Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t7 isoform g2003.t7 14362966 14372625
chr_3 g2003 g2003.t7 exon g2003.t7.exon1 14362966 14363091
chr_3 g2003 g2003.t7 cds g2003.t7.CDS1 14362967 14363091
chr_3 g2003 g2003.t7 exon g2003.t7.exon2 14363160 14363402
chr_3 g2003 g2003.t7 cds g2003.t7.CDS2 14363160 14363402
chr_3 g2003 g2003.t7 exon g2003.t7.exon3 14365013 14365114
chr_3 g2003 g2003.t7 cds g2003.t7.CDS3 14365013 14365114
chr_3 g2003 g2003.t7 exon g2003.t7.exon4 14365438 14365491
chr_3 g2003 g2003.t7 cds g2003.t7.CDS4 14365438 14365491
chr_3 g2003 g2003.t7 exon g2003.t7.exon5 14365563 14365625
chr_3 g2003 g2003.t7 cds g2003.t7.CDS5 14365563 14365625
chr_3 g2003 g2003.t7 exon g2003.t7.exon6 14366695 14366835
chr_3 g2003 g2003.t7 cds g2003.t7.CDS6 14366695 14366835
chr_3 g2003 g2003.t7 exon g2003.t7.exon7 14372586 14372625
chr_3 g2003 g2003.t7 cds g2003.t7.CDS7 14372586 14372625
chr_3 g2003 g2003.t7 TSS g2003.t7 14372675 14372675
chr_3 g2003 g2003.t7 TTS g2003.t7 NA NA

Sequences

>g2003.t7 Gene=g2003 Length=769
ATGTTTCAGAATGCTTTTCAAGCAAATCATTTACAAAATGGACAAAATGGAGCAGTCAAA
GATATTTCAAATGGATGGAATAACAACAATCACAACATCACAACTGACGGCACAGTTAAA
AATGCCACAGCAAATTTTCGTGGAAGGACGACCGAAACGACAGCGTCCGACCCATCAGGG
GCCAGGGGGGTGCGGATCTCGATGGAGAGATCGGGCTCAAAGACGAAGGACACTATTCAA
CTCGAGAAACGGATGGGGTTGTTCAGTGGGATTGCTCTAATCGTTGGAACGATGATAGGC
TCAGGAATTTTCGTATCGCCAAGTGGATTGCTTGTCAGAACAGGCTCTGTTGGCATTAGT
TTCATTATCTGGATGGCGTGCGGTCTTCTCTCATTGTTAGGTGCGCTCTCGTATGCGGAG
TTAGGCACAATGAATACATCTTCAGGTGCGGAGTGGGCATATTTTATGGACGCATTTGGA
TCAGCACCGGCATTTTTGTTCAGTTGGGTATCGACACTTGTCCTGAAGCCCTCACAAATG
GCAATTATATGTTTATCATTTGCGCAATATGCCGTCGAAGCTTTTGTTTCTGAGTGCGAT
CCACCTCCGATTGTTGTAAAAATGGTTGCCTTGCTGGCTATCGTATGCATCTTGTTTGTT
AATTGTTACAGTGTAAATTTGGGAATGGCTGTACAAAATGTATTTACATCTGCAAAAATG
GTTGCTGTTTTGATTGTTATTTGTGGCGGTGCATGGAAACTTTTTCAAG

>g2003.t7 Gene=g2003 Length=256
MFQNAFQANHLQNGQNGAVKDISNGWNNNNHNITTDGTVKNATANFRGRTTETTASDPSG
ARGVRISMERSGSKTKDTIQLEKRMGLFSGIALIVGTMIGSGIFVSPSGLLVRTGSVGIS
FIIWMACGLLSLLGALSYAELGTMNTSSGAEWAYFMDAFGSAPAFLFSWVSTLVLKPSQM
AIICLSFAQYAVEAFVSECDPPPIVVKMVALLAIVCILFVNCYSVNLGMAVQNVFTSAKM
VAVLIVICGGAWKLFQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g2003.t7 Gene3D G3DSA:1.20.1740.10 - 80 256 2.2E-34
2 g2003.t7 PANTHER PTHR11785 AMINO ACID TRANSPORTER 69 256 2.2E-70
3 g2003.t7 PANTHER PTHR11785:SF512 FRUCTOSELYSINE/PSICOSELYSINE TRANSPORTER FRLA-RELATED 69 256 2.2E-70
1 g2003.t7 Pfam PF13520 Amino acid permease 86 249 1.1E-17
10 g2003.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 84 -
22 g2003.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 105 -
16 g2003.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 106 116 -
19 g2003.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 117 139 -
13 g2003.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 140 150 -
17 g2003.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 151 171 -
15 g2003.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 172 176 -
18 g2003.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 177 196 -
12 g2003.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 197 207 -
20 g2003.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 208 231 -
14 g2003.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 232 236 -
21 g2003.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 237 255 -
11 g2003.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 256 256 -
4 g2003.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 85 107 -
6 g2003.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 117 139 -
5 g2003.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 152 174 -
7 g2003.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 204 226 -
8 g2003.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 233 255 -

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. There were no conditions that were differentially expressed