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.t5 TTS g7682.t5 25237172 25237172
chr_2 g7682 g7682.t5 isoform g7682.t5 25237395 25240097
chr_2 g7682 g7682.t5 exon g7682.t5.exon1 25237395 25237662
chr_2 g7682 g7682.t5 cds g7682.t5.CDS1 25237395 25237662
chr_2 g7682 g7682.t5 exon g7682.t5.exon2 25237716 25238041
chr_2 g7682 g7682.t5 cds g7682.t5.CDS2 25237716 25238041
chr_2 g7682 g7682.t5 exon g7682.t5.exon3 25238110 25238233
chr_2 g7682 g7682.t5 cds g7682.t5.CDS3 25238110 25238233
chr_2 g7682 g7682.t5 exon g7682.t5.exon4 25238291 25238661
chr_2 g7682 g7682.t5 cds g7682.t5.CDS4 25238291 25238517
chr_2 g7682 g7682.t5 exon g7682.t5.exon5 25239102 25239217
chr_2 g7682 g7682.t5 exon g7682.t5.exon6 25239286 25239365
chr_2 g7682 g7682.t5 exon g7682.t5.exon7 25239881 25240097
chr_2 g7682 g7682.t5 TSS g7682.t5 25240452 25240452

Sequences

>g7682.t5 Gene=g7682 Length=1502
ATGGGTGAAGATAGCAATAATAAAGTTGTACTTGAACGTAAAATTACGCTATGGAATGGT
GTGGGAATAATTGTTGGATCTATAATCGGTAAATTTCGGACAGTTAACAAATTATTTGGC
GCCGAATTTCTTCTGAATTACTCATAATCTATTAATTTTATTGAATATTAGGATCGGGCA
TCTTTTTGTCACCAGCTGGAGTCTATACTTATACTGAATCAGTAGGCTTCTCTCTCGTTG
TCTGGTGCCTTTCAGGTGTACTCTCAACTCTCGGAGCTCTCTGTTATGCAGAATTGGGCG
TATTAATCACAAGATCGGGCGGTGATTACGCTTATTTACTTGAGGCTTTTGGACCTCTAG
TTGGTTTTCTTCGTTTGTGGATTGCTCTTTTTATCATTCGACCAACTACTCAGGCGATTG
TTGCGCTCACATTTGCAGAATATGCTGCGAAGCCCTTCTTTCCAAACTGTGTGATTCCAC
AAGATTTAATTAAGTTGCTCGGAGCAATTTGCCTCTGTCTACTAACAGCAATCAACTGCA
TATCGACAAAGCTGTCAATGAAAGTTCAAGATATTTTCACAGCTGGTAAATTAATTGCTT
TAATATCGATCATTGCTATGGGAGTTTATGGAATGATTATCAGCGACACAAACAACTTTG
ATGATGCTTGGTCAGGAGATTATGATGCAAAGAAAATTTGTTATGCTTTCATGCAGGGAT
TATTTGCCTTCGGAGGATGGAATTATTTGAATTTTGTTACTGGTGAATTACAGGATCCTT
ACAAAAATTTACCGCGTGCAATTTACATTGGCATGCCAATTGTGACGATAATATACTGTC
TTACAAACTTAGCTTATTTTGCGGTATTGACTGGTGCAGAAATGAAAGCTAGCATCGCTG
TGGCAGTCACATTTGGAAATAAAATATTTGGCTCACTCGCATGGCTGATTCCAATATTTG
TTGCTTTATCAACATTTGGTGGAGTGAATGGTGTGATTTTTACAAGTGCACGACTCTTCG
CCACTGGTGCCAATGAAGGTCATCTTCCATCATTTTTTGCCCTTTTCCATGTCACCAAAC
AGACGCCAATTCCATCACTCATCTTTTCTTGTCTCGTCTCACTTATTATGATAATGTTTG
GAAATGCATTCGAGTTAGTCAACTATTTCAGTCAAGCACTTTGGTTATCAATTGCTGCAT
GCGTTGGCGGACTTATTTGGATGCGAAAAACAAAACCAGACGCGCCAAGACCAATTAAAG
TCAACATAATCATTCCATGGATTTTTCTTATCATTTGCCTTGGTCTTGTTCTAACTCCAT
CATTCACTGAACCTATGAATTTGGCTATAAATATTCTAATTACACTCAGTGGTGTTCCAT
TTTATTTCTTATGTGTCAAATGGAAAAATAAACCAGCTGCATATAAGAAAGTCTCAAAGA
GTGTCGAGAAATTTTGCCAAATTTTATTCTCATCAGTATTCATTGACGAAGAATCTCATT
AG

>g7682.t5 Gene=g7682 Length=314
MKVQDIFTAGKLIALISIIAMGVYGMIISDTNNFDDAWSGDYDAKKICYAFMQGLFAFGG
WNYLNFVTGELQDPYKNLPRAIYIGMPIVTIIYCLTNLAYFAVLTGAEMKASIAVAVTFG
NKIFGSLAWLIPIFVALSTFGGVNGVIFTSARLFATGANEGHLPSFFALFHVTKQTPIPS
LIFSCLVSLIMIMFGNAFELVNYFSQALWLSIAACVGGLIWMRKTKPDAPRPIKVNIIIP
WIFLIICLGLVLTPSFTEPMNLAINILITLSGVPFYFLCVKWKNKPAAYKKVSKSVEKFC
QILFSSVFIDEESH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g7682.t5 Gene3D G3DSA:1.20.1740.10 - 1 303 7.0E-50
2 g7682.t5 PANTHER PTHR11785:SF527 AMINO ACID TRANSPORTER PROTEIN JHI-21 1 310 3.0E-140
3 g7682.t5 PANTHER PTHR11785 AMINO ACID TRANSPORTER 1 310 3.0E-140
1 g7682.t5 Pfam PF13520 Amino acid permease 2 264 7.8E-32
13 g7682.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
29 g7682.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 29 -
19 g7682.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 30 48 -
25 g7682.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 49 69 -
17 g7682.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 70 80 -
23 g7682.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 81 103 -
20 g7682.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 104 122 -
24 g7682.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 123 143 -
16 g7682.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 144 177 -
26 g7682.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 178 197 -
18 g7682.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 198 202 -
22 g7682.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 203 221 -
14 g7682.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 222 232 -
28 g7682.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 233 256 -
21 g7682.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 257 261 -
27 g7682.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 262 280 -
15 g7682.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 281 314 -
8 g7682.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
6 g7682.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 49 68 -
4 g7682.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 81 103 -
10 g7682.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 126 148 -
11 g7682.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 176 198 -
5 g7682.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 203 222 -
9 g7682.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 235 257 -
7 g7682.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 262 280 -

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