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_1 g12948 g12948.t3 TTS g12948.t3 27099013 27099013
chr_1 g12948 g12948.t3 isoform g12948.t3 27099340 27100151
chr_1 g12948 g12948.t3 exon g12948.t3.exon1 27099340 27099882
chr_1 g12948 g12948.t3 cds g12948.t3.CDS1 27099341 27099882
chr_1 g12948 g12948.t3 exon g12948.t3.exon2 27099947 27100017
chr_1 g12948 g12948.t3 cds g12948.t3.CDS2 27099947 27100017
chr_1 g12948 g12948.t3 exon g12948.t3.exon3 27100072 27100151
chr_1 g12948 g12948.t3 cds g12948.t3.CDS3 27100072 27100151
chr_1 g12948 g12948.t3 TSS g12948.t3 27100182 27100182

Sequences

>g12948.t3 Gene=g12948 Length=694
ATGGAAGCAAAAAAGCGACCGTATTTTCTCGATATTAATCCATTCATGTTATGGGTTGCT
GTTATTTATGGATTCACAAGAATTATTGAAATCTTGACAGGTAGCGAGAATTTTTGGAGT
AACTTTTGGAATAGAATTGTTGATCTTTGCGATGACGAATATTATTTCAAAGTCATTCTC
ACAATGGCGTACACAACAATTCTCTATTGGGGTGTCGGAATGTTATTCATTATTATGGAC
ATTACAAATCCAAAGTTTATCCAAAAGTACAAAACACAACCTGAAGCCCATCTTCCACTT
GACATGAAGAAATTTTTACCTGCATGTCGTGTTGTGCTTTTCAATCAATTTGTATTAAAT
GTTTTAGTTTCACATGTTTTGACTATAATTGAAAAAAACTTGGAACGTCCTGGACTTCGA
ACAACACCAACTTTCTATCAGTTGATGGTAGATTTATTTTTATATCAATTCATTTATGAA
TTTGCATTCTTCTATACACATCGTTTGCTACACACGAAATATCTTTACAAAAAAATTCAC
AAAATTCATCATCAATGGCAAGCGCCAGTTTCGATAATGGCAACTTATGCACATCCAATT
GAACACATTTTTAGTAATCTTTTTCCTGTATTTCTTGGAATAGGTTTATTAAAATCGCCA
ATGTCAACAGGATGGGTTATAATGTCTTTGACAA

>g12948.t3 Gene=g12948 Length=231
MEAKKRPYFLDINPFMLWVAVIYGFTRIIEILTGSENFWSNFWNRIVDLCDDEYYFKVIL
TMAYTTILYWGVGMLFIIMDITNPKFIQKYKTQPEAHLPLDMKKFLPACRVVLFNQFVLN
VLVSHVLTIIEKNLERPGLRTTPTFYQLMVDLFLYQFIYEFAFFYTHRLLHTKYLYKKIH
KIHHQWQAPVSIMATYAHPIEHIFSNLFPVFLGIGLLKSPMSTGWVIMSLT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g12948.t3 PANTHER PTHR11863:SF26 FATTY ACID HYDROXYLASE DOMAIN-CONTAINING PROTEIN 2 29 230 4.6E-45
3 g12948.t3 PANTHER PTHR11863 STEROL DESATURASE 29 230 4.6E-45
1 g12948.t3 Pfam PF04116 Fatty acid hydroxylase superfamily 153 229 2.3E-12
8 g12948.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 11 -
15 g12948.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 12 34 -
12 g12948.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 35 53 -
16 g12948.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 79 -
10 g12948.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 80 110 -
14 g12948.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 111 130 -
11 g12948.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 131 144 -
13 g12948.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 145 165 -
9 g12948.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 166 231 -
4 g12948.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 7 29 -
7 g12948.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 59 81 -
6 g12948.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 111 130 -
5 g12948.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 145 167 -

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:0005506 iron ion binding MF
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF
GO:0008610 lipid biosynthetic process BP

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