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.t4 isoform g3175.t4 23443904 23446629
chr_3 g3175 g3175.t4 exon g3175.t4.exon1 23443904 23445221
chr_3 g3175 g3175.t4 cds g3175.t4.CDS1 23444485 23445221
chr_3 g3175 g3175.t4 exon g3175.t4.exon2 23445363 23445836
chr_3 g3175 g3175.t4 cds g3175.t4.CDS2 23445363 23445836
chr_3 g3175 g3175.t4 exon g3175.t4.exon3 23445908 23446007
chr_3 g3175 g3175.t4 cds g3175.t4.CDS3 23445908 23446007
chr_3 g3175 g3175.t4 exon g3175.t4.exon4 23446063 23446318
chr_3 g3175 g3175.t4 cds g3175.t4.CDS4 23446063 23446284
chr_3 g3175 g3175.t4 exon g3175.t4.exon5 23446547 23446629
chr_3 g3175 g3175.t4 TSS g3175.t4 23446668 23446668
chr_3 g3175 g3175.t4 TTS g3175.t4 NA NA

Sequences

>g3175.t4 Gene=g3175 Length=2231
TTCTTGTTATTTACAATATAAATAGACTGCAAGTACTTAGTTAATAACTAAAAATATTAT
GGAAATTCTATAAATCAGGGAAGCTACTACTGTCGTCTTTATTAAATAGATAAAATCATG
CCCAATTTAGTTGAATTAAATAGTCCCACAGATACGGTCATGGAACTCGTACAATCTCCA
TCAAATACAGATTCTTTGAAAGCTGGTAGTTCAATACAGCAAGATGACGACAATTCACCA
AAAGAACGGGTTAAAATGAAAAAAGAACTTGGTCTATTAGAAGGATGTGCAATTATTTTA
GGAATTATTTTTGGTTCTGGCATTTTTATTTCACCGAAAGGCGTAATTAAAGAAGTGAAT
GCACCAGGAACTAGTTTAGTTATTTGGACACTTTGTGGCTTACTATCGATGATTGGAGCA
CTTTGCTATGCAGAATTAGGTTGCTGCATTCCCAAGTCAGGAGGTGATTATGCGTACATA
AATGAAGCTTTTGGCGACTTACCAAGTTTTCTCTACATCTATGATGCGACTGTGATTTTT
GTTCCTGCAACAAATGCTATAATGTCACTTACATTCGCTAATTACGTGTTACAGCCATTT
TACGCAGGAGAGTGCAAAGTGCCTGAACTCGCTGCTCAATTACTTGCTGCAGCCACTATA
TGTGGTTTGACCTATTTAAACTCTTTTAATGTTCGTGCGACTACAAAAATGCAAAACGTC
ATCATGTTCACTAAAATTGCTGCTCTCGTAATGATCATAATCATTGGTCTTGGATATATG
TCATTGGGTCATACAGAAAATTTTGACAATGCATTTGAAAATTCTGAAACTAATCCTGCG
AAATTATCGGTTGCATTCTATTCTGGCATCTTTTCTTATGCAGGATGGAATTATCTAAAC
TTTATGACTGAAGAACTGAGAAATCCATATAAGAATCTTCCACGAGCTATTTACATCAGT
TTACCTCTTGTTACAATCATCTATGTATTAGCAAATGTTGCTTATTTAGCTGTTTTGACA
CCTCAAGAAATGGTCGCAAGTAATGCAATTGCAGTATCTTTTGGAGATAAAGTACTCTCG
TATGGTTCATGGATAATACCAATTATGGTAGCAATTTCTGCATTCGGAGGTCTCTCAGTT
CATATAATGACAAGTTCACGAATGTGTTTTGTTTCCGCTCGGAATGGACATATGCCTGAA
CTTTTGAGTTTTATTAACGTTAAACGTTTTACCCCTACACCTTCTTTGGTATTTTTATGC
GTATTAAGTCTCGTCTATCTGTTCATCGGTGATGTTTATGTATTGATCACATATTCTAGC
ATCGTCGAAACATTCTTTATAATGATGAGTGTTTCTGGAGTTTTATATTTTCGTTGGAAA
CGACCCGATATGGCACGTCCTATAAAAGTTAATATATCAGTTCCAATAATTTTTGTTGGA
ATTTGCATCTTTCTCATTATTGTGCCAGTTTTTGATGCACCTTGGGAAGTTTTCATGGGT
TGTTTCATTACTTTAACAGGCGTTCCTATTTATTTGATCTGTATTGCGTGGAAACGTAAG
CCTAAAAATTTTCAAAATGTCATTGATAAACTCACTATCAACATGCAAAAATTATTCATG
AGTGCCAAAGAAGAGCAAGAGATCGATTAAAAATTGATTGAATATGACGAATATGAAACA
TTTGAATCTCAAAATTTATTTAATTTTAGCATGATCTAAATTTTGTTTATAATTTGCCTA
CCTATCTGAATTTTGAAAAAAAAAACCAAAAAATATTTAGAATCTTTTTCCGTACTTAAG
ACTTGAATTAGAAAAAAATGACAACTAAATCTCACTAAAAAGTAAAAATTTCCCTCCGCT
TTTAGCATATCAAAAATTGATTTTAGTGATTAGTCAAAAGAAAAAGTAATACAGATTTGT
TCTCTTATACTTAAGATTTAATTGATGCAAAAAATTTGAATGACATTATTGTATACTTTT
CTCATTTATATTATTTTTGTAATCATACTTTTATTAAATCATCTGCATCATGATTTTTGT
ATTGAACTTTTTTATATCAAAATATGTAATCAATCAGCATGAAAAAATAAAGAGCAAAAA
AGTAATTTTTCATTAACGAAATCTCAAATGTAATGTATTTTTATTTAAAAATATATCCAA
TCATTTTATAAAATGATGAAATTAATCAAAAAAGTAGTTGAGATAATTATGTCTATTCAT
GTTATAAAATT

