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_3 g4140 g4140.t5 TSS g4140.t5 30903892 30903892
chr_3 g4140 g4140.t5 isoform g4140.t5 30904128 30906789
chr_3 g4140 g4140.t5 exon g4140.t5.exon1 30904128 30904267
chr_3 g4140 g4140.t5 cds g4140.t5.CDS1 30904128 30904267
chr_3 g4140 g4140.t5 exon g4140.t5.exon2 30905882 30905939
chr_3 g4140 g4140.t5 cds g4140.t5.CDS2 30905882 30905939
chr_3 g4140 g4140.t5 exon g4140.t5.exon3 30906000 30906142
chr_3 g4140 g4140.t5 cds g4140.t5.CDS3 30906000 30906142
chr_3 g4140 g4140.t5 exon g4140.t5.exon4 30906342 30906515
chr_3 g4140 g4140.t5 cds g4140.t5.CDS4 30906342 30906396
chr_3 g4140 g4140.t5 exon g4140.t5.exon5 30906581 30906789
chr_3 g4140 g4140.t5 TTS g4140.t5 30906883 30906883

Sequences

>g4140.t5 Gene=g4140 Length=724
ATGCTACGAAATATAAAATCTAAAATATACATATGGATTGAAATTATTATAAGGCTTGCT
CTCTTTGTAGCTTTTTTGAAATTAGAGACATTAGAGCCTTTTCAAAGGAAAATTTTAGCT
GATGATTTATGGAATTATCGTTATCCTAATAAAAAATCATACGTTCCAGTTACATTGTTA
TGGCCAATTCTCACTCTTATCCCAACTTTTGTGTTTATTTTAAATTATATTTTTACGAGA
CATTCAAAAGATTTAAAAGCAGCTATGCTTGGTCATACTTTAGCATTTGGACTTAATGGT
GTTTTAGTAGGTGAGAAAATTCCTTTTATATTTAAATGTTTTTTTGGATGGCAGGAAAAG
TTTCCCGAGCGGTCATTCCTCATTCTCATTCGCTAGTTTAGGATTTTTGACTTTTTATTT
AATTGGAAAGTTGAAAATATTTTCGGATGAAGGAAGAGGAAACAGTTTAAAACTTATAAT
TTCATTTTTTCCTTTTATTGTTGCCATGTTAATAGCAATATCAAGAACATGTGACTATCA
TCATTGGAAAGAAGATGTTGTCGTTGGAAGTTTAATTGGTATTTTAATTGCATATTTATG
CTATCGACAATTTTTTCCACCACTTGCGAGTAAAAAATCAAATTTATGCTATGAAATGCT
TTACCATCTTTCTGCTACAAATGACTCAAATGATCTTCTCGAAAAAGACATTAAATGGAT
CTAA

>g4140.t5 Gene=g4140 Length=131
MLRNIKSKIYIWIEIIIRLALFVAFLKLETLEPFQRKILADDLWNYRYPNKKSYVPVTLL
WPILTLIPTFVFILNYIFTRHSKDLKAAMLGHTLAFGLNGVLVGEKIPFIFKCFFGWQEK
FPERSFLILIR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
3 g4140.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 8 -
6 g4140.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 9 26 -
5 g4140.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 27 58 -
7 g4140.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 59 78 -
4 g4140.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 79 131 -
1 g4140.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 9 26 -
2 g4140.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 57 79 -

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

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. There were no conditions that were differentially expressed