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.t5 isoform g3175.t5 23443904 23447549
chr_3 g3175 g3175.t5 exon g3175.t5.exon1 23443904 23445221
chr_3 g3175 g3175.t5 cds g3175.t5.CDS1 23444485 23445221
chr_3 g3175 g3175.t5 exon g3175.t5.exon2 23445363 23445815
chr_3 g3175 g3175.t5 cds g3175.t5.CDS2 23445363 23445815
chr_3 g3175 g3175.t5 exon g3175.t5.exon3 23445893 23446007
chr_3 g3175 g3175.t5 cds g3175.t5.CDS3 23445893 23446007
chr_3 g3175 g3175.t5 exon g3175.t5.exon4 23446063 23446318
chr_3 g3175 g3175.t5 cds g3175.t5.CDS4 23446063 23446284
chr_3 g3175 g3175.t5 exon g3175.t5.exon5 23446472 23446729
chr_3 g3175 g3175.t5 exon g3175.t5.exon6 23447512 23447549
chr_3 g3175 g3175.t5 TSS g3175.t5 NA NA
chr_3 g3175 g3175.t5 TTS g3175.t5 NA NA

Sequences

>g3175.t5 Gene=g3175 Length=2438
TCTGTAAATAAAGTTTTTCATTATATAACTTTTATAAGTTATAAAAATGAGTGGTTCGCA
ACTCAGAAATTTTCTGATAACTTGGATAAAATGATTTTTTCGGGATAAAAAAAATCAAAC
GTGCTGTTTCATCATCTTTTCTTGTTATTTACAATATAAATAGACTGCAAGTACTTAGTT
AATAACTAAAAATATTATGGAAATTCTATAAATCAGGGAAGGTCAGAAATAGCATTATAA
TAATCAATTGCTTAAATATCAAATAAAAGCGGTAGCGTGAATATAACAAAAGAGCTCTAC
TACTGTCGTCTTTATTAAATAGATAAAATCATGCCCAATTTAGTTGAATTAAATAGTCCC
ACAGATACGGTCATGGAACTCGTACAATCTCCATCAAATACAGATTCTTTGAAAGCTGGT
AGTTCAATACAGCAAGATGACGACAATTCACCAAAAGAACGGGTTAAAATGAAAAAAGAA
CTTGGTCTATTAGAAGGATGTGCAATTATTTTAGGAATTATTTTTGGTTCTGGCATTTTT
ATTTCACCGAAAGGCGTAATTAAAGAAGTGAATGCACCAGGAACTAGTTTAGTTATTTGG
ACACTTTGTGGCTTACTATCGATGATTGGAGCACTTTGCTATGCAGAATTAGGTGTGTTA
ATGCGTAGAGGTGATTATGCGTACATAAATGAAGCTTTTGGCGACTTACCAAGTTTTCTC
TACATCTATGATGCGACTGTGATTTTTGTTCCTGCAACAAATGCTATAATGTCACTTACA
TTCGCTAATTACGTGTTACAGCCATTTTACGCAGGAGAGTGCAAAGTGCCTGAACTCGCT
GCTCAATTACTTGCTGCAGCCACTATATGTGGTTTGACCTATTTAAACTCTTTTAATGTT
CGTGCGACTACAAAAATGCAAAACGTCATCATGTTCACTAAAATTGCTGCTCTCGTAATG
ATCATAATCATTGGTCTTGGATATATGTCATTGGGTCATACAGAAAATTTTGACAATGCA
TTTGAAAATTCTGAAACTAATCCTGCGAAATTATCGGTTGCATTCTATTCTGGCATCTTT
TCTTATGCAGGATGGAATTATCTAAACTTTATGACTGAAGAACTGAGAAATCCATATAAG
AATCTTCCACGAGCTATTTACATCAGTTTACCTCTTGTTACAATCATCTATGTATTAGCA
AATGTTGCTTATTTAGCTGTTTTGACACCTCAAGAAATGGTCGCAAGTAATGCAATTGCA
GTATCTTTTGGAGATAAAGTACTCTCGTATGGTTCATGGATAATACCAATTATGGTAGCA
ATTTCTGCATTCGGAGGTCTCTCAGTTCATATAATGACAAGTTCACGAATGTGTTTTGTT
TCCGCTCGGAATGGACATATGCCTGAACTTTTGAGTTTTATTAACGTTAAACGTTTTACC
CCTACACCTTCTTTGGTATTTTTATGCGTATTAAGTCTCGTCTATCTGTTCATCGGTGAT
GTTTATGTATTGATCACATATTCTAGCATCGTCGAAACATTCTTTATAATGATGAGTGTT
TCTGGAGTTTTATATTTTCGTTGGAAACGACCCGATATGGCACGTCCTATAAAAGTTAAT
ATATCAGTTCCAATAATTTTTGTTGGAATTTGCATCTTTCTCATTATTGTGCCAGTTTTT
GATGCACCTTGGGAAGTTTTCATGGGTTGTTTCATTACTTTAACAGGCGTTCCTATTTAT
TTGATCTGTATTGCGTGGAAACGTAAGCCTAAAAATTTTCAAAATGTCATTGATAAACTC
ACTATCAACATGCAAAAATTATTCATGAGTGCCAAAGAAGAGCAAGAGATCGATTAAAAA
TTGATTGAATATGACGAATATGAAACATTTGAATCTCAAAATTTATTTAATTTTAGCATG
ATCTAAATTTTGTTTATAATTTGCCTACCTATCTGAATTTTGAAAAAAAAAACCAAAAAA
TATTTAGAATCTTTTTCCGTACTTAAGACTTGAATTAGAAAAAAATGACAACTAAATCTC
ACTAAAAAGTAAAAATTTCCCTCCGCTTTTAGCATATCAAAAATTGATTTTAGTGATTAG
TCAAAAGAAAAAGTAATACAGATTTGTTCTCTTATACTTAAGATTTAATTGATGCAAAAA
ATTTGAATGACATTATTGTATACTTTTCTCATTTATATTATTTTTGTAATCATACTTTTA
TTAAATCATCTGCATCATGATTTTTGTATTGAACTTTTTTATATCAAAATATGTAATCAA
TCAGCATGAAAAAATAAAGAGCAAAAAAGTAATTTTTCATTAACGAAATCTCAAATGTAA
TGTATTTTTATTTAAAAATATATCCAATCATTTTATAAAATGATGAAATTAATCAAAAAA
GTAGTTGAGATAATTATGTCTATTCATGTTATAAAATT

