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.t3 isoform g2003.t3 14361316 14365625
chr_3 g2003 g2003.t3 exon g2003.t3.exon1 14361316 14361974
chr_3 g2003 g2003.t3 TTS g2003.t3 14361323 14361323
chr_3 g2003 g2003.t3 cds g2003.t3.CDS1 14361904 14361974
chr_3 g2003 g2003.t3 exon g2003.t3.exon2 14362040 14362683
chr_3 g2003 g2003.t3 cds g2003.t3.CDS2 14362040 14362683
chr_3 g2003 g2003.t3 exon g2003.t3.exon3 14362753 14362897
chr_3 g2003 g2003.t3 cds g2003.t3.CDS3 14362753 14362897
chr_3 g2003 g2003.t3 exon g2003.t3.exon4 14362966 14363091
chr_3 g2003 g2003.t3 cds g2003.t3.CDS4 14362966 14363091
chr_3 g2003 g2003.t3 exon g2003.t3.exon5 14363160 14363402
chr_3 g2003 g2003.t3 cds g2003.t3.CDS5 14363160 14363402
chr_3 g2003 g2003.t3 exon g2003.t3.exon6 14365013 14365114
chr_3 g2003 g2003.t3 cds g2003.t3.CDS6 14365013 14365114
chr_3 g2003 g2003.t3 exon g2003.t3.exon7 14365438 14365489
chr_3 g2003 g2003.t3 cds g2003.t3.CDS7 14365438 14365444
chr_3 g2003 g2003.t3 exon g2003.t3.exon8 14365563 14365625
chr_3 g2003 g2003.t3 TSS g2003.t3 14366269 14366269

Sequences

>g2003.t3 Gene=g2003 Length=2034
CCAGGGGGGTGCGGATCTCGATGGAGAGATCGGGCTCAAAGACGAAGGACACTATTCAAC
TCGAAACGGATGGGGTTGTTCAGTGGGATTGCTCTAATCGTTGGAACGATGATAGGCTCA
GGAATTTTCGTATCGCCAAGTGGATTGCTTGTCAGAACAGGCTCTGTTGGCATTAGTTTC
ATTATCTGGATGGCGTGCGGTCTTCTCTCATTGTTAGGTGCGCTCTCGTATGCGGAGTTA
GGCACAATGAATACATCTTCAGGTGCGGAGTGGGCATATTTTATGGACGCATTTGGATCA
GCACCGGCATTTTTGTTCAGTTGGGTATCGACACTTGTCCTGAAGCCCTCACAAATGGCA
ATTATATGTTTATCATTTGCGCAATATGCCGTCGAAGCTTTTGTTTCTGAGTGCGATCCA
CCTCCGATTGTTGTAAAAATGGTTGCCTTGCTGGCTATCGTATGCATCTTGTTTGTTAAT
TGTTACAGTGTAAATTTGGGAATGGCTGTACAAAATGTATTTACATCTGCAAAAATGGTT
GCTGTTTTGATTGTTATTTGTGGCGGTGCATGGAAACTTTTTCAAGGAAACACACAACAC
TTGTCAAATGCTTTTGATAATCCAACACCATCTATGGGAGTAATTGCCACAGCATTTTAT
ACAGGCTTATGGGCGTATGATGGTTGGAATAATTTAAATTATGTCACTGAGGAAATACAA
AATCCCAGCAAAAATTTACCGAGATCAATTATGATTGCTATTCCATTGGTTACGCTCTGC
TACGCTTTAATCAACATTTCCTATCTTGCCGCAATGTCGCCGCAGGAGATGATCGAATCC
GAAGCTGTTGCTGTCACGTTCGGAAATCGTATTTTAGGAATGTTTGCGTGGATAATGCCA
CTGAGTGTTACAATAAGCACTTTTGGCTCAGCAAATGGAACATTATTTGCGGCAGGAAGA
CTTTGCTTTGCTGCTTCACGAGAGGGACATCTTCTTGATATTCTATCTTATGTTCATGTT
CGTCGTTTAACTCCTGCACCAGGTCTAATTTTTCACTCTCTTATTGCGTCTGCGATGGTG
CTTCATGGCACTATTGACTCATTAATTGACTTCTTTAGCTTTACGGCTTGGATATTTTAT
GGAGGTTCAATGTTTGCACTGATCGTCATGCGCTTCACAAAACCGAACTATCCGCGCCCT
TATAAAGTGCCAATTATCATTCCTGTAATTGTTCTTGTGATTTCGGCTTATTTGGTCATT
GGTCCGATCATCGATAAACCACAAATTGAGTATTTGTATACGGTTCTTTTTATTCTTCTT
GGACTTGTTCTCTATTTGCCATTCGTTCGTTGGCGTATGCATCCTGTATTCATGAATAAA
GTTACAATTTTCTTTCAAATGCTCTTTGAAGTTGTTCCTACAAATCACATGGCAATGTTC
GACTAAATGTCTATCGATCTATTTAACTATAACTGTACACCAGCTTTATGGCGAATTTAT
TTAATTGGGCATATTATCATGCTTTGAGAAAAATATATTTTGTTACTATTGAGTTCACTT
CAATTCAAAAAGACGTTCAAAATTTAGGCAACAAAAATTAATTCTTACGTTGAAGCAATA
ATTTTAGAATGAGAAAATTATGCATTTCAAAAATGAGATTTCGTAAATTATTTAAAAGAG
TAAAAAAGTAATTTTAGAGACTTACAAAAAAGATCATTACGTACATGTTAGAACAAAAAG
AGAATTAAAATTTTTAGAGCTATATTGAAGATAAGAGAAAAATTGCACCTATCTAGAAAA
AAAGTTTCCTTGTAGAAAATGCTAGTCTTTTGGCATTAAAAGAATGAGATTGAAATTTGA
TGTTTCTCTTAGAGAAATTTAAATTATGTGAAAAGAATGTGAGACTAAAGAAAGAAATTA
TCAAAAAATGCCAGCATAAGAACGTAATAAGAAAAATAAAATTCTGTAAATGAAATTTTT
TTTTGAAATAATAAAAGAGTTGAAGGAAATTTATTTTTAAAAGGATTTAAAATT