>g3175.t4 Gene=g3175 Length=510
MPNLVELNSPTDTVMELVQSPSNTDSLKAGSSIQQDDDNSPKERVKMKKELGLLEGCAII
LGIIFGSGIFISPKGVIKEVNAPGTSLVIWTLCGLLSMIGALCYAELGCCIPKSGGDYAY
INEAFGDLPSFLYIYDATVIFVPATNAIMSLTFANYVLQPFYAGECKVPELAAQLLAAAT
ICGLTYLNSFNVRATTKMQNVIMFTKIAALVMIIIIGLGYMSLGHTENFDNAFENSETNP
AKLSVAFYSGIFSYAGWNYLNFMTEELRNPYKNLPRAIYISLPLVTIIYVLANVAYLAVL
TPQEMVASNAIAVSFGDKVLSYGSWIIPIMVAISAFGGLSVHIMTSSRMCFVSARNGHMP
ELLSFINVKRFTPTPSLVFLCVLSLVYLFIGDVYVLITYSSIVETFFIMMSVSGVLYFRW
KRPDMARPIKVNISVPIIFVGICIFLIIVPVFDAPWEVFMGCFITLTGVPIYLICIAWKR
KPKNFQNVIDKLTINMQKLFMSAKEEQEID

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g3175.t4 Gene3D G3DSA:1.20.1740.10 - 45 499 1.3E-90
16 g3175.t4 MobiDBLite mobidb-lite consensus disorder prediction 22 42 -
17 g3175.t4 MobiDBLite mobidb-lite consensus disorder prediction 22 36 -
2 g3175.t4 PANTHER PTHR11785:SF240 GH08870P 35 509 1.6E-256
3 g3175.t4 PANTHER PTHR11785 AMINO ACID TRANSPORTER 35 509 1.6E-256
44 g3175.t4 PIRSF PIRSF006060 AA_transporter 28 496 1.6E-74
1 g3175.t4 Pfam PF13520 Amino acid permease 51 452 4.1E-58
23 g3175.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 50 -
35 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 51 72 -
28 g3175.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 73 86 -
37 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 87 111 -
24 g3175.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 112 131 -
43 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 132 151 -
30 g3175.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 152 170 -
33 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 171 189 -
25 g3175.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 190 200 -
34 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 201 223 -
29 g3175.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 224 242 -
42 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 243 260 -
21 g3175.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 261 279 -
38 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 280 299 -
27 g3175.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 300 318 -
32 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 319 339 -
20 g3175.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 340 370 -
40 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 371 390 -
31 g3175.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 391 395 -
39 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 396 419 -
22 g3175.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 420 430 -
36 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 431 452 -
26 g3175.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 453 457 -
41 g3175.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 458 478 -
19 g3175.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 479 510 -
14 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 51 73 -
6 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 88 110 -
10 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 131 153 -
12 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 168 190 -
8 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 202 224 -
11 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 244 264 -
15 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 277 299 -
9 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 319 341 -
4 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 376 398 -
7 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 402 420 -
13 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 433 452 -
5 g3175.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 456 478 -

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