General information for g2003.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as b-0,+–type amino acid transporter 1.
Parent gene
- The parent gene g2003 is located on chr_3: 14362966..14372625 (- 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 | g2003 | g2003.t4 | isoform | g2003.t4 | 14361316 | 14367440 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon1 | 14361316 | 14361974 |
| chr_3 | g2003 | g2003.t4 | TTS | g2003.t4 | 14361323 | 14361323 |
| chr_3 | g2003 | g2003.t4 | cds | g2003.t4.CDS1 | 14361904 | 14361974 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon2 | 14362040 | 14362683 |
| chr_3 | g2003 | g2003.t4 | cds | g2003.t4.CDS2 | 14362040 | 14362683 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon3 | 14362753 | 14362897 |
| chr_3 | g2003 | g2003.t4 | cds | g2003.t4.CDS3 | 14362753 | 14362897 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon4 | 14362966 | 14363091 |
| chr_3 | g2003 | g2003.t4 | cds | g2003.t4.CDS4 | 14362966 | 14363017 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon5 | 14363156 | 14363402 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon6 | 14365013 | 14365114 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon7 | 14365438 | 14365491 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon8 | 14365563 | 14365625 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon9 | 14366695 | 14366835 |
| chr_3 | g2003 | g2003.t4 | exon | g2003.t4.exon10 | 14367371 | 14367440 |
| chr_3 | g2003 | g2003.t4 | TSS | g2003.t4 | 14367736 | 14367736 |
Sequences
>g2003.t4 Gene=g2003 Length=2251
ATGCGTGATACATTTGTACAAATAATTAAAGAAAAACCTGGATCAAGCTTCAATTCAGAT
AATTGTGAAGGACAAAATGGAGCAGTCAAAGATATTTCAAATGGATGGAATAACAACAAT
CACAACATCACAACTGACGGCACAGTTAAAAATGCCACAGCAAATTTTCGTGGAAGGACG
ACCGAAACGACAGCGTCCGACCCATCAGGGGCCAGGGGGGTGCGGATCTCGATGGAGAGA
TCGGGCTCAAAGACGAAGGACACTATTCAACTCGAGAAACGGATGGGGTTGTTCAGTGGG
ATTGCTCTAATCGTTGGAACGATGATAGGCTCAGGAATTTTCGTATCGCCAAGTGGATTG
CTTGTCAGAACAGGCTCTGTTGGCATTAGTTTCATTATCTGGATGGCGTGCGGTCTTCTC
TCATTGTTAGGTGCGCTCTCGTATGCGGAGTTAGGCACAATGAATACATCTTCAGGTGCG
GAGTGGGCATATTTTATGGACGCATTTGGATCAGCACCGGCATTTTTGTTCAGTTGGGTA
TCGACACTTGTCCTGAAGCCCTCACAAATGGCAATTATATGTTTATCATTTGCGCAATAT
GCCGTCGAAGCTTTTGTTTCTGAGTGCGATCCACCTCCGATTGTTGTAAAAATGGTTGCC
TTGCTGGCTATCGGTTTTATGCATCTTGTTTGTTAATTGTTACAGTGTAAATTTGGGAAT
GGCTGTACAAAATGTATTTACATCTGCAAAAATGGTTGCTGTTTTGATTGTTATTTGTGG
CGGTGCATGGAAACTTTTTCAAGGAAACACACAACACTTGTCAAATGCTTTTGATAATCC
AACACCATCTATGGGAGTAATTGCCACAGCATTTTATACAGGCTTATGGGCGTATGATGG
TTGGAATAATTTAAATTATGTCACTGAGGAAATACAAAATCCCAGCAAAAATTTACCGAG
ATCAATTATGATTGCTATTCCATTGGTTACGCTCTGCTACGCTTTAATCAACATTTCCTA
TCTTGCCGCAATGTCGCCGCAGGAGATGATCGAATCCGAAGCTGTTGCTGTCACGTTCGG
AAATCGTATTTTAGGAATGTTTGCGTGGATAATGCCACTGAGTGTTACAATAAGCACTTT
TGGCTCAGCAAATGGAACATTATTTGCGGCAGGAAGACTTTGCTTTGCTGCTTCACGAGA
GGGACATCTTCTTGATATTCTATCTTATGTTCATGTTCGTCGTTTAACTCCTGCACCAGG
TCTAATTTTTCACTCTCTTATTGCGTCTGCGATGGTGCTTCATGGCACTATTGACTCATT
AATTGACTTCTTTAGCTTTACGGCTTGGATATTTTATGGAGGTTCAATGTTTGCACTGAT
CGTCATGCGCTTCACAAAACCGAACTATCCGCGCCCTTATAAAGTGCCAATTATCATTCC
TGTAATTGTTCTTGTGATTTCGGCTTATTTGGTCATTGGTCCGATCATCGATAAACCACA
AATTGAGTATTTGTATACGGTTCTTTTTATTCTTCTTGGACTTGTTCTCTATTTGCCATT
CGTTCGTTGGCGTATGCATCCTGTATTCATGAATAAAGTTACAATTTTCTTTCAAATGCT
CTTTGAAGTTGTTCCTACAAATCACATGGCAATGTTCGACTAAATGTCTATCGATCTATT
TAACTATAACTGTACACCAGCTTTATGGCGAATTTATTTAATTGGGCATATTATCATGCT
TTGAGAAAAATATATTTTGTTACTATTGAGTTCACTTCAATTCAAAAAGACGTTCAAAAT
