Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Solute carrier family 46 member 3.

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 g7244 g7244.t3 isoform g7244.t3 22335665 22337597
chr_2 g7244 g7244.t3 exon g7244.t3.exon1 22335665 22335959
chr_2 g7244 g7244.t3 exon g7244.t3.exon2 22336036 22337597
chr_2 g7244 g7244.t3 cds g7244.t3.CDS1 22336170 22337597
chr_2 g7244 g7244.t3 TTS g7244.t3 22337665 22337665
chr_2 g7244 g7244.t3 TSS g7244.t3 NA NA

Sequences

>g7244.t3 Gene=g7244 Length=1857
CAAACAACAATTATTAAATTTTAATATGCGCTTATCAACTAACTGTTATTAAGTTCCTTT
ATATTGACGAATAACATTTGCCACAATAAACTTATGTATATGAAGAGAACCTAGTCTTCA
AAAAATATATGAATCACTCTTTGTGTTCCGAAAAATTCTTTCTACATTGTAAGATTGTTA
TTATTTCAGAATCATTAGCTTAAGCTTTAAAAATGATCAGTAGTGATTGAAAAGTATTGA
GATAAAGACGTGAAAGTGTACGAAATTATTTATTCATTACGGTTCATTTTGCAAGATATC
TTTATTGCAAACAATTATATTGTAAAACAATTATTGATAAAATTTTGAGTACAACTTGTT
ATTAAATATTGGTTGTATGCTCGTCAATTATAATTCAGATTTGAACGAGTGAACACTTAA
GCAGAAACTATGGAAGAGGATAAAAGTGAAAATATTCGTGAAAATATTTTGGAACAACTG
CCAACAAATAAGCGTGTAGTAAGATTCAATTATGGATTAGAACCAGCACTCTTCACACTA
TATTTTGCATTCAATTTAACAAATGCTGTTTTGCAGAATCAAATTTTGAAACAAACTTGT
TTGATAACGGGTTATAATATGACAATTTGCACACATCTCAACACAGATAATTATACAAAA
ACAATAGAAGAAGAAATTCAACCTCAAGTGGCAAAAATCAATATGTCGATTCTTCTACTG
AACTCAATTTTTCCAGCACTTTTTAGTTTAATTTTGGGCTCATGGTCTGACATATTTGGA
CGAAAAAAAATTTTAATGCTGGCATTTACTGGTTATACTTGCACAATAGGATTAATTACA
TTGTTTTCATATATTTCTGACAATATCAATCCTCTGACACCTTGGGTGTATTTTTTCGCA
GAAATGCCAATGACTTTTATGGGTGGATGGACATGTTTAGACGTTTCAGTTTGTTGTTAT
GCAGCGGATTTAAGTTCTCAACAAAATCGTTCAATTCGACTTGGAACAATTACATTTCTA
AATTTCTTTGCAAGTGCTATTGCATATTTTTGCAGTTCATATATTTTAAATGCTACCAAC
ATTACATTTGTATTTATAATAGCGATATCATGTGCAGCAGCAGCATTTTTATGGTCCATT
TTTATAATTGATGAGACAATTGAGCCACCGATTGAAGTTTCAAAGTTTGATCAAATTAAA
GAAATTTTCTCTACAAGTCGCATACATGAAATTTTTACTACATTATGCAAAAGACGTCCA
CAAAAATGTAGGAAAACTCTATGGTCTTTGATGACTGTTCCAATTTTAGTAGTCTTTACA
ATGCATGGAAATGGTACGCTTAATTATTTATTTGTTCGAGAAAAATTTGCATGGTCTTTG
AGAGAATGGACAATATTTGAGAGCACAAATACAATCATTTCTGTGTCCGGTCTTTTTATT
GGTTTGTTGTTGTTGAAAAAAACATTCAAATTCTCTGATATCACTCTTGGCATTGTTGCT
CTCACTTCACTACTCGTCGATGCACTCATGAAAGCATTTGCTCAAAAATCATATCTACTT
TATTTGTCATCAGGAATCACACCCTTCCGACTTTTAGCTACACCTATGTTTAGATCTGTA
ATGTCTGTAATAGTTCCACATCAGGAAATAGGGAAAATTTATAGCTTGACAACGTGTTTT
GAAGCATTAAGCGGTTTGGGAGCCGGTCCTTTATATACTGTGATTTATAACAATACGTTT
ACTGTATTTCCTGGAGCATATCATCTTTTGAGTGCTTGCATATTTTTCTTCAATCTGATA
TTATGTGCTTTTATATTCCGATGGAAATCTCAAGTTGTTTCATATCAATATGAATAA

>g7244.t3 Gene=g7244 Length=475
MEEDKSENIRENILEQLPTNKRVVRFNYGLEPALFTLYFAFNLTNAVLQNQILKQTCLIT
GYNMTICTHLNTDNYTKTIEEEIQPQVAKINMSILLLNSIFPALFSLILGSWSDIFGRKK
ILMLAFTGYTCTIGLITLFSYISDNINPLTPWVYFFAEMPMTFMGGWTCLDVSVCCYAAD
LSSQQNRSIRLGTITFLNFFASAIAYFCSSYILNATNITFVFIIAISCAAAAFLWSIFII
DETIEPPIEVSKFDQIKEIFSTSRIHEIFTTLCKRRPQKCRKTLWSLMTVPILVVFTMHG
NGTLNYLFVREKFAWSLREWTIFESTNTIISVSGLFIGLLLLKKTFKFSDITLGIVALTS
LLVDALMKAFAQKSYLLYLSSGITPFRLLATPMFRSVMSVIVPHQEIGKIYSLTTCFEAL
SGLGAGPLYTVIYNNTFTVFPGAYHLLSACIFFFNLILCAFIFRWKSQVVSYQYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g7244.t3 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains 83 464 5.4E-24
2 g7244.t3 PANTHER PTHR23507 ZGC:174356 26 466 3.3E-75
3 g7244.t3 PANTHER PTHR23507:SF1 ZGC:174356 26 466 3.3E-75
1 g7244.t3 Pfam PF07690 Major Facilitator Superfamily 34 423 3.2E-23
25 g7244.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 89 -
32 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 90 109 -
15 g7244.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 110 120 -
26 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 121 142 -
21 g7244.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 143 153 -
31 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 154 179 -
16 g7244.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 180 190 -
36 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 191 212 -
20 g7244.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 213 217 -
30 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 218 240 -
18 g7244.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 241 283 -
28 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 284 308 -
23 g7244.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 309 319 -
35 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 320 342 -
19 g7244.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 343 350 -
34 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 351 371 -
24 g7244.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 372 376 -
27 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 377 398 -
17 g7244.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 399 409 -
29 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 410 432 -
22 g7244.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 433 443 -
33 g7244.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 444 463 -
14 g7244.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 464 475 -
12 g7244.t3 SUPERFAMILY SSF103473 MFS general substrate transporter 94 466 4.32E-27
5 g7244.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 94 116 -
9 g7244.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 121 143 -
7 g7244.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 191 213 -
6 g7244.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 218 240 -
8 g7244.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 283 300 -
10 g7244.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 320 342 -
11 g7244.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 411 433 -
4 g7244.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 443 465 -

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:0055085 transmembrane transport BP
GO:0022857 transmembrane transporter activity MF

KEGG

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