Gene loci information

Transcript annotation

  • This transcript has been annotated as Large neutral amino acids transporter small subunit 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_2 g7682 g7682.t6 TTS g7682.t6 25237172 25237172
chr_2 g7682 g7682.t6 isoform g7682.t6 25237395 25240097
chr_2 g7682 g7682.t6 exon g7682.t6.exon1 25237395 25237662
chr_2 g7682 g7682.t6 cds g7682.t6.CDS1 25237395 25237662
chr_2 g7682 g7682.t6 exon g7682.t6.exon2 25237716 25238041
chr_2 g7682 g7682.t6 cds g7682.t6.CDS2 25237716 25238041
chr_2 g7682 g7682.t6 exon g7682.t6.exon3 25238110 25238233
chr_2 g7682 g7682.t6 cds g7682.t6.CDS3 25238110 25238233
chr_2 g7682 g7682.t6 exon g7682.t6.exon4 25238291 25238661
chr_2 g7682 g7682.t6 cds g7682.t6.CDS4 25238291 25238661
chr_2 g7682 g7682.t6 exon g7682.t6.exon5 25239102 25239217
chr_2 g7682 g7682.t6 cds g7682.t6.CDS5 25239102 25239217
chr_2 g7682 g7682.t6 exon g7682.t6.exon6 25239286 25239365
chr_2 g7682 g7682.t6 cds g7682.t6.CDS6 25239286 25239365
chr_2 g7682 g7682.t6 exon g7682.t6.exon7 25240010 25240097
chr_2 g7682 g7682.t6 cds g7682.t6.CDS7 25240010 25240047
chr_2 g7682 g7682.t6 TSS g7682.t6 25240452 25240452

Sequences

>g7682.t6 Gene=g7682 Length=1373
ATGGGTGAAGATAGCAATAATAAAGTTGTACTTGAACGTAAAATTACGCTATGGAATGGT
GTGGGAATAATTGTTGGATCTATAATCGATCAGTAGGCTTCTCTCTCGTTGTCTGGTGCC
TTTCAGGTGTACTCTCAACTCTCGGAGCTCTCTGTTATGCAGAATTGGGCGTATTAATCA
CAAGATCGGGCGGTGATTACGCTTATTTACTTGAGGCTTTTGGACCTCTAGTTGGTTTTC
TTCGTTTGTGGATTGCTCTTTTTATCATTCGACCAACTACTCAGGCGATTGTTGCGCTCA
CATTTGCAGAATATGCTGCGAAGCCCTTCTTTCCAAACTGTGTGATTCCACAAGATTTAA
TTAAGTTGCTCGGAGCAATTTGCCTCTGTCTACTAACAGCAATCAACTGCATATCGACAA
AGCTGTCAATGAAAGTTCAAGATATTTTCACAGCTGGTAAATTAATTGCTTTAATATCGA
TCATTGCTATGGGAGTTTATGGAATGATTATCAGCGACACAAACAACTTTGATGATGCTT
GGTCAGGAGATTATGATGCAAAGAAAATTTGTTATGCTTTCATGCAGGGATTATTTGCCT
TCGGAGGATGGAATTATTTGAATTTTGTTACTGGTGAATTACAGGATCCTTACAAAAATT
TACCGCGTGCAATTTACATTGGCATGCCAATTGTGACGATAATATACTGTCTTACAAACT
TAGCTTATTTTGCGGTATTGACTGGTGCAGAAATGAAAGCTAGCATCGCTGTGGCAGTCA
CATTTGGAAATAAAATATTTGGCTCACTCGCATGGCTGATTCCAATATTTGTTGCTTTAT
CAACATTTGGTGGAGTGAATGGTGTGATTTTTACAAGTGCACGACTCTTCGCCACTGGTG
CCAATGAAGGTCATCTTCCATCATTTTTTGCCCTTTTCCATGTCACCAAACAGACGCCAA
TTCCATCACTCATCTTTTCTTGTCTCGTCTCACTTATTATGATAATGTTTGGAAATGCAT
TCGAGTTAGTCAACTATTTCAGTCAAGCACTTTGGTTATCAATTGCTGCATGCGTTGGCG
GACTTATTTGGATGCGAAAAACAAAACCAGACGCGCCAAGACCAATTAAAGTCAACATAA
TCATTCCATGGATTTTTCTTATCATTTGCCTTGGTCTTGTTCTAACTCCATCATTCACTG
AACCTATGAATTTGGCTATAAATATTCTAATTACACTCAGTGGTGTTCCATTTTATTTCT
TATGTGTCAAATGGAAAAATAAACCAGCTGCATATAAGAAAGTCTCAAAGAGTGTCGAGA
AATTTTGCCAAATTTTATTCTCATCAGTATTCATTGACGAAGAATCTCATTAG

>g7682.t6 Gene=g7682 Length=440
MEWCGNNCWIYNRSVGFSLVVWCLSGVLSTLGALCYAELGVLITRSGGDYAYLLEAFGPL
VGFLRLWIALFIIRPTTQAIVALTFAEYAAKPFFPNCVIPQDLIKLLGAICLCLLTAINC
ISTKLSMKVQDIFTAGKLIALISIIAMGVYGMIISDTNNFDDAWSGDYDAKKICYAFMQG
LFAFGGWNYLNFVTGELQDPYKNLPRAIYIGMPIVTIIYCLTNLAYFAVLTGAEMKASIA
VAVTFGNKIFGSLAWLIPIFVALSTFGGVNGVIFTSARLFATGANEGHLPSFFALFHVTK
QTPIPSLIFSCLVSLIMIMFGNAFELVNYFSQALWLSIAACVGGLIWMRKTKPDAPRPIK
VNIIIPWIFLIICLGLVLTPSFTEPMNLAINILITLSGVPFYFLCVKWKNKPAAYKKVSK
SVEKFCQILFSSVFIDEESH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g7682.t6 Gene3D G3DSA:1.20.1740.10 - 10 429 1.9E-78
2 g7682.t6 PANTHER PTHR11785:SF527 AMINO ACID TRANSPORTER PROTEIN JHI-21 8 436 3.3E-207
3 g7682.t6 PANTHER PTHR11785 AMINO ACID TRANSPORTER 8 436 3.3E-207
39 g7682.t6 PIRSF PIRSF006060 AA_transporter 8 425 1.6E-62
1 g7682.t6 Pfam PF13520 Amino acid permease 14 390 6.1E-52
27 g7682.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 18 -
31 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 19 43 -
21 g7682.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 44 49 -
37 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 50 73 -
22 g7682.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 74 102 -
30 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 103 122 -
20 g7682.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 123 133 -
28 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 134 155 -
23 g7682.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 156 174 -
34 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 175 195 -
17 g7682.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 196 206 -
29 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 207 229 -
24 g7682.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 230 248 -
33 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 249 269 -
19 g7682.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 270 303 -
36 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 304 323 -
26 g7682.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 324 328 -
38 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 329 347 -
16 g7682.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 348 358 -
35 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 359 382 -
25 g7682.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 383 387 -
32 g7682.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 388 406 -
18 g7682.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 407 440 -
6 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 15 37 -
13 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 50 72 -
14 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 98 120 -
9 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 133 155 -
12 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 175 194 -
7 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 207 229 -
8 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 252 274 -
5 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 302 324 -
4 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 329 348 -
11 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 361 383 -
10 g7682.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 388 406 -

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