136 | 3.6E-42 |
| 1 | g12840.t10 | Pfam | PF01490 | Transmembrane amino acid transporter protein | 7 | 135 | 8.0E-26 |
| 8 | g12840.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 29 | - |
| 11 | g12840.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 30 | 53 | - |
| 10 | g12840.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 54 | 72 | - |
| 13 | g12840.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 73 | 94 | - |
| 7 | g12840.t10 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 95 | 114 | - |
| 12 | g12840.t10 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 132 | - |
| 9 | g12840.t10 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 133 | 136 | - |
| 6 | g12840.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 30 | 52 | - |
| 5 | g12840.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 72 | 94 | - |
| 4 | g12840.t10 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 115 | 132 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
## Warning: Removed 1 row(s) containing missing values (geom_path).
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
