Gene loci information

Transcript annotation

  • This transcript has been annotated as b-0,+–type amino acid transporter 1.

Parent gene

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.t2 TTS g2003.t2 14361323 14361323
chr_3 g2003 g2003.t2 isoform g2003.t2 14361904 14367440
chr_3 g2003 g2003.t2 exon g2003.t2.exon1 14361904 14361974
chr_3 g2003 g2003.t2 cds g2003.t2.CDS1 14361904 14361974
chr_3 g2003 g2003.t2 exon g2003.t2.exon2 14362040 14362683
chr_3 g2003 g2003.t2 cds g2003.t2.CDS2 14362040 14362683
chr_3 g2003 g2003.t2 exon g2003.t2.exon3 14362753 14362897
chr_3 g2003 g2003.t2 cds g2003.t2.CDS3 14362753 14362897
chr_3 g2003 g2003.t2 exon g2003.t2.exon4 14362966 14363091
chr_3 g2003 g2003.t2 cds g2003.t2.CDS4 14362966 14363091
chr_3 g2003 g2003.t2 exon g2003.t2.exon5 14363160 14363402
chr_3 g2003 g2003.t2 cds g2003.t2.CDS5 14363160 14363402
chr_3 g2003 g2003.t2 exon g2003.t2.exon6 14365013 14365114
chr_3 g2003 g2003.t2 cds g2003.t2.CDS6 14365013 14365114
chr_3 g2003 g2003.t2 exon g2003.t2.exon7 14365438 14365491
chr_3 g2003 g2003.t2 cds g2003.t2.CDS7 14365438 14365491
chr_3 g2003 g2003.t2 exon g2003.t2.exon8 14365563 14365625
chr_3 g2003 g2003.t2 cds g2003.t2.CDS8 14365563 14365625
chr_3 g2003 g2003.t2 exon g2003.t2.exon9 14366695 14366835
chr_3 g2003 g2003.t2 cds g2003.t2.CDS9 14366695 14366835
chr_3 g2003 g2003.t2 exon g2003.t2.exon10 14367371 14367440
chr_3 g2003 g2003.t2 cds g2003.t2.CDS10 14367371 14367440
chr_3 g2003 g2003.t2 TSS g2003.t2 14367736 14367736

Sequences

>g2003.t2 Gene=g2003 Length=1659
ATGCGTGATACATTTGTACAAATAATTAAAGAAAAACCTGGATCAAGCTTCAATTCAGAT
AATTGTGAAGGACAAAATGGAGCAGTCAAAGATATTTCAAATGGATGGAATAACAACAAT
CACAACATCACAACTGACGGCACAGTTAAAAATGCCACAGCAAATTTTCGTGGAAGGACG
ACCGAAACGACAGCGTCCGACCCATCAGGGGCCAGGGGGGTGCGGATCTCGATGGAGAGA
TCGGGCTCAAAGACGAAGGACACTATTCAACTCGAGAAACGGATGGGGTTGTTCAGTGGG
ATTGCTCTAATCGTTGGAACGATGATAGGCTCAGGAATTTTCGTATCGCCAAGTGGATTG
CTTGTCAGAACAGGCTCTGTTGGCATTAGTTTCATTATCTGGATGGCGTGCGGTCTTCTC
TCATTGTTAGGTGCGCTCTCGTATGCGGAGTTAGGCACAATGAATACATCTTCAGGTGCG
GAGTGGGCATATTTTATGGACGCATTTGGATCAGCACCGGCATTTTTGTTCAGTTGGGTA
TCGACACTTGTCCTGAAGCCCTCACAAATGGCAATTATATGTTTATCATTTGCGCAATAT
GCCGTCGAAGCTTTTGTTTCTGAGTGCGATCCACCTCCGATTGTTGTAAAAATGGTTGCC
TTGCTGGCTATCGTATGCATCTTGTTTGTTAATTGTTACAGTGTAAATTTGGGAATGGCT
GTACAAAATGTATTTACATCTGCAAAAATGGTTGCTGTTTTGATTGTTATTTGTGGCGGT
GCATGGAAACTTTTTCAAGGAAACACACAACACTTGTCAAATGCTTTTGATAATCCAACA
CCATCTATGGGAGTAATTGCCACAGCATTTTATACAGGCTTATGGGCGTATGATGGTTGG
AATAATTTAAATTATGTCACTGAGGAAATACAAAATCCCAGCAAAAATTTACCGAGATCA
ATTATGATTGCTATTCCATTGGTTACGCTCTGCTACGCTTTAATCAACATTTCCTATCTT
GCCGCAATGTCGCCGCAGGAGATGATCGAATCCGAAGCTGTTGCTGTCACGTTCGGAAAT
CGTATTTTAGGAATGTTTGCGTGGATAATGCCACTGAGTGTTACAATAAGCACTTTTGGC
TCAGCAAATGGAACATTATTTGCGGCAGGAAGACTTTGCTTTGCTGCTTCACGAGAGGGA
CATCTTCTTGATATTCTATCTTATGTTCATGTTCGTCGTTTAACTCCTGCACCAGGTCTA
ATTTTTCACTCTCTTATTGCGTCTGCGATGGTGCTTCATGGCACTATTGACTCATTAATT
GACTTCTTTAGCTTTACGGCTTGGATATTTTATGGAGGTTCAATGTTTGCACTGATCGTC
ATGCGCTTCACAAAACCGAACTATCCGCGCCCTTATAAAGTGCCAATTATCATTCCTGTA
ATTGTTCTTGTGATTTCGGCTTATTTGGTCATTGGTCCGATCATCGATAAACCACAAATT
GAGTATTTGTATACGGTTCTTTTTATTCTTCTTGGACTTGTTCTCTATTTGCCATTCGTT
CGTTGGCGTATGCATCCTGTATTCATGAATAAAGTTACAATTTTCTTTCAAATGCTCTTT
GAAGTTGTTCCTACAAATCACATGGCAATGTTCGACTAA