>g2003.t3 Gene=g2003 Length=445
MIGSGIFVSPSGLLVRTGSVGISFIIWMACGLLSLLGALSYAELGTMNTSSGAEWAYFMD
AFGSAPAFLFSWVSTLVLKPSQMAIICLSFAQYAVEAFVSECDPPPIVVKMVALLAIVCI
LFVNCYSVNLGMAVQNVFTSAKMVAVLIVICGGAWKLFQGNTQHLSNAFDNPTPSMGVIA
TAFYTGLWAYDGWNNLNYVTEEIQNPSKNLPRSIMIAIPLVTLCYALINISYLAAMSPQE
MIESEAVAVTFGNRILGMFAWIMPLSVTISTFGSANGTLFAAGRLCFAASREGHLLDILS
YVHVRRLTPAPGLIFHSLIASAMVLHGTIDSLIDFFSFTAWIFYGGSMFALIVMRFTKPN
YPRPYKVPIIIPVIVLVISAYLVIGPIIDKPQIEYLYTVLFILLGLVLYLPFVRWRMHPV
FMNKVTIFFQMLFEVVPTNHMAMFD

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g2003.t3 Gene3D G3DSA:1.20.1740.10 - 1 434 4.5E-82
2 g2003.t3 PANTHER PTHR11785:SF354 B(0,+)-TYPE AMINO ACID TRANSPORTER 1 1 440 1.2E-174
3 g2003.t3 PANTHER PTHR11785 AMINO ACID TRANSPORTER 1 440 1.2E-174
40 g2003.t3 PIRSF PIRSF006060 AA_transporter 1 434 9.6E-67
1 g2003.t3 Pfam PF13520 Amino acid permease 1 394 2.4E-51
24 g2003.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 19 -
33 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
15 g2003.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 43 53 -
31 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 73 -
22 g2003.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 74 106 -
35 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 107 125 -
16 g2003.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 126 136 -
29 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 137 155 -
23 g2003.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 156 174 -
39 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 175 193 -
20 g2003.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 194 213 -
36 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 214 235 -
21 g2003.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 236 254 -
30 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 255 287 -
19 g2003.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 288 306 -
37 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 307 329 -
27 g2003.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 330 334 -
32 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 335 357 -
17 g2003.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 358 368 -
28 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 369 388 -
26 g2003.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 389 393 -
34 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 394 413 -
18 g2003.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 414 424 -
38 g2003.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 425 444 -
25 g2003.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 445 445 -
10 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 20 42 -
4 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 55 77 -
7 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 107 129 -
6 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 136 158 -
12 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 173 190 -
13 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 213 235 -
11 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 255 277 -
9 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 332 354 -
5 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 369 388 -
8 g2003.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 395 417 -

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.

Raw TPM values