Gene loci information

Transcript annotation

  • This transcript has been annotated as hypothetical.

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 g4466 g4466.t3 isoform g4466.t3 2721340 2722606
chr_2 g4466 g4466.t3 exon g4466.t3.exon1 2721340 2721561
chr_2 g4466 g4466.t3 cds g4466.t3.CDS1 2721340 2721561
chr_2 g4466 g4466.t3 exon g4466.t3.exon2 2721722 2721954
chr_2 g4466 g4466.t3 cds g4466.t3.CDS2 2721722 2721954
chr_2 g4466 g4466.t3 exon g4466.t3.exon3 2722021 2722370
chr_2 g4466 g4466.t3 cds g4466.t3.CDS3 2722021 2722370
chr_2 g4466 g4466.t3 exon g4466.t3.exon4 2722433 2722606
chr_2 g4466 g4466.t3 cds g4466.t3.CDS4 2722433 2722509
chr_2 g4466 g4466.t3 TSS g4466.t3 NA NA
chr_2 g4466 g4466.t3 TTS g4466.t3 NA NA

Sequences

>g4466.t3 Gene=g4466 Length=979
ATGGAAAATATAACAAATGATTCTATTGACTGTATTGATGGCATTCCATCAGCTGATGAG
TTTTTTGCGAGTCTAAATTTCTTATACAAATGGATTTTAGTTATACCAACCGGCTTTTTT
CTAATGACTGTGACGATTTATATACTCAATCTATACACAGTTATTAAATATGGAAAAAGA
GAAACAAAGTCCAACGTGTTGATTCTACTGACATTATATCCAACTGTTGCACTCGTATCA
TTGATCTCGATCTTCATGCCAAAAACATATTTTTTCTGTGACTTTATTGCGCACACATTT
TTCGTCATTTCGTCTTATCAACTTTATCGATATTGTATCAACTGCATCGAAGGTGAATCA
AAATTTATCGCTATATCAAAAAATGAGTCATTTACATTAAAAACACCTCCCGTTTGTTGT
TGCTGTTTGTGCTTTAGTACATCAATGATAACAAAAAAAAAATTTCTATGGATAAGATTA
TTAGTTTTACAAATGGCAGTTGTGCATGTCATCATATTCTCAATTTTAAATCTCATAAAT
ATTGAAAATCCGCCAATAGTTGACTATCTTATGCTTTATTTTCTGCCAGTTATAGCCACT
TCAATCTTATTAGCAGTATGGGGCTTCAATGTTATAATAAGAATGCTTGTGCCTTACTAT
TCAAATTTAAATCTGTTGAAGAAATTTTTAGCCTTCCAATTAGTCCTTGTGTCTTGCAAA
TTTCAACCAGTATTACTTAATCTTATTTTGAGAAACTATATTGAGACTTGTGATGGAGCA
ATCACAGTTGTAGTCAAAATAAGAACTATAACGCAAATATTTATTCAGTTTGAAATGATA
ATATTATCGGTTTGGTCACATTTTTTGTATACGAACAACTAATAAATTTAAACAACATTT
CCTATGAATCAGATGTTTTTAGCAAGTAGCAGTAAATGAGAAGATTATAATTTAGTTTTT
TTAAGCAATACATACTTAA

>g4466.t3 Gene=g4466 Length=293
MENITNDSIDCIDGIPSADEFFASLNFLYKWILVIPTGFFLMTVTIYILNLYTVIKYGKR
ETKSNVLILLTLYPTVALVSLISIFMPKTYFFCDFIAHTFFVISSYQLYRYCINCIEGES
KFIAISKNESFTLKTPPVCCCCLCFSTSMITKKKFLWIRLLVLQMAVVHVIIFSILNLIN
IENPPIVDYLMLYFLPVIATSILLAVWGFNVIIRMLVPYYSNLNLLKKFLAFQLVLVSCK
FQPVLLNLILRNYIETCDGAITVVVKIRTITQIFIQFEMIILSVWSHFLYTNN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g4466.t3 PANTHER PTHR23423:SF21 ORGANIC SOLUTE TRANSPORTER ALPHA-LIKE PROTEIN 4 291 1.9E-38
3 g4466.t3 PANTHER PTHR23423 ORGANIC SOLUTE TRANSPORTER-RELATED 4 291 1.9E-38
1 g4466.t3 Pfam PF03619 Organic solute transporter Ostalpha 34 291 7.0E-24
13 g4466.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 30 -
18 g4466.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 31 54 -
9 g4466.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 55 65 -
19 g4466.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 66 83 -
15 g4466.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 84 88 -
17 g4466.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 109 -
12 g4466.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 110 155 -
22 g4466.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 156 179 -
14 g4466.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 180 190 -
21 g4466.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 191 217 -
10 g4466.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 218 228 -
23 g4466.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 229 250 -
16 g4466.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 251 269 -
20 g4466.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 270 290 -
11 g4466.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 291 293 -
6 g4466.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 31 53 -
5 g4466.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 66 85 -
4 g4466.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 95 113 -
8 g4466.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 157 179 -
7 g4466.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 189 211 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

There are no GO annotations for this transcript.

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