>g2003.t2 Gene=g2003 Length=552
MRDTFVQIIKEKPGSSFNSDNCEGQNGAVKDISNGWNNNNHNITTDGTVKNATANFRGRT
TETTASDPSGARGVRISMERSGSKTKDTIQLEKRMGLFSGIALIVGTMIGSGIFVSPSGL
LVRTGSVGISFIIWMACGLLSLLGALSYAELGTMNTSSGAEWAYFMDAFGSAPAFLFSWV
STLVLKPSQMAIICLSFAQYAVEAFVSECDPPPIVVKMVALLAIVCILFVNCYSVNLGMA
VQNVFTSAKMVAVLIVICGGAWKLFQGNTQHLSNAFDNPTPSMGVIATAFYTGLWAYDGW
NNLNYVTEEIQNPSKNLPRSIMIAIPLVTLCYALINISYLAAMSPQEMIESEAVAVTFGN
RILGMFAWIMPLSVTISTFGSANGTLFAAGRLCFAASREGHLLDILSYVHVRRLTPAPGL
IFHSLIASAMVLHGTIDSLIDFFSFTAWIFYGGSMFALIVMRFTKPNYPRPYKVPIIIPV
IVLVISAYLVIGPIIDKPQIEYLYTVLFILLGLVLYLPFVRWRMHPVFMNKVTIFFQMLF
EVVPTNHMAMFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g2003.t2 Gene3D G3DSA:1.20.1740.10 - 90 541 1.4E-88
2 g2003.t2 PANTHER PTHR11785:SF354 B(0,+)-TYPE AMINO ACID TRANSPORTER 1 80 547 1.2E-186
3 g2003.t2 PANTHER PTHR11785 AMINO ACID TRANSPORTER 80 547 1.2E-186
43 g2003.t2 PIRSF PIRSF006060 AA_transporter 71 540 1.6E-74
1 g2003.t2 Pfam PF13520 Amino acid permease 96 501 3.6E-54
18 g2003.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 94 -
38 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 95 115 -
25 g2003.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 116 126 -
34 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 127 149 -
21 g2003.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 150 160 -
37 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 161 180 -
29 g2003.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 181 213 -
41 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 214 232 -
22 g2003.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 233 243 -
36 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 244 262 -
27 g2003.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 263 281 -
39 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 282 300 -
17 g2003.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 301 320 -
30 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 321 342 -
24 g2003.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 343 361 -
40 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 362 394 -
20 g2003.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 395 413 -
35 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 414 436 -
23 g2003.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 437 441 -
31 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 442 464 -
19 g2003.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 465 475 -
42 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 476 495 -
26 g2003.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 496 500 -
33 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 501 520 -
16 g2003.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 521 531 -
32 g2003.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 532 551 -
28 g2003.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 552 552 -
5 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 95 117 -
8 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 127 149 -
11 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 162 184 -
12 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 214 236 -
9 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 243 265 -
7 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 280 297 -
14 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 320 342 -
10 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 362 384 -
6 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 439 461 -
13 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 476 495 -
4 g2003.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 502 524 -

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

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