Gene loci information

Transcript annotation

  • This transcript has been annotated as Y+L amino acid transporter 2.

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 g3175 g3175.t6 TTS g3175.t6 23444456 23444456
chr_3 g3175 g3175.t6 isoform g3175.t6 23445221 23446629
chr_3 g3175 g3175.t6 exon g3175.t6.exon1 23445221 23445836
chr_3 g3175 g3175.t6 cds g3175.t6.CDS1 23445346 23445836
chr_3 g3175 g3175.t6 exon g3175.t6.exon2 23445908 23446007
chr_3 g3175 g3175.t6 cds g3175.t6.CDS2 23445908 23446007
chr_3 g3175 g3175.t6 exon g3175.t6.exon3 23446063 23446318
chr_3 g3175 g3175.t6 cds g3175.t6.CDS3 23446063 23446284
chr_3 g3175 g3175.t6 exon g3175.t6.exon4 23446472 23446629
chr_3 g3175 g3175.t6 TSS g3175.t6 23446668 23446668

Sequences

>g3175.t6 Gene=g3175 Length=1130
TTCTTGTTATTTACAATATAAATAGACTGCAAGTACTTAGTTAATAACTAAAAATATTAT
GGAAATTCTATAAATCAGGGAAGGTCAGAAATAGCATTATAATAATCAATTGCTTAAATA
TCAAATAAAAGCGGTAGCGTGAATATAACAAAAGAGCTCTACTACTGTCGTCTTTATTAA
ATAGATAAAATCATGCCCAATTTAGTTGAATTAAATAGTCCCACAGATACGGTCATGGAA
CTCGTACAATCTCCATCAAATACAGATTCTTTGAAAGCTGGTAGTTCAATACAGCAAGAT
GACGACAATTCACCAAAAGAACGGGTTAAAATGAAAAAAGAACTTGGTCTATTAGAAGGA
TGTGCAATTATTTTAGGAATTATTTTTGGTTCTGGCATTTTTATTTCACCGAAAGGCGTA
ATTAAAGAAGTGAATGCACCAGGAACTAGTTTAGTTATTTGGACACTTTGTGGCTTACTA
TCGATGATTGGAGCACTTTGCTATGCAGAATTAGGTTGCTGCATTCCCAAGTCAGGAGGT
GATTATGCGTACATAAATGAAGCTTTTGGCGACTTACCAAGTTTTCTCTACATCTATGAT
GCGACTGTGATTTTTGTTCCTGCAACAAATGCTATAATGTCACTTACATTCGCTAATTAC
GTGTTACAGCCATTTTACGCAGGAGAGTGCAAAGTGCCTGAACTCGCTGCTCAATTACTT
GCTGCAGCCACTATATGTGGTTTGACCTATTTAAACTCTTTTAATGTTCGTGCGACTACA
AAAATGCAAAACGTCATCATGTTCACTAAAATTGCTGCTCTCGTAATGATCATAATCATT
GGTCTTGGATATATGTCATTGGGTCATACAGAAAATTTTGACAATGCATTTGAAAATTCT
GAAACTAATCCTGCGAAATTATCGGTTGCATTCTATTCTGGCATCTTTTCTTATGCAGGA
TGGAATTATCTAAACTTTATGACTGAAGGTGATTATAGCATTTAAGCAATAATTTAGTTT
ATCATTTAGTTATGAATCCTTTTAATCAACACTTTCTGCTTCGTTTATAATTATATCTGA
GAGCTGTTTATGTAATAAAAGATTTTCTTCTTTTTATTTCATGTTGAAGA

>g3175.t6 Gene=g3175 Length=270
MPNLVELNSPTDTVMELVQSPSNTDSLKAGSSIQQDDDNSPKERVKMKKELGLLEGCAII
LGIIFGSGIFISPKGVIKEVNAPGTSLVIWTLCGLLSMIGALCYAELGCCIPKSGGDYAY
INEAFGDLPSFLYIYDATVIFVPATNAIMSLTFANYVLQPFYAGECKVPELAAQLLAAAT
ICGLTYLNSFNVRATTKMQNVIMFTKIAALVMIIIIGLGYMSLGHTENFDNAFENSETNP
AKLSVAFYSGIFSYAGWNYLNFMTEGDYSI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g3175.t6 Gene3D G3DSA:1.20.1740.10 - 45 266 1.4E-44
10 g3175.t6 MobiDBLite mobidb-lite consensus disorder prediction 22 42 -
11 g3175.t6 MobiDBLite mobidb-lite consensus disorder prediction 22 36 -
2 g3175.t6 PANTHER PTHR11785:SF240 GH08870P 35 265 8.9E-124
3 g3175.t6 PANTHER PTHR11785 AMINO ACID TRANSPORTER 35 265 8.9E-124
1 g3175.t6 Pfam PF13520 Amino acid permease 51 265 3.4E-28
14 g3175.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 50 -
23 g3175.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 51 72 -
17 g3175.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 73 86 -
25 g3175.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 87 111 -
15 g3175.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 112 131 -
24 g3175.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 132 151 -
19 g3175.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 152 170 -
21 g3175.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 189 -
16 g3175.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 190 200 -
22 g3175.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 201 223 -
18 g3175.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 224 242 -
20 g3175.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 243 260 -
13 g3175.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 261 270 -
6 g3175.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 51 73 -
7 g3175.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 88 110 -
4 g3175.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 131 153 -
5 g3175.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 168 190 -
9 g3175.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 202 224 -
8 g3175.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 244 262 -

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.

Raw TPM values