>g3175.t5 Gene=g3175 Length=508
MPNLVELNSPTDTVMELVQSPSNTDSLKAGSSIQQDDDNSPKERVKMKKELGLLEGCAII
LGIIFGSGIFISPKGVIKEVNAPGTSLVIWTLCGLLSMIGALCYAELGVLMRRGDYAYIN
EAFGDLPSFLYIYDATVIFVPATNAIMSLTFANYVLQPFYAGECKVPELAAQLLAAATIC
GLTYLNSFNVRATTKMQNVIMFTKIAALVMIIIIGLGYMSLGHTENFDNAFENSETNPAK
LSVAFYSGIFSYAGWNYLNFMTEELRNPYKNLPRAIYISLPLVTIIYVLANVAYLAVLTP
QEMVASNAIAVSFGDKVLSYGSWIIPIMVAISAFGGLSVHIMTSSRMCFVSARNGHMPEL
LSFINVKRFTPTPSLVFLCVLSLVYLFIGDVYVLITYSSIVETFFIMMSVSGVLYFRWKR
PDMARPIKVNISVPIIFVGICIFLIIVPVFDAPWEVFMGCFITLTGVPIYLICIAWKRKP
KNFQNVIDKLTINMQKLFMSAKEEQEID

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g3175.t5 Gene3D G3DSA:1.20.1740.10 - 45 497 4.7E-85
16 g3175.t5 MobiDBLite mobidb-lite consensus disorder prediction 22 41 -
17 g3175.t5 MobiDBLite mobidb-lite consensus disorder prediction 22 36 -
2 g3175.t5 PANTHER PTHR11785:SF240 GH08870P 35 507 2.9E-250
3 g3175.t5 PANTHER PTHR11785 AMINO ACID TRANSPORTER 35 507 2.9E-250
44 g3175.t5 PIRSF PIRSF006060 AA_transporter 28 494 2.0E-68
1 g3175.t5 Pfam PF13520 Amino acid permease 51 450 1.2E-53
22 g3175.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 50 -
37 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 51 72 -
27 g3175.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 73 86 -
39 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 87 107 -
21 g3175.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 108 127 -
43 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 128 149 -
29 g3175.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 150 168 -
33 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 169 187 -
25 g3175.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 188 198 -
40 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 199 221 -
26 g3175.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 222 240 -
42 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 241 258 -
19 g3175.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 259 277 -
35 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 278 297 -
31 g3175.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 298 316 -
36 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 317 337 -
24 g3175.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 338 368 -
34 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 369 388 -
30 g3175.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 389 393 -
41 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 394 417 -
20 g3175.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 418 428 -
32 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 429 450 -
28 g3175.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 451 455 -
38 g3175.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 456 476 -
23 g3175.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 477 508 -
12 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 51 73 -
10 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 88 110 -
9 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 129 151 -
15 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 166 188 -
11 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 200 222 -
4 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 242 262 -
5 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 275 297 -
13 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 317 339 -
14 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 374 396 -
7 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 400 418 -
8 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 431 450 -
6 g3175.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 454 476 -

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