TTAGGCAACAAAAATTAATTCTTACGTTGAAGCAATAATTTTAGAATGAGAAAATTATGC
ATTTCAAAAATGAGATTTCGTAAATTATTTAAAAGAGTAAAAAAGTAATTTTAGAGACTT
ACAAAAAAGATCATTACGTACATGTTAGAACAAAAAGAGAATTAAAATTTTTAGAGCTAT
ATTGAAGATAAGAGAAAAATTGCACCTATCTAGAAAAAAAGTTTCCTTGTAGAAAATGCT
AGTCTTTTGGCATTAAAAGAATGAGATTGAAATTTGATGTTTCTCTTAGAGAAATTTAAA
TTATGTGAAAAGAATGTGAGACTAAAGAAAGAAATTATCAAAAAATGCCAGCATAAGAAC
GTAATAAGAAAAATAAAATTCTGTAAATGAAATTTTTTTTTGAAATAATAAAAGAGTTGA
AGGAAATTTATTTTTAAAAGGATTTAAAATT
>g2003.t4 Gene=g2003 Length=303
MVAVLIVICGGAWKLFQGNTQHLSNAFDNPTPSMGVIATAFYTGLWAYDGWNNLNYVTEE
IQNPSKNLPRSIMIAIPLVTLCYALINISYLAAMSPQEMIESEAVAVTFGNRILGMFAWI
MPLSVTISTFGSANGTLFAAGRLCFAASREGHLLDILSYVHVRRLTPAPGLIFHSLIASA
MVLHGTIDSLIDFFSFTAWIFYGGSMFALIVMRFTKPNYPRPYKVPIIIPVIVLVISAYL
VIGPIIDKPQIEYLYTVLFILLGLVLYLPFVRWRMHPVFMNKVTIFFQMLFEVVPTNHMA
MFD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g2003.t4 | Gene3D | G3DSA:1.20.1740.10 | - | 1 | 293 | 4.5E-51 |
| 2 | g2003.t4 | PANTHER | PTHR11785:SF340 | AROMATIC-PREFERRING AMINO ACID TRANSPORTER | 2 | 298 | 1.1E-119 |
| 3 | g2003.t4 | PANTHER | PTHR11785 | AMINO ACID TRANSPORTER | 2 | 298 | 1.1E-119 |
| 1 | g2003.t4 | Pfam | PF13520 | Amino acid permease | 3 | 252 | 1.7E-33 |
| 19 | g2003.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 18 | - |
| 20 | g2003.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 1 | - |
| 21 | g2003.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 2 | 13 | - |
| 30 | g2003.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 14 | 18 | - |
| 14 | g2003.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 19 | 33 | - |
| 28 | g2003.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 34 | 51 | - |
| 13 | g2003.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 52 | 71 | - |
| 29 | g2003.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 72 | 93 | - |
| 17 | g2003.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 94 | 112 | - |
| 23 | g2003.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 145 | - |
| 11 | g2003.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 146 | 164 | - |
| 26 | g2003.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 165 | 187 | - |
| 15 | g2003.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 188 | 192 | - |
| 22 | g2003.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 193 | 215 | - |
| 10 | g2003.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 216 | 226 | - |
| 25 | g2003.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 227 | 246 | - |
| 18 | g2003.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 247 | 251 | - |
| 27 | g2003.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 252 | 271 | - |
| 12 | g2003.t4 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 272 | 282 | - |
| 24 | g2003.t4 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 283 | 302 | - |
| 16 | g2003.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 303 | 303 | - |
| 8 | g2003.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 71 | 93 | - |
| 7 | g2003.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 113 | 135 | - |
| 5 | g2003.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 190 | 212 | - |
| 4 | g2003.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 225 | 247 | - |
| 6 | g2003.t4 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 251 | 273 | - |
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.
